Main Page

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    <text bytes="449" xml:space="preserve">&lt;big&gt;'''MediaWiki has been successfully installed.'''&lt;/big&gt;

Consult the [http://meta.wikimedia.org/wiki/Help:Contents User's Guide] for information on using the wiki software.

== Getting started ==
* [http://www.mediawiki.org/wiki/Manual:Configuration_settings Configuration settings list]
* [http://www.mediawiki.org/wiki/Manual:FAQ MediaWiki FAQ]
* [https://lists.wikimedia.org/mailman/listinfo/mediawiki-announce MediaWiki release mailing list]</text>
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    <text bytes="490" xml:space="preserve">== jV ==
Welcome to jV wiki.


&lt;br/&gt;
&lt;big&gt;'''MediaWiki has been successfully installed.'''&lt;/big&gt;

Consult the [http://meta.wikimedia.org/wiki/Help:Contents User's Guide] for information on using the wiki software.

== Getting started ==
* [http://www.mediawiki.org/wiki/Manual:Configuration_settings Configuration settings list]
* [http://www.mediawiki.org/wiki/Manual:FAQ MediaWiki FAQ]
* [https://lists.wikimedia.org/mailman/listinfo/mediawiki-announce MediaWiki release mailing list]</text>
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    <text bytes="1300" xml:space="preserve">'Welcome to jV wiki.'&lt;br /&gt;
jV is a program to display molecular graphics of proteins and nucleic acids. jV version 3 is used as PDBjViewer. &lt;br/&gt;
jV supports the following features:
* jV can read and display PDBML files, the canonical XML format for the Protein Data Bank.
* Of course, jV can read and display the traditional PDB format files, too.
* RasMol-like usability.
* jV can process more than one molecules.
* jV can display polygons specified by XML. (XML Schema for polygons is available.)
* Multiple polygons can be processed simultaneously, and be superimposed onto molecular images.
* Animation can be realized.
* jV runs on the Java Runtime Environment (JRE) so that it can work as a stand-alone application as well as an applet.
* The graphics of jV is based on OpenGL (JOGL), thereby producing fairly beautiful pictures.


&lt;br/&gt;
&lt;big&gt;'''MediaWiki has been successfully installed.'''&lt;/big&gt;

Consult the [http://meta.wikimedia.org/wiki/Help:Contents User's Guide] for information on using the wiki software.

== Getting started ==
* [http://www.mediawiki.org/wiki/Manual:Configuration_settings Configuration settings list]
* [http://www.mediawiki.org/wiki/Manual:FAQ MediaWiki FAQ]
* [https://lists.wikimedia.org/mailman/listinfo/mediawiki-announce MediaWiki release mailing list]</text>
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    <text bytes="1304" xml:space="preserve">'''Welcome to jV wiki.'''&lt;br /&gt;
jV is a program to display molecular graphics of proteins and nucleic acids. jV version 3 is used as PDBjViewer. &lt;br/&gt;
jV supports the following features:
* jV can read and display PDBML files, the canonical XML format for the Protein Data Bank.
* Of course, jV can read and display the traditional PDB format files, too.
* RasMol-like usability.
* jV can process more than one molecules.
* jV can display polygons specified by XML. (XML Schema for polygons is available.)
* Multiple polygons can be processed simultaneously, and be superimposed onto molecular images.
* Animation can be realized.
* jV runs on the Java Runtime Environment (JRE) so that it can work as a stand-alone application as well as an applet.
* The graphics of jV is based on OpenGL (JOGL), thereby producing fairly beautiful pictures.


&lt;br/&gt;
&lt;big&gt;'''MediaWiki has been successfully installed.'''&lt;/big&gt;

Consult the [http://meta.wikimedia.org/wiki/Help:Contents User's Guide] for information on using the wiki software.

== Getting started ==
* [http://www.mediawiki.org/wiki/Manual:Configuration_settings Configuration settings list]
* [http://www.mediawiki.org/wiki/Manual:FAQ MediaWiki FAQ]
* [https://lists.wikimedia.org/mailman/listinfo/mediawiki-announce MediaWiki release mailing list]</text>
    <sha1>8f8c6f39b7181e80f25f388436fda35dc7a9f1c1</sha1>
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    <text bytes="1420" xml:space="preserve">'''Welcome to jV wiki.'''&lt;br /&gt;
Version 3.6 was released on 11, Aug, 2008.&lt;br /&gt;
This version is fully compativle with applet-launcher.&lt;br /&gt;&lt;br /&gt;
jV is a program to display molecular graphics of proteins and nucleic acids. jV version 3 is used as PDBjViewer. &lt;br/&gt;
jV supports the following features:
* jV can read and display PDBML files, the canonical XML format for the Protein Data Bank.
* Of course, jV can read and display the traditional PDB format files, too.
* RasMol-like usability.
* jV can process more than one molecules.
* jV can display polygons specified by XML. (XML Schema for polygons is available.)
* Multiple polygons can be processed simultaneously, and be superimposed onto molecular images.
* Animation can be realized.
* jV runs on the Java Runtime Environment (JRE) so that it can work as a stand-alone application as well as an applet.
* The graphics of jV is based on OpenGL (JOGL), thereby producing fairly beautiful pictures.


&lt;br/&gt;
&lt;big&gt;'''MediaWiki has been successfully installed.'''&lt;/big&gt;

Consult the [http://meta.wikimedia.org/wiki/Help:Contents User's Guide] for information on using the wiki software.

== Getting started ==
* [http://www.mediawiki.org/wiki/Manual:Configuration_settings Configuration settings list]
* [http://www.mediawiki.org/wiki/Manual:FAQ MediaWiki FAQ]
* [https://lists.wikimedia.org/mailman/listinfo/mediawiki-announce MediaWiki release mailing list]</text>
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    <format>text/x-wiki</format>
    <text bytes="1451" xml:space="preserve">'''Welcome to jV wiki.'''&lt;br /&gt;
Version 3.6 was released on 11, Aug, 2008.&lt;br /&gt;
This version is fully compativle with applet-launcher.&lt;br /&gt;&lt;br /&gt;
&lt;font color="red"&gt;jV version 3&lt;/font&gt; (formerly known as PDBjViewer) is a program to display molecular graphics of proteins and nucleic acids. &lt;br /&gt;
jV supports the following features:
* jV can read and display PDBML files, the canonical XML format for the Protein Data Bank.
* Of course, jV can read and display the traditional PDB format files, too.
* RasMol-like usability.
* jV can process more than one molecules.
* jV can display polygons specified by XML. (XML Schema for polygons is available.)
* Multiple polygons can be processed simultaneously, and be superimposed onto molecular images.
* Animation can be realized.
* jV runs on the Java Runtime Environment (JRE) so that it can work as a stand-alone application as well as an applet.
* The graphics of jV is based on OpenGL (JOGL), thereby producing fairly beautiful pictures.


&lt;br/&gt;
&lt;big&gt;'''MediaWiki has been successfully installed.'''&lt;/big&gt;

Consult the [http://meta.wikimedia.org/wiki/Help:Contents User's Guide] for information on using the wiki software.

== Getting started ==
* [http://www.mediawiki.org/wiki/Manual:Configuration_settings Configuration settings list]
* [http://www.mediawiki.org/wiki/Manual:FAQ MediaWiki FAQ]
* [https://lists.wikimedia.org/mailman/listinfo/mediawiki-announce MediaWiki release mailing list]</text>
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    <text bytes="1473" xml:space="preserve">'''Welcome to jV wiki.'''&lt;br /&gt;
&lt;font size="1"&gt;Version 3.6 was released on 11, Aug, 2008.&lt;br /&gt;
This version is fully compativle with applet-launcher.&lt;/font&gt;&lt;br /&gt;&lt;br /&gt;
&lt;font color="red"&gt;jV version 3&lt;/font&gt; (formerly known as PDBjViewer) is a program to display molecular graphics of proteins and nucleic acids. &lt;br /&gt;
jV supports the following features:
* jV can read and display PDBML files, the canonical XML format for the Protein Data Bank.
* Of course, jV can read and display the traditional PDB format files, too.
* RasMol-like usability.
* jV can process more than one molecules.
* jV can display polygons specified by XML. (XML Schema for polygons is available.)
* Multiple polygons can be processed simultaneously, and be superimposed onto molecular images.
* Animation can be realized.
* jV runs on the Java Runtime Environment (JRE) so that it can work as a stand-alone application as well as an applet.
* The graphics of jV is based on OpenGL (JOGL), thereby producing fairly beautiful pictures.


&lt;br/&gt;
&lt;big&gt;'''MediaWiki has been successfully installed.'''&lt;/big&gt;

Consult the [http://meta.wikimedia.org/wiki/Help:Contents User's Guide] for information on using the wiki software.

== Getting started ==
* [http://www.mediawiki.org/wiki/Manual:Configuration_settings Configuration settings list]
* [http://www.mediawiki.org/wiki/Manual:FAQ MediaWiki FAQ]
* [https://lists.wikimedia.org/mailman/listinfo/mediawiki-announce MediaWiki release mailing list]</text>
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    <text bytes="1685" xml:space="preserve">'''Welcome to jV wiki.'''&lt;br /&gt;
&lt;font size="1"&gt;Version 3.6 was released on 11, Aug, 2008.&lt;br /&gt;
This version is fully compativle with applet-launcher.&lt;/font&gt;&lt;br /&gt;&lt;br /&gt;
&lt;font color="red"&gt;jV version 3&lt;/font&gt; (formerly known as PDBjViewer) is a program to display molecular graphics of proteins and nucleic acids. &lt;br /&gt;
jV supports the following features:
* jV can read and display PDBML files, the canonical XML format for the Protein Data Bank.
* Of course, jV can read and display the traditional PDB format files, too.
* RasMol-like usability.
* jV can process more than one molecules.
* jV can display polygons specified by XML. ([http://ef-site.hgc.jp/eF-site/schema/polygon12.xsd XML Schema for polygons] is available.)
* Multiple polygons can be processed simultaneously, and be superimposed onto molecular images.
* Animation can be realized.
* jV runs on the Java Runtime Environment ([jV version 3 (formerly known as PDBjViewer) is a program to display molecular graphics of proteins and nucleic acids. jV supports the following features:


 JRE]) so that it can work as a stand-alone application as well as an applet.
* The graphics of jV is based on OpenGL (JOGL), thereby producing fairly beautiful pictures.


&lt;br/&gt;
&lt;big&gt;'''MediaWiki has been successfully installed.'''&lt;/big&gt;

Consult the [http://meta.wikimedia.org/wiki/Help:Contents User's Guide] for information on using the wiki software.

== Getting started ==
* [http://www.mediawiki.org/wiki/Manual:Configuration_settings Configuration settings list]
* [http://www.mediawiki.org/wiki/Manual:FAQ MediaWiki FAQ]
* [https://lists.wikimedia.org/mailman/listinfo/mediawiki-announce MediaWiki release mailing list]</text>
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    <text bytes="1565" xml:space="preserve">'''Welcome to jV wiki.'''&lt;br /&gt;
&lt;font size="1"&gt;Version 3.6 was released on 11, Aug, 2008.&lt;br /&gt;
This version is fully compativle with applet-launcher.&lt;/font&gt;&lt;br /&gt;&lt;br /&gt;
&lt;font color="red"&gt;jV version 3&lt;/font&gt; (formerly known as PDBjViewer) is a program to display molecular graphics of proteins and nucleic acids. &lt;br /&gt;
jV supports the following features:
* jV can read and display PDBML files, the canonical XML format for the Protein Data Bank.
* Of course, jV can read and display the traditional PDB format files, too.
* RasMol-like usability.
* jV can process more than one molecules.
* jV can display polygons specified by XML. ([http://ef-site.hgc.jp/eF-site/schema/polygon12.xsd XML Schema for polygons] is available.)
* Multiple polygons can be processed simultaneously, and be superimposed onto molecular images.
* Animation can be realized.
* jV runs on the Java Runtime Environment ([http://java.sun.com/javase/index.jsp JRE]) so that it can work as a stand-alone application as well as an applet.
* The graphics of jV is based on OpenGL (JOGL), thereby producing fairly beautiful pictures.


&lt;br/&gt;
&lt;big&gt;'''MediaWiki has been successfully installed.'''&lt;/big&gt;

Consult the [http://meta.wikimedia.org/wiki/Help:Contents User's Guide] for information on using the wiki software.

== Getting started ==
* [http://www.mediawiki.org/wiki/Manual:Configuration_settings Configuration settings list]
* [http://www.mediawiki.org/wiki/Manual:FAQ MediaWiki FAQ]
* [https://lists.wikimedia.org/mailman/listinfo/mediawiki-announce MediaWiki release mailing list]</text>
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    <text bytes="1602" xml:space="preserve">'''Welcome to jV wiki.'''&lt;br /&gt;
&lt;font size="1"&gt;Version 3.6 was released on 11, Aug, 2008.&lt;br /&gt;[[File:Download.png|right|Download]]]
This version is fully compativle with applet-launcher.&lt;/font&gt;&lt;br /&gt;&lt;br /&gt;
&lt;font color="red"&gt;jV version 3&lt;/font&gt; (formerly known as PDBjViewer) is a program to display molecular graphics of proteins and nucleic acids. &lt;br /&gt;
jV supports the following features:
* jV can read and display PDBML files, the canonical XML format for the Protein Data Bank.
* Of course, jV can read and display the traditional PDB format files, too.
* RasMol-like usability.
* jV can process more than one molecules.
* jV can display polygons specified by XML. ([http://ef-site.hgc.jp/eF-site/schema/polygon12.xsd XML Schema for polygons] is available.)
* Multiple polygons can be processed simultaneously, and be superimposed onto molecular images.
* Animation can be realized.
* jV runs on the Java Runtime Environment ([http://java.sun.com/javase/index.jsp JRE]) so that it can work as a stand-alone application as well as an applet.
* The graphics of jV is based on OpenGL (JOGL), thereby producing fairly beautiful pictures.


&lt;br/&gt;
&lt;big&gt;'''MediaWiki has been successfully installed.'''&lt;/big&gt;

Consult the [http://meta.wikimedia.org/wiki/Help:Contents User's Guide] for information on using the wiki software.

== Getting started ==
* [http://www.mediawiki.org/wiki/Manual:Configuration_settings Configuration settings list]
* [http://www.mediawiki.org/wiki/Manual:FAQ MediaWiki FAQ]
* [https://lists.wikimedia.org/mailman/listinfo/mediawiki-announce MediaWiki release mailing list]</text>
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    <text bytes="1611" xml:space="preserve">'''Welcome to jV wiki.'''&lt;br /&gt;
&lt;font size="1"&gt;Version 3.6 was released on 11, Aug, 2008.&lt;br /&gt;
This version is fully compativle with applet-launcher.&lt;/font&gt;&lt;br /&gt;&lt;br /&gt; [[File:/images/Download.png|right|Download]]]
&lt;font color="red"&gt;jV version 3&lt;/font&gt; (formerly known as PDBjViewer) is a program to display molecular graphics of proteins and nucleic acids. &lt;br /&gt;
jV supports the following features:
* jV can read and display PDBML files, the canonical XML format for the Protein Data Bank.
* Of course, jV can read and display the traditional PDB format files, too.
* RasMol-like usability.
* jV can process more than one molecules.
* jV can display polygons specified by XML. ([http://ef-site.hgc.jp/eF-site/schema/polygon12.xsd XML Schema for polygons] is available.)
* Multiple polygons can be processed simultaneously, and be superimposed onto molecular images.
* Animation can be realized.
* jV runs on the Java Runtime Environment ([http://java.sun.com/javase/index.jsp JRE]) so that it can work as a stand-alone application as well as an applet.
* The graphics of jV is based on OpenGL (JOGL), thereby producing fairly beautiful pictures.


&lt;br/&gt;
&lt;big&gt;'''MediaWiki has been successfully installed.'''&lt;/big&gt;

Consult the [http://meta.wikimedia.org/wiki/Help:Contents User's Guide] for information on using the wiki software.

== Getting started ==
* [http://www.mediawiki.org/wiki/Manual:Configuration_settings Configuration settings list]
* [http://www.mediawiki.org/wiki/Manual:FAQ MediaWiki FAQ]
* [https://lists.wikimedia.org/mailman/listinfo/mediawiki-announce MediaWiki release mailing list]</text>
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    <text bytes="1602" xml:space="preserve">'''Welcome to jV wiki.'''&lt;br /&gt;
&lt;font size="1"&gt;Version 3.6 was released on 11, Aug, 2008.&lt;br /&gt;
This version is fully compativle with applet-launcher.&lt;/font&gt;&lt;br /&gt;&lt;br /&gt; [[File:Download.png|right|Download]]
&lt;font color="red"&gt;jV version 3&lt;/font&gt; (formerly known as PDBjViewer) is a program to display molecular graphics of proteins and nucleic acids. &lt;br /&gt;
jV supports the following features:
* jV can read and display PDBML files, the canonical XML format for the Protein Data Bank.
* Of course, jV can read and display the traditional PDB format files, too.
* RasMol-like usability.
* jV can process more than one molecules.
* jV can display polygons specified by XML. ([http://ef-site.hgc.jp/eF-site/schema/polygon12.xsd XML Schema for polygons] is available.)
* Multiple polygons can be processed simultaneously, and be superimposed onto molecular images.
* Animation can be realized.
* jV runs on the Java Runtime Environment ([http://java.sun.com/javase/index.jsp JRE]) so that it can work as a stand-alone application as well as an applet.
* The graphics of jV is based on OpenGL (JOGL), thereby producing fairly beautiful pictures.


&lt;br/&gt;
&lt;big&gt;'''MediaWiki has been successfully installed.'''&lt;/big&gt;

Consult the [http://meta.wikimedia.org/wiki/Help:Contents User's Guide] for information on using the wiki software.

== Getting started ==
* [http://www.mediawiki.org/wiki/Manual:Configuration_settings Configuration settings list]
* [http://www.mediawiki.org/wiki/Manual:FAQ MediaWiki FAQ]
* [https://lists.wikimedia.org/mailman/listinfo/mediawiki-announce MediaWiki release mailing list]</text>
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    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="1601" xml:space="preserve">'''Welcome to jV wiki.'''&lt;br /&gt;
&lt;font size="1"&gt;Version 3.6 was released on 11, Aug, 2008.&lt;br /&gt;This version is fully compativle with applet-launcher.&lt;/font&gt;&lt;br /&gt;[[File:Download.png|right|Download]]
&lt;br /&gt;
&lt;font color="red"&gt;jV version 3&lt;/font&gt; (formerly known as PDBjViewer) is a program to display molecular graphics of proteins and nucleic acids. &lt;br /&gt;
jV supports the following features:
* jV can read and display PDBML files, the canonical XML format for the Protein Data Bank.
* Of course, jV can read and display the traditional PDB format files, too.
* RasMol-like usability.
* jV can process more than one molecules.
* jV can display polygons specified by XML. ([http://ef-site.hgc.jp/eF-site/schema/polygon12.xsd XML Schema for polygons] is available.)
* Multiple polygons can be processed simultaneously, and be superimposed onto molecular images.
* Animation can be realized.
* jV runs on the Java Runtime Environment ([http://java.sun.com/javase/index.jsp JRE]) so that it can work as a stand-alone application as well as an applet.
* The graphics of jV is based on OpenGL (JOGL), thereby producing fairly beautiful pictures.


&lt;br/&gt;
&lt;big&gt;'''MediaWiki has been successfully installed.'''&lt;/big&gt;

Consult the [http://meta.wikimedia.org/wiki/Help:Contents User's Guide] for information on using the wiki software.

== Getting started ==
* [http://www.mediawiki.org/wiki/Manual:Configuration_settings Configuration settings list]
* [http://www.mediawiki.org/wiki/Manual:FAQ MediaWiki FAQ]
* [https://lists.wikimedia.org/mailman/listinfo/mediawiki-announce MediaWiki release mailing list]</text>
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    <text bytes="1601" xml:space="preserve">'''Welcome to jV wiki.'''&lt;br /&gt;
&lt;font size="1"&gt;Version 3.6 was released on 11, Aug, 2008.&lt;br /&gt;[[File:Download.png|right|Download]]This version is fully compativle with applet-launcher.&lt;/font&gt;&lt;br /&gt;
&lt;br /&gt;
&lt;font color="red"&gt;jV version 3&lt;/font&gt; (formerly known as PDBjViewer) is a program to display molecular graphics of proteins and nucleic acids. &lt;br /&gt;
jV supports the following features:
* jV can read and display PDBML files, the canonical XML format for the Protein Data Bank.
* Of course, jV can read and display the traditional PDB format files, too.
* RasMol-like usability.
* jV can process more than one molecules.
* jV can display polygons specified by XML. ([http://ef-site.hgc.jp/eF-site/schema/polygon12.xsd XML Schema for polygons] is available.)
* Multiple polygons can be processed simultaneously, and be superimposed onto molecular images.
* Animation can be realized.
* jV runs on the Java Runtime Environment ([http://java.sun.com/javase/index.jsp JRE]) so that it can work as a stand-alone application as well as an applet.
* The graphics of jV is based on OpenGL (JOGL), thereby producing fairly beautiful pictures.


&lt;br/&gt;
&lt;big&gt;'''MediaWiki has been successfully installed.'''&lt;/big&gt;

Consult the [http://meta.wikimedia.org/wiki/Help:Contents User's Guide] for information on using the wiki software.

== Getting started ==
* [http://www.mediawiki.org/wiki/Manual:Configuration_settings Configuration settings list]
* [http://www.mediawiki.org/wiki/Manual:FAQ MediaWiki FAQ]
* [https://lists.wikimedia.org/mailman/listinfo/mediawiki-announce MediaWiki release mailing list]</text>
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&lt;font size="1"&gt;Version 3.6 was released on 11, Aug, 2008.&lt;br /&gt;This version is fully compativle with applet-launcher.&lt;/font&gt;&lt;br /&gt;
&lt;br /&gt;
&lt;font color="red"&gt;jV version 3&lt;/font&gt; (formerly known as PDBjViewer) is a program to display molecular graphics of proteins and nucleic acids. &lt;br /&gt;
jV supports the following features:
* jV can read and display PDBML files, the canonical XML format for the Protein Data Bank.
* Of course, jV can read and display the traditional PDB format files, too.
* RasMol-like usability.
* jV can process more than one molecules.
* jV can display polygons specified by XML. ([http://ef-site.hgc.jp/eF-site/schema/polygon12.xsd XML Schema for polygons] is available.)
* Multiple polygons can be processed simultaneously, and be superimposed onto molecular images.
* Animation can be realized.
* jV runs on the Java Runtime Environment ([http://java.sun.com/javase/index.jsp JRE]) so that it can work as a stand-alone application as well as an applet.
* The graphics of jV is based on OpenGL (JOGL), thereby producing fairly beautiful pictures.


&lt;br/&gt;
&lt;big&gt;'''MediaWiki has been successfully installed.'''&lt;/big&gt;

Consult the [http://meta.wikimedia.org/wiki/Help:Contents User's Guide] for information on using the wiki software.

== Getting started ==
* [http://www.mediawiki.org/wiki/Manual:Configuration_settings Configuration settings list]
* [http://www.mediawiki.org/wiki/Manual:FAQ MediaWiki FAQ]
* [https://lists.wikimedia.org/mailman/listinfo/mediawiki-announce MediaWiki release mailing list]</text>
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&lt;font size="1"&gt;Version 3.6 was released on 11, Aug, 2008.&lt;br /&gt;This version is fully compativle with applet-launcher.&lt;/font&gt;&lt;br /&gt;
&lt;br /&gt;
&lt;font color="red"&gt;jV version 3&lt;/font&gt; (formerly known as PDBjViewer) is a program to display molecular graphics of proteins and nucleic acids. &lt;br /&gt;
jV supports the following features:
* jV can read and display PDBML files, the canonical XML format for the Protein Data Bank.
* Of course, jV can read and display the traditional PDB format files, too.
* RasMol-like usability.
* jV can process more than one molecules.
* jV can display polygons specified by XML. ([http://ef-site.hgc.jp/eF-site/schema/polygon12.xsd XML Schema for polygons] is available.)
* Multiple polygons can be processed simultaneously, and be superimposed onto molecular images.
* Animation can be realized.
* jV runs on the Java Runtime Environment ([http://java.sun.com/javase/index.jsp JRE]) so that it can work as a stand-alone application as well as an applet.
* The graphics of jV is based on OpenGL (JOGL), thereby producing fairly beautiful pictures.


&lt;br/&gt;
&lt;big&gt;'''MediaWiki has been successfully installed.'''&lt;/big&gt;

Consult the [http://meta.wikimedia.org/wiki/Help:Contents User's Guide] for information on using the wiki software.

== Getting started ==
* [http://www.mediawiki.org/wiki/Manual:Configuration_settings Configuration settings list]
* [http://www.mediawiki.org/wiki/Manual:FAQ MediaWiki FAQ]
* [https://lists.wikimedia.org/mailman/listinfo/mediawiki-announce MediaWiki release mailing list]</text>
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    <text bytes="1668" xml:space="preserve">&lt;big&gt;'''Welcome to jV wiki.'''&lt;/big&gt;&lt;br /&gt;[[File:Download.png|right|link=http://ef-site.hgc.jp/eF-site/servlet/Registration|Download]]
&lt;font size="1"&gt;Version 3.6 was released on 11, Aug, 2008.&lt;br /&gt;This version is fully compativle with applet-launcher.&lt;/font&gt;&lt;br /&gt;
&lt;br /&gt;
&lt;font color="red"&gt;jV version 3&lt;/font&gt; (formerly known as PDBjViewer) is a program to display molecular graphics of proteins and nucleic acids. &lt;br /&gt;
jV supports the following features:
* jV can read and display PDBML files, the canonical XML format for the Protein Data Bank.
* Of course, jV can read and display the traditional PDB format files, too.
* RasMol-like usability.
* jV can process more than one molecules.
* jV can display polygons specified by XML. ([http://ef-site.hgc.jp/eF-site/schema/polygon12.xsd XML Schema for polygons] is available.)
* Multiple polygons can be processed simultaneously, and be superimposed onto molecular images.
* Animation can be realized.
* jV runs on the Java Runtime Environment ([http://java.sun.com/javase/index.jsp JRE]) so that it can work as a stand-alone application as well as an applet.
* The graphics of jV is based on OpenGL (JOGL), thereby producing fairly beautiful pictures.


&lt;br/&gt;
&lt;big&gt;'''MediaWiki has been successfully installed.'''&lt;/big&gt;

Consult the [http://meta.wikimedia.org/wiki/Help:Contents User's Guide] for information on using the wiki software.

== Getting started ==
* [http://www.mediawiki.org/wiki/Manual:Configuration_settings Configuration settings list]
* [http://www.mediawiki.org/wiki/Manual:FAQ MediaWiki FAQ]
* [https://lists.wikimedia.org/mailman/listinfo/mediawiki-announce MediaWiki release mailing list]</text>
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    <text bytes="1708" xml:space="preserve">&lt;big&gt;'''Welcome to jV wiki.'''&lt;/big&gt;&lt;br /&gt;[[File:Download.png|right|link=http://ef-site.hgc.jp/eF-site/servlet/Registration|Download]]
&lt;font size="1"&gt;Version 3.6 was released on 11, Aug, 2008.&lt;br /&gt;This version is fully compativle with [https://applet-launcher.dev.java.net/ applet-launcher].&lt;/font&gt;&lt;br /&gt;
&lt;br /&gt;
&lt;font color="red"&gt;jV version 3&lt;/font&gt; (formerly known as PDBjViewer) is a program to display molecular graphics of proteins and nucleic acids. &lt;br /&gt;
jV supports the following features:
* jV can read and display PDBML files, the canonical XML format for the Protein Data Bank.
* Of course, jV can read and display the traditional PDB format files, too.
* RasMol-like usability.
* jV can process more than one molecules.
* jV can display polygons specified by XML. ([http://ef-site.hgc.jp/eF-site/schema/polygon12.xsd XML Schema for polygons] is available.)
* Multiple polygons can be processed simultaneously, and be superimposed onto molecular images.
* Animation can be realized.
* jV runs on the Java Runtime Environment ([http://java.sun.com/javase/index.jsp JRE]) so that it can work as a stand-alone application as well as an applet.
* The graphics of jV is based on OpenGL (JOGL), thereby producing fairly beautiful pictures.


&lt;br/&gt;
&lt;big&gt;'''MediaWiki has been successfully installed.'''&lt;/big&gt;

Consult the [http://meta.wikimedia.org/wiki/Help:Contents User's Guide] for information on using the wiki software.

== Getting started ==
* [http://www.mediawiki.org/wiki/Manual:Configuration_settings Configuration settings list]
* [http://www.mediawiki.org/wiki/Manual:FAQ MediaWiki FAQ]
* [https://lists.wikimedia.org/mailman/listinfo/mediawiki-announce MediaWiki release mailing list]</text>
    <sha1>c3714e7b6e95355cac59cc45c6e189955bb1d4e4</sha1>
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    <text bytes="2077" xml:space="preserve">&lt;big&gt;'''Welcome to jV wiki.'''&lt;/big&gt;

jV(formerly known as PDBjViewer) is a program to display molecular graphics of protein and nucleic acids. The program 'jV' has been developed by Kengo Kinoshita (Graduate School of Integrated Science, Yokohama City University) and Haruki Nakamura (Institute for Protein Research, Osaka Univeristy), as one of the activities of Protein Data Bank Japan (PDBj), supported by grant-in-aid from Institute for Bioinformatics Research and Development, Japan Science and TechnologyCorporation (BIRD-JST).

== jV version 3 ==
&lt;br /&gt;[[File:Download.png|right|link=http://ef-site.hgc.jp/eF-site/servlet/Registration|Download]]
&lt;font size="1"&gt;Version 3.6 was released on 11, Aug, 2008.&lt;br /&gt;This version is fully compativle with [https://applet-launcher.dev.java.net/ applet-launcher].&lt;/font&gt;&lt;br /&gt;
&lt;br /&gt;
jV supports the following features:
* jV can read and display PDBML files, the canonical XML format for the Protein Data Bank.
* Of course, jV can read and display the traditional PDB format files, too.
* RasMol-like usability.
* jV can process more than one molecules.
* jV can display polygons specified by XML. ([http://ef-site.hgc.jp/eF-site/schema/polygon12.xsd XML Schema for polygons] is available.)
* Multiple polygons can be processed simultaneously, and be superimposed onto molecular images.
* Animation can be realized.
* jV runs on the Java Runtime Environment ([http://java.sun.com/javase/index.jsp JRE]) so that it can work as a stand-alone application as well as an applet.
* The graphics of jV is based on OpenGL (JOGL), thereby producing fairly beautiful pictures.


&lt;br/&gt;
&lt;big&gt;'''MediaWiki has been successfully installed.'''&lt;/big&gt;

Consult the [http://meta.wikimedia.org/wiki/Help:Contents User's Guide] for information on using the wiki software.

== Getting started ==
* [http://www.mediawiki.org/wiki/Manual:Configuration_settings Configuration settings list]
* [http://www.mediawiki.org/wiki/Manual:FAQ MediaWiki FAQ]
* [https://lists.wikimedia.org/mailman/listinfo/mediawiki-announce MediaWiki release mailing list]</text>
    <sha1>303ffd70557280d273b6cc60364070c0de6e4eb7</sha1>
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    <parentid>26</parentid>
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      <id>2</id>
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    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="2243" xml:space="preserve">&lt;big&gt;'''Welcome to jV wiki.'''&lt;/big&gt;

jV(formerly known as PDBjViewer) is a program to display molecular graphics of protein and nucleic acids. The program 'jV' has been developed by [http://www.hgc.jp/~kinosita/TOP.html Kengo Kinoshita] ([http://www.hgc.jp/english/ Human Genome Center], [http://www.ims.u-tokyo.ac.jp/imsut/en/ Insutitute for Medical Science],[http://www.u-tokyo.ac.jp/index_e.html University of Tokyo]) and [http://www.protein.osaka-u.ac.jp/rcsfp/pi/ Haruki Nakamura] ([http://www.protein.osaka-u.ac.jp/index_e.php Institute for Protein Research], [http://www.osaka-u.ac.jp/eng/index.html Osaka Univeristy]), with the support from [http://www-bird.jst.go.jp/index_e.html JST-BIRD].

== jV version 3 ==
&lt;br /&gt;[[File:Download.png|right|link=http://ef-site.hgc.jp/eF-site/servlet/Registration|Download]]
&lt;font size="1"&gt;Version 3.6 was released on 11, Aug, 2008.&lt;br /&gt;This version is fully compativle with [https://applet-launcher.dev.java.net/ applet-launcher].&lt;/font&gt;&lt;br /&gt;
&lt;br /&gt;
jV supports the following features:
* jV can read and display PDBML files, the canonical XML format for the Protein Data Bank.
* Of course, jV can read and display the traditional PDB format files, too.
* RasMol-like usability.
* jV can process more than one molecules.
* jV can display polygons specified by XML. ([http://ef-site.hgc.jp/eF-site/schema/polygon12.xsd XML Schema for polygons] is available.)
* Multiple polygons can be processed simultaneously, and be superimposed onto molecular images.
* Animation can be realized.
* jV runs on the Java Runtime Environment ([http://java.sun.com/javase/index.jsp JRE]) so that it can work as a stand-alone application as well as an applet.
* The graphics of jV is based on OpenGL (JOGL), thereby producing fairly beautiful pictures.


&lt;br/&gt;
&lt;big&gt;'''MediaWiki has been successfully installed.'''&lt;/big&gt;

Consult the [http://meta.wikimedia.org/wiki/Help:Contents User's Guide] for information on using the wiki software.

== Getting started ==
* [http://www.mediawiki.org/wiki/Manual:Configuration_settings Configuration settings list]
* [http://www.mediawiki.org/wiki/Manual:FAQ MediaWiki FAQ]
* [https://lists.wikimedia.org/mailman/listinfo/mediawiki-announce MediaWiki release mailing list]</text>
    <sha1>c8d0e2fbf4a87e9c68522f9ed67305a32b196662</sha1>
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  <revision>
    <id>28</id>
    <parentid>27</parentid>
    <timestamp>2009-03-03T08:11:32Z</timestamp>
    <contributor>
      <username>JVuser</username>
      <id>2</id>
    </contributor>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="2294" xml:space="preserve">&lt;big&gt;'''Welcome to jV wiki.'''&lt;/big&gt;

jV(formerly known as PDBjViewer) is a program to display molecular graphics of protein and nucleic acids. 


jV supports the following features:
* jV can read and display PDBML files, the canonical XML format for the Protein Data Bank.
* Of course, jV can read and display the traditional PDB format files, too.
* RasMol-like usability.
* jV can process more than one molecules.
* jV can display polygons specified by XML. ([http://ef-site.hgc.jp/eF-site/schema/polygon12.xsd XML Schema for polygons] is available.)
* Multiple polygons can be processed simultaneously, and be superimposed onto molecular images.
* Animation can be realized.


The program 'jV' has been developed by [http://www.hgc.jp/~kinosita/TOP.html Kengo Kinoshita] ([http://www.hgc.jp/english/ Human Genome Center], [http://www.ims.u-tokyo.ac.jp/imsut/en/ Insutitute for Medical Science],[http://www.u-tokyo.ac.jp/index_e.html University of Tokyo]) and [http://www.protein.osaka-u.ac.jp/rcsfp/pi/ Haruki Nakamura] ([http://www.protein.osaka-u.ac.jp/index_e.php Institute for Protein Research], [http://www.osaka-u.ac.jp/eng/index.html Osaka Univeristy]), with the support from [http://www-bird.jst.go.jp/index_e.html JST-BIRD].

== jV version 3 ==
&lt;br /&gt;[[File:Download.png|right|link=http://ef-site.hgc.jp/eF-site/servlet/Registration|Download]]
&lt;font size="1"&gt;Version 3.6 was released on 11, Aug, 2008.&lt;br /&gt;This version is fully compativle with [https://applet-launcher.dev.java.net/ applet-launcher].&lt;/font&gt;&lt;br /&gt;
&lt;br /&gt;
jV version 3 supports the following features:
* jV runs on the Java Runtime Environment ([http://java.sun.com/javase/index.jsp JRE]) so that it can work as a stand-alone application as well as an applet.
* The graphics of jV is based on OpenGL (JOGL), thereby producing fairly beautiful pictures.


&lt;br/&gt;
&lt;big&gt;'''MediaWiki has been successfully installed.'''&lt;/big&gt;

Consult the [http://meta.wikimedia.org/wiki/Help:Contents User's Guide] for information on using the wiki software.

== Getting started ==
* [http://www.mediawiki.org/wiki/Manual:Configuration_settings Configuration settings list]
* [http://www.mediawiki.org/wiki/Manual:FAQ MediaWiki FAQ]
* [https://lists.wikimedia.org/mailman/listinfo/mediawiki-announce MediaWiki release mailing list]</text>
    <sha1>fa3e56ff509801c3b40ec95b633b720fe4bcc7db</sha1>
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  <revision>
    <id>29</id>
    <parentid>28</parentid>
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    <contributor>
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      <id>2</id>
    </contributor>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="2345" xml:space="preserve">&lt;big&gt;'''Welcome to jV wiki.'''&lt;/big&gt;

jV(formerly known as PDBjViewer) is a program to display molecular graphics of protein and nucleic acids. 


jV supports the following features:
* jV can read and display PDBML files, the canonical XML format for the Protein Data Bank.
* Of course, jV can read and display the traditional PDB format files, too.
* RasMol-like usability.
* jV can process more than one molecules.
* jV can display polygons specified by XML. ([http://ef-site.hgc.jp/eF-site/schema/polygon12.xsd XML Schema for polygons] is available.)
* Multiple polygons can be processed simultaneously, and be superimposed onto molecular images.
* Animation can be realized.


The program 'jV' has been developed by [http://www.hgc.jp/~kinosita/TOP.html Kengo Kinoshita] ([http://www.hgc.jp/english/ Human Genome Center], [http://www.ims.u-tokyo.ac.jp/imsut/en/ Insutitute for Medical Science],[http://www.u-tokyo.ac.jp/index_e.html University of Tokyo]) and [http://www.protein.osaka-u.ac.jp/rcsfp/pi/ Haruki Nakamura] ([http://www.protein.osaka-u.ac.jp/index_e.php Institute for Protein Research], [http://www.osaka-u.ac.jp/eng/index.html Osaka Univeristy]), with the support from [http://www-bird.jst.go.jp/index_e.html JST-BIRD].

== jV version 3 ==
&lt;br /&gt;[[File:Download.png|right|link=http://ef-site.hgc.jp/eF-site/servlet/Registration|Download]]
&lt;font size="1"&gt;Version 3.6 was released on 11, Aug, 2008.&lt;br /&gt;This version is fully compativle with [https://applet-launcher.dev.java.net/ applet-launcher].&lt;/font&gt;&lt;br /&gt;
&lt;br /&gt;
jV version 3 supports the following features:
* jV runs on the Java Runtime Environment ([http://java.sun.com/javase/index.jsp JRE]) so that it can work as a stand-alone application as well as an applet.
* The graphics of jV is based on OpenGL (JOGL), thereby producing fairly beautiful pictures.


== jV version 2 ==


== jV version 1 (PDBjViewer) ==


&lt;br/&gt;
&lt;big&gt;'''MediaWiki has been successfully installed.'''&lt;/big&gt;

Consult the [http://meta.wikimedia.org/wiki/Help:Contents User's Guide] for information on using the wiki software.

== Getting started ==
* [http://www.mediawiki.org/wiki/Manual:Configuration_settings Configuration settings list]
* [http://www.mediawiki.org/wiki/Manual:FAQ MediaWiki FAQ]
* [https://lists.wikimedia.org/mailman/listinfo/mediawiki-announce MediaWiki release mailing list]</text>
    <sha1>3b2215a8e46c09245ee3ea64678a77eaf60a2928</sha1>
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  <revision>
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    <parentid>29</parentid>
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    <contributor>
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    <model>wikitext</model>
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    <text bytes="2381" xml:space="preserve">&lt;big&gt;'''Welcome to jV wiki.'''&lt;/big&gt;
{| style="float:right"
 |__TOC__
 |}
jV(formerly known as PDBjViewer) is a program to display molecular graphics of protein and nucleic acids. 


jV supports the following features:
* jV can read and display PDBML files, the canonical XML format for the Protein Data Bank.
* Of course, jV can read and display the traditional PDB format files, too.
* RasMol-like usability.
* jV can process more than one molecules.
* jV can display polygons specified by XML. ([http://ef-site.hgc.jp/eF-site/schema/polygon12.xsd XML Schema for polygons] is available.)
* Multiple polygons can be processed simultaneously, and be superimposed onto molecular images.
* Animation can be realized.


The program 'jV' has been developed by [http://www.hgc.jp/~kinosita/TOP.html Kengo Kinoshita] ([http://www.hgc.jp/english/ Human Genome Center], [http://www.ims.u-tokyo.ac.jp/imsut/en/ Insutitute for Medical Science],[http://www.u-tokyo.ac.jp/index_e.html University of Tokyo]) and [http://www.protein.osaka-u.ac.jp/rcsfp/pi/ Haruki Nakamura] ([http://www.protein.osaka-u.ac.jp/index_e.php Institute for Protein Research], [http://www.osaka-u.ac.jp/eng/index.html Osaka Univeristy]), with the support from [http://www-bird.jst.go.jp/index_e.html JST-BIRD].

== jV version 3 ==
&lt;br /&gt;[[File:Download.png|right|link=http://ef-site.hgc.jp/eF-site/servlet/Registration|Download]]
&lt;font size="1"&gt;Version 3.6 was released on 11, Aug, 2008.&lt;br /&gt;This version is fully compativle with [https://applet-launcher.dev.java.net/ applet-launcher].&lt;/font&gt;&lt;br /&gt;
&lt;br /&gt;
jV version 3 supports the following features:
* jV runs on the Java Runtime Environment ([http://java.sun.com/javase/index.jsp JRE]) so that it can work as a stand-alone application as well as an applet.
* The graphics of jV is based on OpenGL (JOGL), thereby producing fairly beautiful pictures.


== jV version 2 ==


== jV version 1 (PDBjViewer) ==


&lt;br/&gt;
&lt;big&gt;'''MediaWiki has been successfully installed.'''&lt;/big&gt;

Consult the [http://meta.wikimedia.org/wiki/Help:Contents User's Guide] for information on using the wiki software.

== Getting started ==
* [http://www.mediawiki.org/wiki/Manual:Configuration_settings Configuration settings list]
* [http://www.mediawiki.org/wiki/Manual:FAQ MediaWiki FAQ]
* [https://lists.wikimedia.org/mailman/listinfo/mediawiki-announce MediaWiki release mailing list]</text>
    <sha1>1ecfabc22dab20d7f4c5529d5e5fad8a02bdfc55</sha1>
  </revision>
  <revision>
    <id>31</id>
    <parentid>30</parentid>
    <timestamp>2009-03-03T08:44:37Z</timestamp>
    <contributor>
      <username>JVuser</username>
      <id>2</id>
    </contributor>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="2672" xml:space="preserve">&lt;big&gt;'''Welcome to jV wiki.'''&lt;/big&gt;
{| style="float:right"
 |__TOC__
 |}
jV(formerly known as PDBjViewer) is a program to display molecular graphics of protein and nucleic acids. 
jV can use as a stand-alone program and can operate on a web browser as an Java applet. jV is used by PDBj services([http://ef-site.hgc.jp/eF-site/index.jsp eF-site], [http://ef-site.hgc.jp/eF-seek/index.jsp eF-seek], the molecular structure surface database of the protein functional part).

jV supports the following features:
* jV can read and display PDBML files, the canonical XML format for the Protein Data Bank.
* Of course, jV can read and display the traditional PDB format files, too.
* RasMol-like usability.
* jV can process more than one molecules.
* jV can display polygons specified by XML. ([http://ef-site.hgc.jp/eF-site/schema/polygon12.xsd XML Schema for polygons] is available.)
* Multiple polygons can be processed simultaneously, and be superimposed onto molecular images.
* Animation can be realized.


The program 'jV' has been developed by [http://www.hgc.jp/~kinosita/TOP.html Kengo Kinoshita] ([http://www.hgc.jp/english/ Human Genome Center], [http://www.ims.u-tokyo.ac.jp/imsut/en/ Insutitute for Medical Science],[http://www.u-tokyo.ac.jp/index_e.html University of Tokyo]) and [http://www.protein.osaka-u.ac.jp/rcsfp/pi/ Haruki Nakamura] ([http://www.protein.osaka-u.ac.jp/index_e.php Institute for Protein Research], [http://www.osaka-u.ac.jp/eng/index.html Osaka Univeristy]), with the support from [http://www-bird.jst.go.jp/index_e.html JST-BIRD].

== jV version 3 ==
&lt;br /&gt;[[File:Download.png|right|link=http://ef-site.hgc.jp/eF-site/servlet/Registration|Download]]
&lt;font size="1"&gt;Version 3.6 was released on 11, Aug, 2008.&lt;br /&gt;This version is fully compativle with [https://applet-launcher.dev.java.net/ applet-launcher].&lt;/font&gt;&lt;br /&gt;
&lt;br /&gt;
jV version 3 supports the following features:
* jV runs on the Java Runtime Environment ([http://java.sun.com/javase/index.jsp JRE]) so that it can work as a stand-alone application as well as an applet.
* The graphics of jV is based on OpenGL (JOGL), thereby producing fairly beautiful pictures.


== jV version 2 ==


== jV version 1 (PDBjViewer) ==


&lt;br/&gt;
&lt;big&gt;'''MediaWiki has been successfully installed.'''&lt;/big&gt;

Consult the [http://meta.wikimedia.org/wiki/Help:Contents User's Guide] for information on using the wiki software.

== Getting started ==
* [http://www.mediawiki.org/wiki/Manual:Configuration_settings Configuration settings list]
* [http://www.mediawiki.org/wiki/Manual:FAQ MediaWiki FAQ]
* [https://lists.wikimedia.org/mailman/listinfo/mediawiki-announce MediaWiki release mailing list]</text>
    <sha1>2165942e31d1674e32ba3f472d41b02b570a14bf</sha1>
  </revision>
  <revision>
    <id>32</id>
    <parentid>31</parentid>
    <timestamp>2009-03-03T08:46:59Z</timestamp>
    <contributor>
      <username>JVuser</username>
      <id>2</id>
    </contributor>
    <comment>/* jV version 3 */</comment>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="2827" xml:space="preserve">&lt;big&gt;'''Welcome to jV wiki.'''&lt;/big&gt;
{| style="float:right"
 |__TOC__
 |}
jV(formerly known as PDBjViewer) is a program to display molecular graphics of protein and nucleic acids. 
jV can use as a stand-alone program and can operate on a web browser as an Java applet. jV is used by PDBj services([http://ef-site.hgc.jp/eF-site/index.jsp eF-site], [http://ef-site.hgc.jp/eF-seek/index.jsp eF-seek], the molecular structure surface database of the protein functional part).

jV supports the following features:
* jV can read and display PDBML files, the canonical XML format for the Protein Data Bank.
* Of course, jV can read and display the traditional PDB format files, too.
* RasMol-like usability.
* jV can process more than one molecules.
* jV can display polygons specified by XML. ([http://ef-site.hgc.jp/eF-site/schema/polygon12.xsd XML Schema for polygons] is available.)
* Multiple polygons can be processed simultaneously, and be superimposed onto molecular images.
* Animation can be realized.


The program 'jV' has been developed by [http://www.hgc.jp/~kinosita/TOP.html Kengo Kinoshita] ([http://www.hgc.jp/english/ Human Genome Center], [http://www.ims.u-tokyo.ac.jp/imsut/en/ Insutitute for Medical Science],[http://www.u-tokyo.ac.jp/index_e.html University of Tokyo]) and [http://www.protein.osaka-u.ac.jp/rcsfp/pi/ Haruki Nakamura] ([http://www.protein.osaka-u.ac.jp/index_e.php Institute for Protein Research], [http://www.osaka-u.ac.jp/eng/index.html Osaka Univeristy]), with the support from [http://www-bird.jst.go.jp/index_e.html JST-BIRD].

== jV version 3 ==
[[File:Download.png|right|link=http://ef-site.hgc.jp/eF-site/servlet/Registration|Download]]&lt;br /&gt;
[http://ef-site.hgc.jp/jV/ jV version 3] is now used to display molecules and their surfaces as a Java applet program.
It requires the following softwares.
&lt;font size="1"&gt;Version 3.6 was released on 11, Aug, 2008.&lt;br /&gt;This version is fully compativle with [https://applet-launcher.dev.java.net/ applet-launcher].&lt;/font&gt;&lt;br /&gt;
&lt;br /&gt;
jV version 3 supports the following features:
* jV runs on the Java Runtime Environment ([http://java.sun.com/javase/index.jsp JRE]) so that it can work as a stand-alone application as well as an applet.
* The graphics of jV is based on OpenGL (JOGL), thereby producing fairly beautiful pictures.

== jV version 2 ==


== jV version 1 (PDBjViewer) ==


&lt;br/&gt;
&lt;big&gt;'''MediaWiki has been successfully installed.'''&lt;/big&gt;

Consult the [http://meta.wikimedia.org/wiki/Help:Contents User's Guide] for information on using the wiki software.

== Getting started ==
* [http://www.mediawiki.org/wiki/Manual:Configuration_settings Configuration settings list]
* [http://www.mediawiki.org/wiki/Manual:FAQ MediaWiki FAQ]
* [https://lists.wikimedia.org/mailman/listinfo/mediawiki-announce MediaWiki release mailing list]</text>
    <sha1>52b57d4d57b86ff587a9f6a533e5e77cbfb67761</sha1>
  </revision>
  <revision>
    <id>33</id>
    <parentid>32</parentid>
    <timestamp>2009-03-03T08:47:36Z</timestamp>
    <contributor>
      <username>JVuser</username>
      <id>2</id>
    </contributor>
    <comment>/* jV version 3 */</comment>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="2830" xml:space="preserve">&lt;big&gt;'''Welcome to jV wiki.'''&lt;/big&gt;
{| style="float:right"
 |__TOC__
 |}
jV(formerly known as PDBjViewer) is a program to display molecular graphics of protein and nucleic acids. 
jV can use as a stand-alone program and can operate on a web browser as an Java applet. jV is used by PDBj services([http://ef-site.hgc.jp/eF-site/index.jsp eF-site], [http://ef-site.hgc.jp/eF-seek/index.jsp eF-seek], the molecular structure surface database of the protein functional part).

jV supports the following features:
* jV can read and display PDBML files, the canonical XML format for the Protein Data Bank.
* Of course, jV can read and display the traditional PDB format files, too.
* RasMol-like usability.
* jV can process more than one molecules.
* jV can display polygons specified by XML. ([http://ef-site.hgc.jp/eF-site/schema/polygon12.xsd XML Schema for polygons] is available.)
* Multiple polygons can be processed simultaneously, and be superimposed onto molecular images.
* Animation can be realized.


The program 'jV' has been developed by [http://www.hgc.jp/~kinosita/TOP.html Kengo Kinoshita] ([http://www.hgc.jp/english/ Human Genome Center], [http://www.ims.u-tokyo.ac.jp/imsut/en/ Insutitute for Medical Science],[http://www.u-tokyo.ac.jp/index_e.html University of Tokyo]) and [http://www.protein.osaka-u.ac.jp/rcsfp/pi/ Haruki Nakamura] ([http://www.protein.osaka-u.ac.jp/index_e.php Institute for Protein Research], [http://www.osaka-u.ac.jp/eng/index.html Osaka Univeristy]), with the support from [http://www-bird.jst.go.jp/index_e.html JST-BIRD].

== jV version 3 ==
[[File:Download.png|right|link=http://ef-site.hgc.jp/eF-site/servlet/Registration|Download]][http://ef-site.hgc.jp/jV/ jV version 3] is now used to display molecules and their surfaces as a Java applet program.&lt;br /&gt;It requires the following softwares.&lt;br /&gt;&lt;font size="1"&gt;Version 3.6 was released on 11, Aug, 2008.&lt;br /&gt;This version is fully compativle with [https://applet-launcher.dev.java.net/ applet-launcher].&lt;/font&gt;&lt;br /&gt;
&lt;br /&gt;
jV version 3 supports the following features:
* jV runs on the Java Runtime Environment ([http://java.sun.com/javase/index.jsp JRE]) so that it can work as a stand-alone application as well as an applet.
* The graphics of jV is based on OpenGL (JOGL), thereby producing fairly beautiful pictures.

== jV version 2 ==


== jV version 1 (PDBjViewer) ==


&lt;br/&gt;
&lt;big&gt;'''MediaWiki has been successfully installed.'''&lt;/big&gt;

Consult the [http://meta.wikimedia.org/wiki/Help:Contents User's Guide] for information on using the wiki software.

== Getting started ==
* [http://www.mediawiki.org/wiki/Manual:Configuration_settings Configuration settings list]
* [http://www.mediawiki.org/wiki/Manual:FAQ MediaWiki FAQ]
* [https://lists.wikimedia.org/mailman/listinfo/mediawiki-announce MediaWiki release mailing list]</text>
    <sha1>cd0f2ff264ec385e7e2bee3af3631a6c6488d38c</sha1>
  </revision>
  <revision>
    <id>34</id>
    <parentid>33</parentid>
    <timestamp>2009-03-03T08:48:37Z</timestamp>
    <contributor>
      <username>JVuser</username>
      <id>2</id>
    </contributor>
    <comment>/* jV version 3 */</comment>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="2831" xml:space="preserve">&lt;big&gt;'''Welcome to jV wiki.'''&lt;/big&gt;
{| style="float:right"
 |__TOC__
 |}
jV(formerly known as PDBjViewer) is a program to display molecular graphics of protein and nucleic acids. 
jV can use as a stand-alone program and can operate on a web browser as an Java applet. jV is used by PDBj services([http://ef-site.hgc.jp/eF-site/index.jsp eF-site], [http://ef-site.hgc.jp/eF-seek/index.jsp eF-seek], the molecular structure surface database of the protein functional part).

jV supports the following features:
* jV can read and display PDBML files, the canonical XML format for the Protein Data Bank.
* Of course, jV can read and display the traditional PDB format files, too.
* RasMol-like usability.
* jV can process more than one molecules.
* jV can display polygons specified by XML. ([http://ef-site.hgc.jp/eF-site/schema/polygon12.xsd XML Schema for polygons] is available.)
* Multiple polygons can be processed simultaneously, and be superimposed onto molecular images.
* Animation can be realized.


The program 'jV' has been developed by [http://www.hgc.jp/~kinosita/TOP.html Kengo Kinoshita] ([http://www.hgc.jp/english/ Human Genome Center], [http://www.ims.u-tokyo.ac.jp/imsut/en/ Insutitute for Medical Science],[http://www.u-tokyo.ac.jp/index_e.html University of Tokyo]) and [http://www.protein.osaka-u.ac.jp/rcsfp/pi/ Haruki Nakamura] ([http://www.protein.osaka-u.ac.jp/index_e.php Institute for Protein Research], [http://www.osaka-u.ac.jp/eng/index.html Osaka Univeristy]), with the support from [http://www-bird.jst.go.jp/index_e.html JST-BIRD].

== jV version 3 ==
[[File:Download.png|right|link=http://ef-site.hgc.jp/eF-site/servlet/Registration|Download]][http://ef-site.hgc.jp/jV/ jV version 3] is now used to display molecules and their surfaces as a Java applet program.&lt;br /&gt;&lt;font size="1"&gt;Version 3.6 was released on 11, Aug, 2008.&lt;br /&gt;This version is fully compativle with [https://applet-launcher.dev.java.net/ applet-launcher].&lt;/font&gt;&lt;br /&gt;
&lt;br /&gt;
It requires the following softwares.&lt;br /&gt;
jV version 3 supports the following features:
* jV runs on the Java Runtime Environment ([http://java.sun.com/javase/index.jsp JRE]) so that it can work as a stand-alone application as well as an applet.
* The graphics of jV is based on OpenGL (JOGL), thereby producing fairly beautiful pictures.

== jV version 2 ==


== jV version 1 (PDBjViewer) ==


&lt;br/&gt;
&lt;big&gt;'''MediaWiki has been successfully installed.'''&lt;/big&gt;

Consult the [http://meta.wikimedia.org/wiki/Help:Contents User's Guide] for information on using the wiki software.

== Getting started ==
* [http://www.mediawiki.org/wiki/Manual:Configuration_settings Configuration settings list]
* [http://www.mediawiki.org/wiki/Manual:FAQ MediaWiki FAQ]
* [https://lists.wikimedia.org/mailman/listinfo/mediawiki-announce MediaWiki release mailing list]</text>
    <sha1>9dcfaab7e3e3937a04c95ee09bf16b926c750cdb</sha1>
  </revision>
  <revision>
    <id>35</id>
    <parentid>34</parentid>
    <timestamp>2009-03-03T08:57:27Z</timestamp>
    <contributor>
      <username>JVuser</username>
      <id>2</id>
    </contributor>
    <comment>/* jV version 3 */</comment>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="2890" xml:space="preserve">&lt;big&gt;'''Welcome to jV wiki.'''&lt;/big&gt;
{| style="float:right"
 |__TOC__
 |}
jV(formerly known as PDBjViewer) is a program to display molecular graphics of protein and nucleic acids. 
jV can use as a stand-alone program and can operate on a web browser as an Java applet. jV is used by PDBj services([http://ef-site.hgc.jp/eF-site/index.jsp eF-site], [http://ef-site.hgc.jp/eF-seek/index.jsp eF-seek], the molecular structure surface database of the protein functional part).

jV supports the following features:
* jV can read and display PDBML files, the canonical XML format for the Protein Data Bank.
* Of course, jV can read and display the traditional PDB format files, too.
* RasMol-like usability.
* jV can process more than one molecules.
* jV can display polygons specified by XML. ([http://ef-site.hgc.jp/eF-site/schema/polygon12.xsd XML Schema for polygons] is available.)
* Multiple polygons can be processed simultaneously, and be superimposed onto molecular images.
* Animation can be realized.


The program 'jV' has been developed by [http://www.hgc.jp/~kinosita/TOP.html Kengo Kinoshita] ([http://www.hgc.jp/english/ Human Genome Center], [http://www.ims.u-tokyo.ac.jp/imsut/en/ Insutitute for Medical Science],[http://www.u-tokyo.ac.jp/index_e.html University of Tokyo]) and [http://www.protein.osaka-u.ac.jp/rcsfp/pi/ Haruki Nakamura] ([http://www.protein.osaka-u.ac.jp/index_e.php Institute for Protein Research], [http://www.osaka-u.ac.jp/eng/index.html Osaka Univeristy]), with the support from [http://www-bird.jst.go.jp/index_e.html JST-BIRD].

== jV version 3 ==
[[File:Download.png|right|link=http://ef-site.hgc.jp/eF-site/servlet/Registration|Download]][http://ef-site.hgc.jp/jV/ jV version 3] is now used to display molecules and their surfaces as a Java applet program.&lt;br /&gt;&lt;font size="1"&gt;Version 3.6 was released on 11, Aug, 2008.&lt;br /&gt;This version is fully compativle with [https://applet-launcher.dev.java.net/ applet-launcher].&lt;/font&gt;&lt;br /&gt;
&lt;br /&gt;
It requires the following softwares.&lt;br /&gt;
** JRE 1.4.2 or later  (recommend 1.4.2_12)&lt;br&gt;jV runs on the Java Runtime Environment ([http://java.sun.com/javase/index.jsp JRE]) so that it can work as a stand-alone application as well as an applet.
** JOGL 1.0, 1.1.1 or JSR-231 1.0.0  (recommend JSR-231)&lt;br /&gt;The graphics of jV is based on OpenGL (JOGL), thereby producing fairly beautiful pictures.

== jV version 2 ==


== jV version 1 (PDBjViewer) ==


&lt;br/&gt;
&lt;big&gt;'''MediaWiki has been successfully installed.'''&lt;/big&gt;

Consult the [http://meta.wikimedia.org/wiki/Help:Contents User's Guide] for information on using the wiki software.

== Getting started ==
* [http://www.mediawiki.org/wiki/Manual:Configuration_settings Configuration settings list]
* [http://www.mediawiki.org/wiki/Manual:FAQ MediaWiki FAQ]
* [https://lists.wikimedia.org/mailman/listinfo/mediawiki-announce MediaWiki release mailing list]</text>
    <sha1>a94258319e5cc9805cd70d0e66b9257ccd2020b8</sha1>
  </revision>
  <revision>
    <id>36</id>
    <parentid>35</parentid>
    <timestamp>2009-03-03T08:58:50Z</timestamp>
    <contributor>
      <username>JVuser</username>
      <id>2</id>
    </contributor>
    <comment>/* jV version 3 */</comment>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="4075" xml:space="preserve">&lt;big&gt;'''Welcome to jV wiki.'''&lt;/big&gt;
{| style="float:right"
 |__TOC__
 |}
jV(formerly known as PDBjViewer) is a program to display molecular graphics of protein and nucleic acids. 
jV can use as a stand-alone program and can operate on a web browser as an Java applet. jV is used by PDBj services([http://ef-site.hgc.jp/eF-site/index.jsp eF-site], [http://ef-site.hgc.jp/eF-seek/index.jsp eF-seek], the molecular structure surface database of the protein functional part).

jV supports the following features:
* jV can read and display PDBML files, the canonical XML format for the Protein Data Bank.
* Of course, jV can read and display the traditional PDB format files, too.
* RasMol-like usability.
* jV can process more than one molecules.
* jV can display polygons specified by XML. ([http://ef-site.hgc.jp/eF-site/schema/polygon12.xsd XML Schema for polygons] is available.)
* Multiple polygons can be processed simultaneously, and be superimposed onto molecular images.
* Animation can be realized.


The program 'jV' has been developed by [http://www.hgc.jp/~kinosita/TOP.html Kengo Kinoshita] ([http://www.hgc.jp/english/ Human Genome Center], [http://www.ims.u-tokyo.ac.jp/imsut/en/ Insutitute for Medical Science],[http://www.u-tokyo.ac.jp/index_e.html University of Tokyo]) and [http://www.protein.osaka-u.ac.jp/rcsfp/pi/ Haruki Nakamura] ([http://www.protein.osaka-u.ac.jp/index_e.php Institute for Protein Research], [http://www.osaka-u.ac.jp/eng/index.html Osaka Univeristy]), with the support from [http://www-bird.jst.go.jp/index_e.html JST-BIRD].

== jV version 3 ==
[[File:Download.png|right|link=http://ef-site.hgc.jp/eF-site/servlet/Registration|Download]][http://ef-site.hgc.jp/jV/ jV version 3] is now used to display molecules and their surfaces as a Java applet program.&lt;br /&gt;&lt;font size="1"&gt;Version 3.6 was released on 11, Aug, 2008.&lt;br /&gt;This version is fully compativle with [https://applet-launcher.dev.java.net/ applet-launcher].&lt;/font&gt;&lt;br /&gt;
&lt;br /&gt;
It requires the following softwares.&lt;br /&gt;
* JRE 1.4.2 or later  (recommend 1.4.2_12)&lt;br&gt;jV runs on the Java Runtime Environment ([http://java.sun.com/javase/index.jsp JRE]) so that it can work as a stand-alone application as well as an applet.
* JOGL 1.0, 1.1.1 or JSR-231 1.0.0  (recommend JSR-231)&lt;br /&gt;The graphics of jV is based on OpenGL (JOGL), thereby producing fairly beautiful pictures.

[https://jogl.dev.java.net/ JOGL](Java bindings for OpenGL) library is available here.

* version 1.0 [[http://ef-site.hgc.jp/eF-site/jV/JOGL1.0_win32.zip Windows],[http://ef-site.hgc.jp/eF-site/jV/JOGL1.0_macosx.tar.gz Mac OS X],[http://ef-site.hgc.jp/eF-site/jV/JOGL1.0_linux.tar.gz Linux]]
* version 1.1.1 [[http://ef-site.hgc.jp/eF-site/jV/JOGL1.1.1_win32.zip Windows],[http://ef-site.hgc.jp/eF-site/jV/JOGL1.1.1_macosx.tar.gz Mac OS X], [http://ef-site.hgc.jp/eF-site/jV/JOGL1.1.1_linux.tar.gz Linux]]
* JSR-231 1.0.0 [[http://ef-site.hgc.jp/eF-site/jV/JOGL_JSR231_win32.zip Windows], [http://ef-site.hgc.jp/eF-site/jV/JOGL_JSR231_macosx_ppc.tar.gz Mac OS X ppc], [http://ef-site.hgc.jp/eF-site/jV/JOGL_JSR231_macosx_universal.tar.gz Mac OS X universal], [http://ef-site.hgc.jp/eF-site/jV/JOGL_JSR231_linux_i586.tar.gz Linux]]

&lt;font size="-1"&gt;Note: &amp;nbsp; JOGL 1.0 and 1.1.1 are not available for Intel Mac.The latest version of JOGL, JSR-231 1.0.0, runs on Intel Mac.
&lt;/font&gt;
&lt;br /&gt;
&lt;div align="center"&gt;
&lt;b&gt;Download jV &amp; PDBjViewer&lt;/b&gt;
[[http://ef-site.hgc.jp/eF-site/servlet/DownloadViewerBinary binary], [http://ef-site.hgc.jp/eF-site/servlet/Registration source code]]
&lt;/div&gt;

== jV version 2 ==


== jV version 1 (PDBjViewer) ==


&lt;br/&gt;
&lt;big&gt;'''MediaWiki has been successfully installed.'''&lt;/big&gt;

Consult the [http://meta.wikimedia.org/wiki/Help:Contents User's Guide] for information on using the wiki software.

== Getting started ==
* [http://www.mediawiki.org/wiki/Manual:Configuration_settings Configuration settings list]
* [http://www.mediawiki.org/wiki/Manual:FAQ MediaWiki FAQ]
* [https://lists.wikimedia.org/mailman/listinfo/mediawiki-announce MediaWiki release mailing list]</text>
    <sha1>c71189dacdc3967274cb85f554522b2695c2960e</sha1>
  </revision>
  <revision>
    <id>37</id>
    <parentid>36</parentid>
    <timestamp>2009-03-03T09:00:38Z</timestamp>
    <contributor>
      <username>JVuser</username>
      <id>2</id>
    </contributor>
    <comment>/* jV version 3 */</comment>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="3815" xml:space="preserve">&lt;big&gt;'''Welcome to jV wiki.'''&lt;/big&gt;
{| style="float:right"
 |__TOC__
 |}
jV(formerly known as PDBjViewer) is a program to display molecular graphics of protein and nucleic acids. 
jV can use as a stand-alone program and can operate on a web browser as an Java applet. jV is used by PDBj services([http://ef-site.hgc.jp/eF-site/index.jsp eF-site], [http://ef-site.hgc.jp/eF-seek/index.jsp eF-seek], the molecular structure surface database of the protein functional part).

jV supports the following features:
* jV can read and display PDBML files, the canonical XML format for the Protein Data Bank.
* Of course, jV can read and display the traditional PDB format files, too.
* RasMol-like usability.
* jV can process more than one molecules.
* jV can display polygons specified by XML. ([http://ef-site.hgc.jp/eF-site/schema/polygon12.xsd XML Schema for polygons] is available.)
* Multiple polygons can be processed simultaneously, and be superimposed onto molecular images.
* Animation can be realized.


The program 'jV' has been developed by [http://www.hgc.jp/~kinosita/TOP.html Kengo Kinoshita] ([http://www.hgc.jp/english/ Human Genome Center], [http://www.ims.u-tokyo.ac.jp/imsut/en/ Insutitute for Medical Science],[http://www.u-tokyo.ac.jp/index_e.html University of Tokyo]) and [http://www.protein.osaka-u.ac.jp/rcsfp/pi/ Haruki Nakamura] ([http://www.protein.osaka-u.ac.jp/index_e.php Institute for Protein Research], [http://www.osaka-u.ac.jp/eng/index.html Osaka Univeristy]), with the support from [http://www-bird.jst.go.jp/index_e.html JST-BIRD].

== jV version 3 ==
[[File:Download.png|right|link=http://ef-site.hgc.jp/eF-site/servlet/Registration|Download]][http://ef-site.hgc.jp/jV/ jV version 3] is now used to display molecules and their surfaces as a Java applet program.&lt;br /&gt;&lt;font size="1"&gt;Version 3.6 was released on 11, Aug, 2008.&lt;br /&gt;This version is fully compativle with [https://applet-launcher.dev.java.net/ applet-launcher].&lt;/font&gt;&lt;br /&gt;
&lt;br /&gt;
It requires the following softwares.&lt;br /&gt;
* JRE 1.4.2 or later  (recommend 1.4.2_12)&lt;br&gt;jV runs on the Java Runtime Environment ([http://java.sun.com/javase/index.jsp JRE]) so that it can work as a stand-alone application as well as an applet.
* JOGL 1.0, 1.1.1 or JSR-231 1.0.0  (recommend JSR-231)&lt;br /&gt;The graphics of jV is based on OpenGL ([https://jogl.dev.java.net/ JOGL]), thereby producing fairly beautiful pictures.
** version 1.0 [[http://ef-site.hgc.jp/eF-site/jV/JOGL1.0_win32.zip Windows],[http://ef-site.hgc.jp/eF-site/jV/JOGL1.0_macosx.tar.gz Mac OS X],[http://ef-site.hgc.jp/eF-site/jV/JOGL1.0_linux.tar.gz Linux]]
** version 1.1.1 [[http://ef-site.hgc.jp/eF-site/jV/JOGL1.1.1_win32.zip Windows],[http://ef-site.hgc.jp/eF-site/jV/JOGL1.1.1_macosx.tar.gz Mac OS X], [http://ef-site.hgc.jp/eF-site/jV/JOGL1.1.1_linux.tar.gz Linux]]
** JSR-231 1.0.0 [[http://ef-site.hgc.jp/eF-site/jV/JOGL_JSR231_win32.zip Windows], [http://ef-site.hgc.jp/eF-site/jV/JOGL_JSR231_macosx_ppc.tar.gz Mac OS X ppc], [http://ef-site.hgc.jp/eF-site/jV/JOGL_JSR231_macosx_universal.tar.gz Mac OS X universal], [http://ef-site.hgc.jp/eF-site/jV/JOGL_JSR231_linux_i586.tar.gz Linux]]

&lt;font size="-1"&gt;Note: &amp;nbsp; JOGL 1.0 and 1.1.1 are not available for Intel Mac.The latest version of JOGL, JSR-231 1.0.0, runs on Intel Mac.
&lt;/font&gt;

== jV version 2 ==


== jV version 1 (PDBjViewer) ==


&lt;br/&gt;
&lt;big&gt;'''MediaWiki has been successfully installed.'''&lt;/big&gt;

Consult the [http://meta.wikimedia.org/wiki/Help:Contents User's Guide] for information on using the wiki software.

== Getting started ==
* [http://www.mediawiki.org/wiki/Manual:Configuration_settings Configuration settings list]
* [http://www.mediawiki.org/wiki/Manual:FAQ MediaWiki FAQ]
* [https://lists.wikimedia.org/mailman/listinfo/mediawiki-announce MediaWiki release mailing list]</text>
    <sha1>a852e3463f36c57340b75fd4c216ff39daf27db5</sha1>
  </revision>
  <revision>
    <id>38</id>
    <parentid>37</parentid>
    <timestamp>2009-03-03T09:01:13Z</timestamp>
    <contributor>
      <username>JVuser</username>
      <id>2</id>
    </contributor>
    <comment>/* jV version 3 */</comment>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="3813" xml:space="preserve">&lt;big&gt;'''Welcome to jV wiki.'''&lt;/big&gt;
{| style="float:right"
 |__TOC__
 |}
jV(formerly known as PDBjViewer) is a program to display molecular graphics of protein and nucleic acids. 
jV can use as a stand-alone program and can operate on a web browser as an Java applet. jV is used by PDBj services([http://ef-site.hgc.jp/eF-site/index.jsp eF-site], [http://ef-site.hgc.jp/eF-seek/index.jsp eF-seek], the molecular structure surface database of the protein functional part).

jV supports the following features:
* jV can read and display PDBML files, the canonical XML format for the Protein Data Bank.
* Of course, jV can read and display the traditional PDB format files, too.
* RasMol-like usability.
* jV can process more than one molecules.
* jV can display polygons specified by XML. ([http://ef-site.hgc.jp/eF-site/schema/polygon12.xsd XML Schema for polygons] is available.)
* Multiple polygons can be processed simultaneously, and be superimposed onto molecular images.
* Animation can be realized.


The program 'jV' has been developed by [http://www.hgc.jp/~kinosita/TOP.html Kengo Kinoshita] ([http://www.hgc.jp/english/ Human Genome Center], [http://www.ims.u-tokyo.ac.jp/imsut/en/ Insutitute for Medical Science],[http://www.u-tokyo.ac.jp/index_e.html University of Tokyo]) and [http://www.protein.osaka-u.ac.jp/rcsfp/pi/ Haruki Nakamura] ([http://www.protein.osaka-u.ac.jp/index_e.php Institute for Protein Research], [http://www.osaka-u.ac.jp/eng/index.html Osaka Univeristy]), with the support from [http://www-bird.jst.go.jp/index_e.html JST-BIRD].

== jV version 3 ==
[[File:Download.png|right|link=http://ef-site.hgc.jp/eF-site/servlet/Registration|Download]][http://ef-site.hgc.jp/jV/ jV version 3] is now used to display molecules and their surfaces as a Java applet program.&lt;br /&gt;&lt;font size="1"&gt;Version 3.6 was released on 11, Aug, 2008.&lt;br /&gt;This version is fully compativle with [https://applet-launcher.dev.java.net/ applet-launcher].&lt;/font&gt;&lt;br /&gt;
&lt;br /&gt;
It requires the following softwares.&lt;br /&gt;
* JRE 1.4.2 or later  (recommend 1.4.2_12)&lt;br&gt;jV runs on the Java Runtime Environment ([http://java.sun.com/javase/index.jsp JRE]) so that it can work as a stand-alone application as well as an applet.
* JOGL 1.0, 1.1.1 or JSR-231 1.0.0  (recommend JSR-231)&lt;br /&gt;The graphics of jV is based on OpenGL ([https://jogl.dev.java.net/ JOGL]), thereby producing fairly beautiful pictures.
** version 1.0 [[http://ef-site.hgc.jp/eF-site/jV/JOGL1.0_win32.zip Windows],[http://ef-site.hgc.jp/eF-site/jV/JOGL1.0_macosx.tar.gz Mac OS X],[http://ef-site.hgc.jp/eF-site/jV/JOGL1.0_linux.tar.gz Linux]]
** version 1.1.1 [[http://ef-site.hgc.jp/eF-site/jV/JOGL1.1.1_win32.zip Windows],[http://ef-site.hgc.jp/eF-site/jV/JOGL1.1.1_macosx.tar.gz Mac OS X], [http://ef-site.hgc.jp/eF-site/jV/JOGL1.1.1_linux.tar.gz Linux]]
** JSR-231 1.0.0 [[http://ef-site.hgc.jp/eF-site/jV/JOGL_JSR231_win32.zip Windows], [http://ef-site.hgc.jp/eF-site/jV/JOGL_JSR231_macosx_ppc.tar.gz Mac OS X ppc], [http://ef-site.hgc.jp/eF-site/jV/JOGL_JSR231_macosx_universal.tar.gz Mac OS X universal], [http://ef-site.hgc.jp/eF-site/jV/JOGL_JSR231_linux_i586.tar.gz Linux]]

&lt;font size="1"&gt;Note: &amp;nbsp; JOGL 1.0 and 1.1.1 are not available for Intel Mac.The latest version of JOGL, JSR-231 1.0.0, runs on Intel Mac.&lt;/font&gt;

== jV version 2 ==


== jV version 1 (PDBjViewer) ==


&lt;br/&gt;
&lt;big&gt;'''MediaWiki has been successfully installed.'''&lt;/big&gt;

Consult the [http://meta.wikimedia.org/wiki/Help:Contents User's Guide] for information on using the wiki software.

== Getting started ==
* [http://www.mediawiki.org/wiki/Manual:Configuration_settings Configuration settings list]
* [http://www.mediawiki.org/wiki/Manual:FAQ MediaWiki FAQ]
* [https://lists.wikimedia.org/mailman/listinfo/mediawiki-announce MediaWiki release mailing list]</text>
    <sha1>d3910bd54cfba5abb2ace1821f54c3df09f663eb</sha1>
  </revision>
  <revision>
    <id>39</id>
    <parentid>38</parentid>
    <timestamp>2009-03-03T09:03:13Z</timestamp>
    <contributor>
      <username>JVuser</username>
      <id>2</id>
    </contributor>
    <comment>/* jV version 3 */</comment>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="3786" xml:space="preserve">&lt;big&gt;'''Welcome to jV wiki.'''&lt;/big&gt;
{| style="float:right"
 |__TOC__
 |}
jV(formerly known as PDBjViewer) is a program to display molecular graphics of protein and nucleic acids. 
jV can use as a stand-alone program and can operate on a web browser as an Java applet. jV is used by PDBj services([http://ef-site.hgc.jp/eF-site/index.jsp eF-site], [http://ef-site.hgc.jp/eF-seek/index.jsp eF-seek], the molecular structure surface database of the protein functional part).

jV supports the following features:
* jV can read and display PDBML files, the canonical XML format for the Protein Data Bank.
* Of course, jV can read and display the traditional PDB format files, too.
* RasMol-like usability.
* jV can process more than one molecules.
* jV can display polygons specified by XML. ([http://ef-site.hgc.jp/eF-site/schema/polygon12.xsd XML Schema for polygons] is available.)
* Multiple polygons can be processed simultaneously, and be superimposed onto molecular images.
* Animation can be realized.


The program 'jV' has been developed by [http://www.hgc.jp/~kinosita/TOP.html Kengo Kinoshita] ([http://www.hgc.jp/english/ Human Genome Center], [http://www.ims.u-tokyo.ac.jp/imsut/en/ Insutitute for Medical Science],[http://www.u-tokyo.ac.jp/index_e.html University of Tokyo]) and [http://www.protein.osaka-u.ac.jp/rcsfp/pi/ Haruki Nakamura] ([http://www.protein.osaka-u.ac.jp/index_e.php Institute for Protein Research], [http://www.osaka-u.ac.jp/eng/index.html Osaka Univeristy]), with the support from [http://www-bird.jst.go.jp/index_e.html JST-BIRD].

== jV version 3 ==
[[File:Download.png|right|link=http://ef-site.hgc.jp/eF-site/servlet/Registration|Download]] jV version 3 is now used to display molecules and their surfaces as a Java applet program.&lt;br /&gt;&lt;font size="1"&gt;Version 3.6 was released on 11, Aug, 2008.&lt;br /&gt;This version is fully compativle with [https://applet-launcher.dev.java.net/ applet-launcher].&lt;/font&gt;&lt;br /&gt;
&lt;br /&gt;
It requires the following softwares.&lt;br /&gt;
* JRE 1.4.2 or later  (recommend 1.4.2_12)&lt;br&gt;jV runs on the Java Runtime Environment ([http://java.sun.com/javase/index.jsp JRE]) so that it can work as a stand-alone application as well as an applet.
* JOGL 1.0, 1.1.1 or JSR-231 1.0.0  (recommend JSR-231)&lt;br /&gt;The graphics of jV is based on OpenGL ([https://jogl.dev.java.net/ JOGL]), thereby producing fairly beautiful pictures.
** version 1.0 [[http://ef-site.hgc.jp/eF-site/jV/JOGL1.0_win32.zip Windows],[http://ef-site.hgc.jp/eF-site/jV/JOGL1.0_macosx.tar.gz Mac OS X],[http://ef-site.hgc.jp/eF-site/jV/JOGL1.0_linux.tar.gz Linux]]
** version 1.1.1 [[http://ef-site.hgc.jp/eF-site/jV/JOGL1.1.1_win32.zip Windows],[http://ef-site.hgc.jp/eF-site/jV/JOGL1.1.1_macosx.tar.gz Mac OS X], [http://ef-site.hgc.jp/eF-site/jV/JOGL1.1.1_linux.tar.gz Linux]]
** JSR-231 1.0.0 [[http://ef-site.hgc.jp/eF-site/jV/JOGL_JSR231_win32.zip Windows], [http://ef-site.hgc.jp/eF-site/jV/JOGL_JSR231_macosx_ppc.tar.gz Mac OS X ppc], [http://ef-site.hgc.jp/eF-site/jV/JOGL_JSR231_macosx_universal.tar.gz Mac OS X universal], [http://ef-site.hgc.jp/eF-site/jV/JOGL_JSR231_linux_i586.tar.gz Linux]]

&lt;font size="1"&gt;Note: &amp;nbsp; JOGL 1.0 and 1.1.1 are not available for Intel Mac.The latest version of JOGL, JSR-231 1.0.0, runs on Intel Mac.&lt;/font&gt;

== jV version 2 ==


== jV version 1 (PDBjViewer) ==


&lt;br/&gt;
&lt;big&gt;'''MediaWiki has been successfully installed.'''&lt;/big&gt;

Consult the [http://meta.wikimedia.org/wiki/Help:Contents User's Guide] for information on using the wiki software.

== Getting started ==
* [http://www.mediawiki.org/wiki/Manual:Configuration_settings Configuration settings list]
* [http://www.mediawiki.org/wiki/Manual:FAQ MediaWiki FAQ]
* [https://lists.wikimedia.org/mailman/listinfo/mediawiki-announce MediaWiki release mailing list]</text>
    <sha1>69c71d005a3a3b83682c02b5b97b7bac1efae29b</sha1>
  </revision>
  <revision>
    <id>40</id>
    <parentid>39</parentid>
    <timestamp>2009-03-03T09:04:09Z</timestamp>
    <contributor>
      <username>JVuser</username>
      <id>2</id>
    </contributor>
    <comment>/* jV version 2 */</comment>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="4203" xml:space="preserve">&lt;big&gt;'''Welcome to jV wiki.'''&lt;/big&gt;
{| style="float:right"
 |__TOC__
 |}
jV(formerly known as PDBjViewer) is a program to display molecular graphics of protein and nucleic acids. 
jV can use as a stand-alone program and can operate on a web browser as an Java applet. jV is used by PDBj services([http://ef-site.hgc.jp/eF-site/index.jsp eF-site], [http://ef-site.hgc.jp/eF-seek/index.jsp eF-seek], the molecular structure surface database of the protein functional part).

jV supports the following features:
* jV can read and display PDBML files, the canonical XML format for the Protein Data Bank.
* Of course, jV can read and display the traditional PDB format files, too.
* RasMol-like usability.
* jV can process more than one molecules.
* jV can display polygons specified by XML. ([http://ef-site.hgc.jp/eF-site/schema/polygon12.xsd XML Schema for polygons] is available.)
* Multiple polygons can be processed simultaneously, and be superimposed onto molecular images.
* Animation can be realized.


The program 'jV' has been developed by [http://www.hgc.jp/~kinosita/TOP.html Kengo Kinoshita] ([http://www.hgc.jp/english/ Human Genome Center], [http://www.ims.u-tokyo.ac.jp/imsut/en/ Insutitute for Medical Science],[http://www.u-tokyo.ac.jp/index_e.html University of Tokyo]) and [http://www.protein.osaka-u.ac.jp/rcsfp/pi/ Haruki Nakamura] ([http://www.protein.osaka-u.ac.jp/index_e.php Institute for Protein Research], [http://www.osaka-u.ac.jp/eng/index.html Osaka Univeristy]), with the support from [http://www-bird.jst.go.jp/index_e.html JST-BIRD].

== jV version 3 ==
[[File:Download.png|right|link=http://ef-site.hgc.jp/eF-site/servlet/Registration|Download]] jV version 3 is now used to display molecules and their surfaces as a Java applet program.&lt;br /&gt;&lt;font size="1"&gt;Version 3.6 was released on 11, Aug, 2008.&lt;br /&gt;This version is fully compativle with [https://applet-launcher.dev.java.net/ applet-launcher].&lt;/font&gt;&lt;br /&gt;
&lt;br /&gt;
It requires the following softwares.&lt;br /&gt;
* JRE 1.4.2 or later  (recommend 1.4.2_12)&lt;br&gt;jV runs on the Java Runtime Environment ([http://java.sun.com/javase/index.jsp JRE]) so that it can work as a stand-alone application as well as an applet.
* JOGL 1.0, 1.1.1 or JSR-231 1.0.0  (recommend JSR-231)&lt;br /&gt;The graphics of jV is based on OpenGL ([https://jogl.dev.java.net/ JOGL]), thereby producing fairly beautiful pictures.
** version 1.0 [[http://ef-site.hgc.jp/eF-site/jV/JOGL1.0_win32.zip Windows],[http://ef-site.hgc.jp/eF-site/jV/JOGL1.0_macosx.tar.gz Mac OS X],[http://ef-site.hgc.jp/eF-site/jV/JOGL1.0_linux.tar.gz Linux]]
** version 1.1.1 [[http://ef-site.hgc.jp/eF-site/jV/JOGL1.1.1_win32.zip Windows],[http://ef-site.hgc.jp/eF-site/jV/JOGL1.1.1_macosx.tar.gz Mac OS X], [http://ef-site.hgc.jp/eF-site/jV/JOGL1.1.1_linux.tar.gz Linux]]
** JSR-231 1.0.0 [[http://ef-site.hgc.jp/eF-site/jV/JOGL_JSR231_win32.zip Windows], [http://ef-site.hgc.jp/eF-site/jV/JOGL_JSR231_macosx_ppc.tar.gz Mac OS X ppc], [http://ef-site.hgc.jp/eF-site/jV/JOGL_JSR231_macosx_universal.tar.gz Mac OS X universal], [http://ef-site.hgc.jp/eF-site/jV/JOGL_JSR231_linux_i586.tar.gz Linux]]

&lt;font size="1"&gt;Note: &amp;nbsp; JOGL 1.0 and 1.1.1 are not available for Intel Mac.The latest version of JOGL, JSR-231 1.0.0, runs on Intel Mac.&lt;/font&gt;

== jV version 2 ==
jV version 2 is an advanced version of PDBjViewer, which can be used only as a stand-alone program. It enables to display more than one molecule images at the same time and their display models and transforms can be operated separately. An animation of molecules can be also performed. jV version 2 runs with .NET framework 1.1 on the Windows platform. Therefore the .NET framework must be installed on your computer.

== jV version 1 (PDBjViewer) ==


&lt;br/&gt;
&lt;big&gt;'''MediaWiki has been successfully installed.'''&lt;/big&gt;

Consult the [http://meta.wikimedia.org/wiki/Help:Contents User's Guide] for information on using the wiki software.

== Getting started ==
* [http://www.mediawiki.org/wiki/Manual:Configuration_settings Configuration settings list]
* [http://www.mediawiki.org/wiki/Manual:FAQ MediaWiki FAQ]
* [https://lists.wikimedia.org/mailman/listinfo/mediawiki-announce MediaWiki release mailing list]</text>
    <sha1>53250dbe43af11d5185e1507931a8620bdf87af2</sha1>
  </revision>
  <revision>
    <id>41</id>
    <parentid>40</parentid>
    <timestamp>2009-03-03T09:06:02Z</timestamp>
    <contributor>
      <username>JVuser</username>
      <id>2</id>
    </contributor>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="3744" xml:space="preserve">&lt;big&gt;'''Welcome to jV wiki.'''&lt;/big&gt;
{| style="float:right"
 |__TOC__
 |}
jV(formerly known as PDBjViewer) is a program to display molecular graphics of protein and nucleic acids. 
jV can use as a stand-alone program and can operate on a web browser as an Java applet. jV is used by PDBj services([http://ef-site.hgc.jp/eF-site/index.jsp eF-site], [http://ef-site.hgc.jp/eF-seek/index.jsp eF-seek], the molecular structure surface database of the protein functional part).

jV supports the following features:
* jV can read and display PDBML files, the canonical XML format for the Protein Data Bank.
* Of course, jV can read and display the traditional PDB format files, too.
* RasMol-like usability.
* jV can process more than one molecules.
* jV can display polygons specified by XML. ([http://ef-site.hgc.jp/eF-site/schema/polygon12.xsd XML Schema for polygons] is available.)
* Multiple polygons can be processed simultaneously, and be superimposed onto molecular images.
* Animation can be realized.


The program 'jV' has been developed by [http://www.hgc.jp/~kinosita/TOP.html Kengo Kinoshita] ([http://www.hgc.jp/english/ Human Genome Center], [http://www.ims.u-tokyo.ac.jp/imsut/en/ Insutitute for Medical Science],[http://www.u-tokyo.ac.jp/index_e.html University of Tokyo]) and [http://www.protein.osaka-u.ac.jp/rcsfp/pi/ Haruki Nakamura] ([http://www.protein.osaka-u.ac.jp/index_e.php Institute for Protein Research], [http://www.osaka-u.ac.jp/eng/index.html Osaka Univeristy]), with the support from [http://www-bird.jst.go.jp/index_e.html JST-BIRD].

== jV version 3 ==
[[File:Download.png|right|link=http://ef-site.hgc.jp/eF-site/servlet/Registration|Download]] jV version 3 is now used to display molecules and their surfaces as a Java applet program.&lt;br /&gt;&lt;font size="1"&gt;Version 3.6 was released on 11, Aug, 2008.&lt;br /&gt;This version is fully compativle with [https://applet-launcher.dev.java.net/ applet-launcher].&lt;/font&gt;&lt;br /&gt;
&lt;br /&gt;
It requires the following softwares.&lt;br /&gt;
* JRE 1.4.2 or later  (recommend 1.4.2_12)&lt;br&gt;jV runs on the Java Runtime Environment ([http://java.sun.com/javase/index.jsp JRE]) so that it can work as a stand-alone application as well as an applet.
* JOGL 1.0, 1.1.1 or JSR-231 1.0.0  (recommend JSR-231)&lt;br /&gt;The graphics of jV is based on OpenGL ([https://jogl.dev.java.net/ JOGL]), thereby producing fairly beautiful pictures.
** version 1.0 [[http://ef-site.hgc.jp/eF-site/jV/JOGL1.0_win32.zip Windows],[http://ef-site.hgc.jp/eF-site/jV/JOGL1.0_macosx.tar.gz Mac OS X],[http://ef-site.hgc.jp/eF-site/jV/JOGL1.0_linux.tar.gz Linux]]
** version 1.1.1 [[http://ef-site.hgc.jp/eF-site/jV/JOGL1.1.1_win32.zip Windows],[http://ef-site.hgc.jp/eF-site/jV/JOGL1.1.1_macosx.tar.gz Mac OS X], [http://ef-site.hgc.jp/eF-site/jV/JOGL1.1.1_linux.tar.gz Linux]]
** JSR-231 1.0.0 [[http://ef-site.hgc.jp/eF-site/jV/JOGL_JSR231_win32.zip Windows], [http://ef-site.hgc.jp/eF-site/jV/JOGL_JSR231_macosx_ppc.tar.gz Mac OS X ppc], [http://ef-site.hgc.jp/eF-site/jV/JOGL_JSR231_macosx_universal.tar.gz Mac OS X universal], [http://ef-site.hgc.jp/eF-site/jV/JOGL_JSR231_linux_i586.tar.gz Linux]]

&lt;font size="1"&gt;Note: &amp;nbsp; JOGL 1.0 and 1.1.1 are not available for Intel Mac.The latest version of JOGL, JSR-231 1.0.0, runs on Intel Mac.&lt;/font&gt;

== jV version 2 ==
jV version 2 is an advanced version of PDBjViewer, which can be used only as a stand-alone program. It enables to display more than one molecule images at the same time and their display models and transforms can be operated separately. An animation of molecules can be also performed. jV version 2 runs with .NET framework 1.1 on the Windows platform. Therefore the .NET framework must be installed on your computer.

== jV version 1 (PDBjViewer) ==</text>
    <sha1>b9e65e85a8c0ce811b318abd90ac86d619809d07</sha1>
  </revision>
  <revision>
    <id>42</id>
    <parentid>41</parentid>
    <timestamp>2009-03-03T09:07:56Z</timestamp>
    <contributor>
      <username>JVuser</username>
      <id>2</id>
    </contributor>
    <comment>/* jV version 3 */</comment>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="3767" xml:space="preserve">&lt;big&gt;'''Welcome to jV wiki.'''&lt;/big&gt;
{| style="float:right"
 |__TOC__
 |}
jV(formerly known as PDBjViewer) is a program to display molecular graphics of protein and nucleic acids. 
jV can use as a stand-alone program and can operate on a web browser as an Java applet. jV is used by PDBj services([http://ef-site.hgc.jp/eF-site/index.jsp eF-site], [http://ef-site.hgc.jp/eF-seek/index.jsp eF-seek], the molecular structure surface database of the protein functional part).

jV supports the following features:
* jV can read and display PDBML files, the canonical XML format for the Protein Data Bank.
* Of course, jV can read and display the traditional PDB format files, too.
* RasMol-like usability.
* jV can process more than one molecules.
* jV can display polygons specified by XML. ([http://ef-site.hgc.jp/eF-site/schema/polygon12.xsd XML Schema for polygons] is available.)
* Multiple polygons can be processed simultaneously, and be superimposed onto molecular images.
* Animation can be realized.


The program 'jV' has been developed by [http://www.hgc.jp/~kinosita/TOP.html Kengo Kinoshita] ([http://www.hgc.jp/english/ Human Genome Center], [http://www.ims.u-tokyo.ac.jp/imsut/en/ Insutitute for Medical Science],[http://www.u-tokyo.ac.jp/index_e.html University of Tokyo]) and [http://www.protein.osaka-u.ac.jp/rcsfp/pi/ Haruki Nakamura] ([http://www.protein.osaka-u.ac.jp/index_e.php Institute for Protein Research], [http://www.osaka-u.ac.jp/eng/index.html Osaka Univeristy]), with the support from [http://www-bird.jst.go.jp/index_e.html JST-BIRD].

== jV version 3 ==
[[File:Download.png|right|link=http://ef-site.hgc.jp/eF-site/servlet/Registration|Download]] jV version 3 is now used to display molecules and their surfaces as a Java applet program.&lt;br /&gt;&lt;font size="1"&gt;Version 3.6 was released on 11, Aug, 2008.&lt;br /&gt;This version is fully compativle with [https://applet-launcher.dev.java.net/ applet-launcher].&lt;/font&gt;&lt;br /&gt;
&lt;br /&gt;Go to [[jV version 3]].
It requires the following softwares.&lt;br /&gt;
* JRE 1.4.2 or later  (recommend 1.4.2_12)&lt;br&gt;jV runs on the Java Runtime Environment ([http://java.sun.com/javase/index.jsp JRE]) so that it can work as a stand-alone application as well as an applet.
* JOGL 1.0, 1.1.1 or JSR-231 1.0.0  (recommend JSR-231)&lt;br /&gt;The graphics of jV is based on OpenGL ([https://jogl.dev.java.net/ JOGL]), thereby producing fairly beautiful pictures.
** version 1.0 [[http://ef-site.hgc.jp/eF-site/jV/JOGL1.0_win32.zip Windows],[http://ef-site.hgc.jp/eF-site/jV/JOGL1.0_macosx.tar.gz Mac OS X],[http://ef-site.hgc.jp/eF-site/jV/JOGL1.0_linux.tar.gz Linux]]
** version 1.1.1 [[http://ef-site.hgc.jp/eF-site/jV/JOGL1.1.1_win32.zip Windows],[http://ef-site.hgc.jp/eF-site/jV/JOGL1.1.1_macosx.tar.gz Mac OS X], [http://ef-site.hgc.jp/eF-site/jV/JOGL1.1.1_linux.tar.gz Linux]]
** JSR-231 1.0.0 [[http://ef-site.hgc.jp/eF-site/jV/JOGL_JSR231_win32.zip Windows], [http://ef-site.hgc.jp/eF-site/jV/JOGL_JSR231_macosx_ppc.tar.gz Mac OS X ppc], [http://ef-site.hgc.jp/eF-site/jV/JOGL_JSR231_macosx_universal.tar.gz Mac OS X universal], [http://ef-site.hgc.jp/eF-site/jV/JOGL_JSR231_linux_i586.tar.gz Linux]]

&lt;font size="1"&gt;Note: &amp;nbsp; JOGL 1.0 and 1.1.1 are not available for Intel Mac.The latest version of JOGL, JSR-231 1.0.0, runs on Intel Mac.&lt;/font&gt;

== jV version 2 ==
jV version 2 is an advanced version of PDBjViewer, which can be used only as a stand-alone program. It enables to display more than one molecule images at the same time and their display models and transforms can be operated separately. An animation of molecules can be also performed. jV version 2 runs with .NET framework 1.1 on the Windows platform. Therefore the .NET framework must be installed on your computer.

== jV version 1 (PDBjViewer) ==</text>
    <sha1>7ba1dab147236d73f6bc679b22e53edfb194d7f3</sha1>
  </revision>
  <revision>
    <id>43</id>
    <parentid>42</parentid>
    <timestamp>2009-03-03T09:08:24Z</timestamp>
    <contributor>
      <username>JVuser</username>
      <id>2</id>
    </contributor>
    <comment>/* jV version 3 */</comment>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="3767" xml:space="preserve">&lt;big&gt;'''Welcome to jV wiki.'''&lt;/big&gt;
{| style="float:right"
 |__TOC__
 |}
jV(formerly known as PDBjViewer) is a program to display molecular graphics of protein and nucleic acids. 
jV can use as a stand-alone program and can operate on a web browser as an Java applet. jV is used by PDBj services([http://ef-site.hgc.jp/eF-site/index.jsp eF-site], [http://ef-site.hgc.jp/eF-seek/index.jsp eF-seek], the molecular structure surface database of the protein functional part).

jV supports the following features:
* jV can read and display PDBML files, the canonical XML format for the Protein Data Bank.
* Of course, jV can read and display the traditional PDB format files, too.
* RasMol-like usability.
* jV can process more than one molecules.
* jV can display polygons specified by XML. ([http://ef-site.hgc.jp/eF-site/schema/polygon12.xsd XML Schema for polygons] is available.)
* Multiple polygons can be processed simultaneously, and be superimposed onto molecular images.
* Animation can be realized.


The program 'jV' has been developed by [http://www.hgc.jp/~kinosita/TOP.html Kengo Kinoshita] ([http://www.hgc.jp/english/ Human Genome Center], [http://www.ims.u-tokyo.ac.jp/imsut/en/ Insutitute for Medical Science],[http://www.u-tokyo.ac.jp/index_e.html University of Tokyo]) and [http://www.protein.osaka-u.ac.jp/rcsfp/pi/ Haruki Nakamura] ([http://www.protein.osaka-u.ac.jp/index_e.php Institute for Protein Research], [http://www.osaka-u.ac.jp/eng/index.html Osaka Univeristy]), with the support from [http://www-bird.jst.go.jp/index_e.html JST-BIRD].

== jV version 3 ==
[[File:Download.png|right|link=http://ef-site.hgc.jp/eF-site/servlet/Registration|Download]] jV version 3 is now used to display molecules and their surfaces as a Java applet program.&lt;br /&gt;&lt;font size="1"&gt;Version 3.6 was released on 11, Aug, 2008.&lt;br /&gt;This version is fully compativle with [https://applet-launcher.dev.java.net/ applet-launcher].&lt;/font&gt;&lt;br /&gt;Go to [[jV version 3]].
&lt;br /&gt;
It requires the following softwares.&lt;br /&gt;
* JRE 1.4.2 or later  (recommend 1.4.2_12)&lt;br&gt;jV runs on the Java Runtime Environment ([http://java.sun.com/javase/index.jsp JRE]) so that it can work as a stand-alone application as well as an applet.
* JOGL 1.0, 1.1.1 or JSR-231 1.0.0  (recommend JSR-231)&lt;br /&gt;The graphics of jV is based on OpenGL ([https://jogl.dev.java.net/ JOGL]), thereby producing fairly beautiful pictures.
** version 1.0 [[http://ef-site.hgc.jp/eF-site/jV/JOGL1.0_win32.zip Windows],[http://ef-site.hgc.jp/eF-site/jV/JOGL1.0_macosx.tar.gz Mac OS X],[http://ef-site.hgc.jp/eF-site/jV/JOGL1.0_linux.tar.gz Linux]]
** version 1.1.1 [[http://ef-site.hgc.jp/eF-site/jV/JOGL1.1.1_win32.zip Windows],[http://ef-site.hgc.jp/eF-site/jV/JOGL1.1.1_macosx.tar.gz Mac OS X], [http://ef-site.hgc.jp/eF-site/jV/JOGL1.1.1_linux.tar.gz Linux]]
** JSR-231 1.0.0 [[http://ef-site.hgc.jp/eF-site/jV/JOGL_JSR231_win32.zip Windows], [http://ef-site.hgc.jp/eF-site/jV/JOGL_JSR231_macosx_ppc.tar.gz Mac OS X ppc], [http://ef-site.hgc.jp/eF-site/jV/JOGL_JSR231_macosx_universal.tar.gz Mac OS X universal], [http://ef-site.hgc.jp/eF-site/jV/JOGL_JSR231_linux_i586.tar.gz Linux]]

&lt;font size="1"&gt;Note: &amp;nbsp; JOGL 1.0 and 1.1.1 are not available for Intel Mac.The latest version of JOGL, JSR-231 1.0.0, runs on Intel Mac.&lt;/font&gt;

== jV version 2 ==
jV version 2 is an advanced version of PDBjViewer, which can be used only as a stand-alone program. It enables to display more than one molecule images at the same time and their display models and transforms can be operated separately. An animation of molecules can be also performed. jV version 2 runs with .NET framework 1.1 on the Windows platform. Therefore the .NET framework must be installed on your computer.

== jV version 1 (PDBjViewer) ==</text>
    <sha1>206dd6ca9b9adb9e0a810d01645da21fc136af76</sha1>
  </revision>
  <revision>
    <id>44</id>
    <parentid>43</parentid>
    <timestamp>2009-03-03T09:11:07Z</timestamp>
    <contributor>
      <username>JVuser</username>
      <id>2</id>
    </contributor>
    <comment>/* jV version 1 (PDBjViewer) */</comment>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="5450" xml:space="preserve">&lt;big&gt;'''Welcome to jV wiki.'''&lt;/big&gt;
{| style="float:right"
 |__TOC__
 |}
jV(formerly known as PDBjViewer) is a program to display molecular graphics of protein and nucleic acids. 
jV can use as a stand-alone program and can operate on a web browser as an Java applet. jV is used by PDBj services([http://ef-site.hgc.jp/eF-site/index.jsp eF-site], [http://ef-site.hgc.jp/eF-seek/index.jsp eF-seek], the molecular structure surface database of the protein functional part).

jV supports the following features:
* jV can read and display PDBML files, the canonical XML format for the Protein Data Bank.
* Of course, jV can read and display the traditional PDB format files, too.
* RasMol-like usability.
* jV can process more than one molecules.
* jV can display polygons specified by XML. ([http://ef-site.hgc.jp/eF-site/schema/polygon12.xsd XML Schema for polygons] is available.)
* Multiple polygons can be processed simultaneously, and be superimposed onto molecular images.
* Animation can be realized.


The program 'jV' has been developed by [http://www.hgc.jp/~kinosita/TOP.html Kengo Kinoshita] ([http://www.hgc.jp/english/ Human Genome Center], [http://www.ims.u-tokyo.ac.jp/imsut/en/ Insutitute for Medical Science],[http://www.u-tokyo.ac.jp/index_e.html University of Tokyo]) and [http://www.protein.osaka-u.ac.jp/rcsfp/pi/ Haruki Nakamura] ([http://www.protein.osaka-u.ac.jp/index_e.php Institute for Protein Research], [http://www.osaka-u.ac.jp/eng/index.html Osaka Univeristy]), with the support from [http://www-bird.jst.go.jp/index_e.html JST-BIRD].

== jV version 3 ==
[[File:Download.png|right|link=http://ef-site.hgc.jp/eF-site/servlet/Registration|Download]] jV version 3 is now used to display molecules and their surfaces as a Java applet program.&lt;br /&gt;&lt;font size="1"&gt;Version 3.6 was released on 11, Aug, 2008.&lt;br /&gt;This version is fully compativle with [https://applet-launcher.dev.java.net/ applet-launcher].&lt;/font&gt;&lt;br /&gt;Go to [[jV version 3]].
&lt;br /&gt;
It requires the following softwares.&lt;br /&gt;
* JRE 1.4.2 or later  (recommend 1.4.2_12)&lt;br&gt;jV runs on the Java Runtime Environment ([http://java.sun.com/javase/index.jsp JRE]) so that it can work as a stand-alone application as well as an applet.
* JOGL 1.0, 1.1.1 or JSR-231 1.0.0  (recommend JSR-231)&lt;br /&gt;The graphics of jV is based on OpenGL ([https://jogl.dev.java.net/ JOGL]), thereby producing fairly beautiful pictures.
** version 1.0 [[http://ef-site.hgc.jp/eF-site/jV/JOGL1.0_win32.zip Windows],[http://ef-site.hgc.jp/eF-site/jV/JOGL1.0_macosx.tar.gz Mac OS X],[http://ef-site.hgc.jp/eF-site/jV/JOGL1.0_linux.tar.gz Linux]]
** version 1.1.1 [[http://ef-site.hgc.jp/eF-site/jV/JOGL1.1.1_win32.zip Windows],[http://ef-site.hgc.jp/eF-site/jV/JOGL1.1.1_macosx.tar.gz Mac OS X], [http://ef-site.hgc.jp/eF-site/jV/JOGL1.1.1_linux.tar.gz Linux]]
** JSR-231 1.0.0 [[http://ef-site.hgc.jp/eF-site/jV/JOGL_JSR231_win32.zip Windows], [http://ef-site.hgc.jp/eF-site/jV/JOGL_JSR231_macosx_ppc.tar.gz Mac OS X ppc], [http://ef-site.hgc.jp/eF-site/jV/JOGL_JSR231_macosx_universal.tar.gz Mac OS X universal], [http://ef-site.hgc.jp/eF-site/jV/JOGL_JSR231_linux_i586.tar.gz Linux]]

&lt;font size="1"&gt;Note: &amp;nbsp; JOGL 1.0 and 1.1.1 are not available for Intel Mac.The latest version of JOGL, JSR-231 1.0.0, runs on Intel Mac.&lt;/font&gt;

== jV version 2 ==
jV version 2 is an advanced version of PDBjViewer, which can be used only as a stand-alone program. It enables to display more than one molecule images at the same time and their display models and transforms can be operated separately. An animation of molecules can be also performed. jV version 2 runs with .NET framework 1.1 on the Windows platform. Therefore the .NET framework must be installed on your computer.

== jV version 1 (PDBjViewer) ==
Visualization of structure and surface of molecules is performed by a Java applet program called 'PDBjViewer'.The PDBjViewer Version 1.0 is freely distributed from this Web page. 

Two image windows are opened. The structure of the molecule is shown in the left window and the molecular surface is displayed in the right window. The mouse control is as follows. 
&lt;br /&gt;
&lt;br&gt;
&lt;div align="center"&gt;
&lt;table border="1" cellpadding="5"&gt;
  &lt;tr&gt;
    &lt;td width="100" align="center"&gt;&lt;b&gt;action&lt;/b&gt;&lt;/td&gt;
    &lt;td width="100" align="center"&gt;&lt;b&gt;Windows&lt;/b&gt;&lt;/td&gt;
  &lt;/tr&gt;
  &lt;tr&gt;
    &lt;td&gt;rotate x, y&lt;br&gt;zoom&lt;br&gt;translate x, y&lt;/td&gt;
    &lt;td&gt;left&lt;br&gt;Alt + left&lt;br&gt;right&lt;/td&gt;
  &lt;/tr&gt;
&lt;/table&gt;
&lt;/div&gt;
&lt;br&gt;
In order to use PDBjViewer, [http://java.sun.com/products/plugin/ Java Plug-in] and
[http://java.sun.com/products/java-media/3D/ Java 3D API] must be installed on your computer.
The version requirements are as follows.&lt;br /&gt;
&lt;div align="center"&gt;
&lt;table border="0"&gt;
&lt;tr&gt;
&lt;td width="20"&gt;&amp;middot;&lt;/td&gt;
&lt;td align="left" &gt;JRE (includes Java Plug-in) 1.4.1 or later&lt;/td&gt;
&lt;td width="10"&gt;&lt;/td&gt;
&lt;td&gt;(recommend 1.4.2)&lt;/td&gt;
&lt;/tr&gt;
&lt;tr&gt;
&lt;td width="20"&gt;&amp;middot;&lt;/td&gt;
&lt;td align="left"&gt;Java 3D API (OpenGL) 1.2.1 or later&lt;/td&gt;
&lt;td width="10"&gt;&lt;/td&gt;
&lt;td&gt;(recommend 1.2.1_04)&lt;/td&gt;
&lt;/tr&gt;
&lt;/table&gt;
&lt;/div&gt;
Important notes
* You can select two kinds of implementation of Java 3D, OpenGL version and DirectX version. But, PDBjViewer only work with OpenGL version at present.
* PDBjViewer does not work with JRE from 1.4.1_03 to 1.4.1_06.&lt;br /&gt;
PDBjViewer can be used as a stand-alone program as well as an applet
with the same requirements as above.
In addition to mouse controls, a command line interface is provided.
&lt;br&gt;</text>
    <sha1>0dc59c2a2e440d926b1d1a571508421757f36036</sha1>
  </revision>
  <revision>
    <id>45</id>
    <parentid>44</parentid>
    <timestamp>2009-03-03T09:12:27Z</timestamp>
    <contributor>
      <username>JVuser</username>
      <id>2</id>
    </contributor>
    <comment>/* jV version 1 (PDBjViewer) */</comment>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="5381" xml:space="preserve">&lt;big&gt;'''Welcome to jV wiki.'''&lt;/big&gt;
{| style="float:right"
 |__TOC__
 |}
jV(formerly known as PDBjViewer) is a program to display molecular graphics of protein and nucleic acids. 
jV can use as a stand-alone program and can operate on a web browser as an Java applet. jV is used by PDBj services([http://ef-site.hgc.jp/eF-site/index.jsp eF-site], [http://ef-site.hgc.jp/eF-seek/index.jsp eF-seek], the molecular structure surface database of the protein functional part).

jV supports the following features:
* jV can read and display PDBML files, the canonical XML format for the Protein Data Bank.
* Of course, jV can read and display the traditional PDB format files, too.
* RasMol-like usability.
* jV can process more than one molecules.
* jV can display polygons specified by XML. ([http://ef-site.hgc.jp/eF-site/schema/polygon12.xsd XML Schema for polygons] is available.)
* Multiple polygons can be processed simultaneously, and be superimposed onto molecular images.
* Animation can be realized.


The program 'jV' has been developed by [http://www.hgc.jp/~kinosita/TOP.html Kengo Kinoshita] ([http://www.hgc.jp/english/ Human Genome Center], [http://www.ims.u-tokyo.ac.jp/imsut/en/ Insutitute for Medical Science],[http://www.u-tokyo.ac.jp/index_e.html University of Tokyo]) and [http://www.protein.osaka-u.ac.jp/rcsfp/pi/ Haruki Nakamura] ([http://www.protein.osaka-u.ac.jp/index_e.php Institute for Protein Research], [http://www.osaka-u.ac.jp/eng/index.html Osaka Univeristy]), with the support from [http://www-bird.jst.go.jp/index_e.html JST-BIRD].

== jV version 3 ==
[[File:Download.png|right|link=http://ef-site.hgc.jp/eF-site/servlet/Registration|Download]] jV version 3 is now used to display molecules and their surfaces as a Java applet program.&lt;br /&gt;&lt;font size="1"&gt;Version 3.6 was released on 11, Aug, 2008.&lt;br /&gt;This version is fully compativle with [https://applet-launcher.dev.java.net/ applet-launcher].&lt;/font&gt;&lt;br /&gt;Go to [[jV version 3]].
&lt;br /&gt;
It requires the following softwares.&lt;br /&gt;
* JRE 1.4.2 or later  (recommend 1.4.2_12)&lt;br&gt;jV runs on the Java Runtime Environment ([http://java.sun.com/javase/index.jsp JRE]) so that it can work as a stand-alone application as well as an applet.
* JOGL 1.0, 1.1.1 or JSR-231 1.0.0  (recommend JSR-231)&lt;br /&gt;The graphics of jV is based on OpenGL ([https://jogl.dev.java.net/ JOGL]), thereby producing fairly beautiful pictures.
** version 1.0 [[http://ef-site.hgc.jp/eF-site/jV/JOGL1.0_win32.zip Windows],[http://ef-site.hgc.jp/eF-site/jV/JOGL1.0_macosx.tar.gz Mac OS X],[http://ef-site.hgc.jp/eF-site/jV/JOGL1.0_linux.tar.gz Linux]]
** version 1.1.1 [[http://ef-site.hgc.jp/eF-site/jV/JOGL1.1.1_win32.zip Windows],[http://ef-site.hgc.jp/eF-site/jV/JOGL1.1.1_macosx.tar.gz Mac OS X], [http://ef-site.hgc.jp/eF-site/jV/JOGL1.1.1_linux.tar.gz Linux]]
** JSR-231 1.0.0 [[http://ef-site.hgc.jp/eF-site/jV/JOGL_JSR231_win32.zip Windows], [http://ef-site.hgc.jp/eF-site/jV/JOGL_JSR231_macosx_ppc.tar.gz Mac OS X ppc], [http://ef-site.hgc.jp/eF-site/jV/JOGL_JSR231_macosx_universal.tar.gz Mac OS X universal], [http://ef-site.hgc.jp/eF-site/jV/JOGL_JSR231_linux_i586.tar.gz Linux]]

&lt;font size="1"&gt;Note: &amp;nbsp; JOGL 1.0 and 1.1.1 are not available for Intel Mac.The latest version of JOGL, JSR-231 1.0.0, runs on Intel Mac.&lt;/font&gt;

== jV version 2 ==
jV version 2 is an advanced version of PDBjViewer, which can be used only as a stand-alone program. It enables to display more than one molecule images at the same time and their display models and transforms can be operated separately. An animation of molecules can be also performed. jV version 2 runs with .NET framework 1.1 on the Windows platform. Therefore the .NET framework must be installed on your computer.

== jV version 1 (PDBjViewer) ==
Visualization of structure and surface of molecules is performed by a Java applet program called 'PDBjViewer'.

Two image windows are opened. The structure of the molecule is shown in the left window and the molecular surface is displayed in the right window. The mouse control is as follows. 
&lt;br /&gt;
&lt;br&gt;
&lt;div align="center"&gt;
&lt;table border="1" cellpadding="5"&gt;
  &lt;tr&gt;
    &lt;td width="100" align="center"&gt;&lt;b&gt;action&lt;/b&gt;&lt;/td&gt;
    &lt;td width="100" align="center"&gt;&lt;b&gt;Windows&lt;/b&gt;&lt;/td&gt;
  &lt;/tr&gt;
  &lt;tr&gt;
    &lt;td&gt;rotate x, y&lt;br&gt;zoom&lt;br&gt;translate x, y&lt;/td&gt;
    &lt;td&gt;left&lt;br&gt;Alt + left&lt;br&gt;right&lt;/td&gt;
  &lt;/tr&gt;
&lt;/table&gt;
&lt;/div&gt;
&lt;br&gt;
In order to use PDBjViewer, [http://java.sun.com/products/plugin/ Java Plug-in] and
[http://java.sun.com/products/java-media/3D/ Java 3D API] must be installed on your computer.
The version requirements are as follows.&lt;br /&gt;
&lt;div align="center"&gt;
&lt;table border="0"&gt;
&lt;tr&gt;
&lt;td width="20"&gt;&amp;middot;&lt;/td&gt;
&lt;td align="left" &gt;JRE (includes Java Plug-in) 1.4.1 or later&lt;/td&gt;
&lt;td width="10"&gt;&lt;/td&gt;
&lt;td&gt;(recommend 1.4.2)&lt;/td&gt;
&lt;/tr&gt;
&lt;tr&gt;
&lt;td width="20"&gt;&amp;middot;&lt;/td&gt;
&lt;td align="left"&gt;Java 3D API (OpenGL) 1.2.1 or later&lt;/td&gt;
&lt;td width="10"&gt;&lt;/td&gt;
&lt;td&gt;(recommend 1.2.1_04)&lt;/td&gt;
&lt;/tr&gt;
&lt;/table&gt;
&lt;/div&gt;
Important notes
* You can select two kinds of implementation of Java 3D, OpenGL version and DirectX version. But, PDBjViewer only work with OpenGL version at present.
* PDBjViewer does not work with JRE from 1.4.1_03 to 1.4.1_06.&lt;br /&gt;
PDBjViewer can be used as a stand-alone program as well as an applet
with the same requirements as above.
In addition to mouse controls, a command line interface is provided.
&lt;br&gt;</text>
    <sha1>8015d50c3e1f2cc6f7468aa1d4060aa367abce69</sha1>
  </revision>
  <revision>
    <id>46</id>
    <parentid>45</parentid>
    <timestamp>2009-03-03T09:31:58Z</timestamp>
    <contributor>
      <username>JVuser</username>
      <id>2</id>
    </contributor>
    <comment>/* jV version 1 (PDBjViewer) */</comment>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="5268" xml:space="preserve">&lt;big&gt;'''Welcome to jV wiki.'''&lt;/big&gt;
{| style="float:right"
 |__TOC__
 |}
jV(formerly known as PDBjViewer) is a program to display molecular graphics of protein and nucleic acids. 
jV can use as a stand-alone program and can operate on a web browser as an Java applet. jV is used by PDBj services([http://ef-site.hgc.jp/eF-site/index.jsp eF-site], [http://ef-site.hgc.jp/eF-seek/index.jsp eF-seek], the molecular structure surface database of the protein functional part).

jV supports the following features:
* jV can read and display PDBML files, the canonical XML format for the Protein Data Bank.
* Of course, jV can read and display the traditional PDB format files, too.
* RasMol-like usability.
* jV can process more than one molecules.
* jV can display polygons specified by XML. ([http://ef-site.hgc.jp/eF-site/schema/polygon12.xsd XML Schema for polygons] is available.)
* Multiple polygons can be processed simultaneously, and be superimposed onto molecular images.
* Animation can be realized.


The program 'jV' has been developed by [http://www.hgc.jp/~kinosita/TOP.html Kengo Kinoshita] ([http://www.hgc.jp/english/ Human Genome Center], [http://www.ims.u-tokyo.ac.jp/imsut/en/ Insutitute for Medical Science],[http://www.u-tokyo.ac.jp/index_e.html University of Tokyo]) and [http://www.protein.osaka-u.ac.jp/rcsfp/pi/ Haruki Nakamura] ([http://www.protein.osaka-u.ac.jp/index_e.php Institute for Protein Research], [http://www.osaka-u.ac.jp/eng/index.html Osaka Univeristy]), with the support from [http://www-bird.jst.go.jp/index_e.html JST-BIRD].

== jV version 3 ==
[[File:Download.png|right|link=http://ef-site.hgc.jp/eF-site/servlet/Registration|Download]] jV version 3 is now used to display molecules and their surfaces as a Java applet program.&lt;br /&gt;&lt;font size="1"&gt;Version 3.6 was released on 11, Aug, 2008.&lt;br /&gt;This version is fully compativle with [https://applet-launcher.dev.java.net/ applet-launcher].&lt;/font&gt;&lt;br /&gt;Go to [[jV version 3]].
&lt;br /&gt;
It requires the following softwares.&lt;br /&gt;
* JRE 1.4.2 or later  (recommend 1.4.2_12)&lt;br&gt;jV runs on the Java Runtime Environment ([http://java.sun.com/javase/index.jsp JRE]) so that it can work as a stand-alone application as well as an applet.
* JOGL 1.0, 1.1.1 or JSR-231 1.0.0  (recommend JSR-231)&lt;br /&gt;The graphics of jV is based on OpenGL ([https://jogl.dev.java.net/ JOGL]), thereby producing fairly beautiful pictures.
** version 1.0 [[http://ef-site.hgc.jp/eF-site/jV/JOGL1.0_win32.zip Windows],[http://ef-site.hgc.jp/eF-site/jV/JOGL1.0_macosx.tar.gz Mac OS X],[http://ef-site.hgc.jp/eF-site/jV/JOGL1.0_linux.tar.gz Linux]]
** version 1.1.1 [[http://ef-site.hgc.jp/eF-site/jV/JOGL1.1.1_win32.zip Windows],[http://ef-site.hgc.jp/eF-site/jV/JOGL1.1.1_macosx.tar.gz Mac OS X], [http://ef-site.hgc.jp/eF-site/jV/JOGL1.1.1_linux.tar.gz Linux]]
** JSR-231 1.0.0 [[http://ef-site.hgc.jp/eF-site/jV/JOGL_JSR231_win32.zip Windows], [http://ef-site.hgc.jp/eF-site/jV/JOGL_JSR231_macosx_ppc.tar.gz Mac OS X ppc], [http://ef-site.hgc.jp/eF-site/jV/JOGL_JSR231_macosx_universal.tar.gz Mac OS X universal], [http://ef-site.hgc.jp/eF-site/jV/JOGL_JSR231_linux_i586.tar.gz Linux]]

&lt;font size="1"&gt;Note: &amp;nbsp; JOGL 1.0 and 1.1.1 are not available for Intel Mac.The latest version of JOGL, JSR-231 1.0.0, runs on Intel Mac.&lt;/font&gt;

== jV version 2 ==
jV version 2 is an advanced version of PDBjViewer, which can be used only as a stand-alone program. It enables to display more than one molecule images at the same time and their display models and transforms can be operated separately. An animation of molecules can be also performed. jV version 2 runs with .NET framework 1.1 on the Windows platform. Therefore the .NET framework must be installed on your computer.

== jV version 1 (PDBjViewer) ==
Visualization of structure and surface of molecules is performed by a Java applet program called 'PDBjViewer'.

Two image windows are opened. The structure of the molecule is shown in the left window and the molecular surface is displayed in the right window. The mouse control is as follows. 
&lt;br /&gt;
&lt;div align="center"&gt;
{| class="wikitable" cellspacing="0" border="1"
 ! action !! Windows 
 |-
 | rotate x, y || left
 |-
 | zoom || Alt + left
 |-
 | tranlate x, y || right
 |-
|}
&lt;br /&gt;
&lt;/div&gt;
&lt;br&gt;
In order to use PDBjViewer, [http://java.sun.com/products/plugin/ Java Plug-in] and
[http://java.sun.com/products/java-media/3D/ Java 3D API] must be installed on your computer.
The version requirements are as follows.&lt;br /&gt;
&lt;div align="center"&gt;
&lt;table border="0"&gt;
&lt;tr&gt;
&lt;td width="20"&gt;&amp;middot;&lt;/td&gt;
&lt;td align="left" &gt;JRE (includes Java Plug-in) 1.4.1 or later&lt;/td&gt;
&lt;td width="10"&gt;&lt;/td&gt;
&lt;td&gt;(recommend 1.4.2)&lt;/td&gt;
&lt;/tr&gt;
&lt;tr&gt;
&lt;td width="20"&gt;&amp;middot;&lt;/td&gt;
&lt;td align="left"&gt;Java 3D API (OpenGL) 1.2.1 or later&lt;/td&gt;
&lt;td width="10"&gt;&lt;/td&gt;
&lt;td&gt;(recommend 1.2.1_04)&lt;/td&gt;
&lt;/tr&gt;
&lt;/table&gt;
&lt;/div&gt;
Important notes
* You can select two kinds of implementation of Java 3D, OpenGL version and DirectX version. But, PDBjViewer only work with OpenGL version at present.
* PDBjViewer does not work with JRE from 1.4.1_03 to 1.4.1_06.&lt;br /&gt;
PDBjViewer can be used as a stand-alone program as well as an applet
with the same requirements as above.
In addition to mouse controls, a command line interface is provided.
&lt;br&gt;</text>
    <sha1>78a77927405aa0fdea0c5d144f31586ef4b80d02</sha1>
  </revision>
  <revision>
    <id>47</id>
    <parentid>46</parentid>
    <timestamp>2009-03-03T09:33:02Z</timestamp>
    <contributor>
      <username>JVuser</username>
      <id>2</id>
    </contributor>
    <comment>/* jV version 1 (PDBjViewer) */</comment>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="5031" xml:space="preserve">&lt;big&gt;'''Welcome to jV wiki.'''&lt;/big&gt;
{| style="float:right"
 |__TOC__
 |}
jV(formerly known as PDBjViewer) is a program to display molecular graphics of protein and nucleic acids. 
jV can use as a stand-alone program and can operate on a web browser as an Java applet. jV is used by PDBj services([http://ef-site.hgc.jp/eF-site/index.jsp eF-site], [http://ef-site.hgc.jp/eF-seek/index.jsp eF-seek], the molecular structure surface database of the protein functional part).

jV supports the following features:
* jV can read and display PDBML files, the canonical XML format for the Protein Data Bank.
* Of course, jV can read and display the traditional PDB format files, too.
* RasMol-like usability.
* jV can process more than one molecules.
* jV can display polygons specified by XML. ([http://ef-site.hgc.jp/eF-site/schema/polygon12.xsd XML Schema for polygons] is available.)
* Multiple polygons can be processed simultaneously, and be superimposed onto molecular images.
* Animation can be realized.


The program 'jV' has been developed by [http://www.hgc.jp/~kinosita/TOP.html Kengo Kinoshita] ([http://www.hgc.jp/english/ Human Genome Center], [http://www.ims.u-tokyo.ac.jp/imsut/en/ Insutitute for Medical Science],[http://www.u-tokyo.ac.jp/index_e.html University of Tokyo]) and [http://www.protein.osaka-u.ac.jp/rcsfp/pi/ Haruki Nakamura] ([http://www.protein.osaka-u.ac.jp/index_e.php Institute for Protein Research], [http://www.osaka-u.ac.jp/eng/index.html Osaka Univeristy]), with the support from [http://www-bird.jst.go.jp/index_e.html JST-BIRD].

== jV version 3 ==
[[File:Download.png|right|link=http://ef-site.hgc.jp/eF-site/servlet/Registration|Download]] jV version 3 is now used to display molecules and their surfaces as a Java applet program.&lt;br /&gt;&lt;font size="1"&gt;Version 3.6 was released on 11, Aug, 2008.&lt;br /&gt;This version is fully compativle with [https://applet-launcher.dev.java.net/ applet-launcher].&lt;/font&gt;&lt;br /&gt;Go to [[jV version 3]].
&lt;br /&gt;
It requires the following softwares.&lt;br /&gt;
* JRE 1.4.2 or later  (recommend 1.4.2_12)&lt;br&gt;jV runs on the Java Runtime Environment ([http://java.sun.com/javase/index.jsp JRE]) so that it can work as a stand-alone application as well as an applet.
* JOGL 1.0, 1.1.1 or JSR-231 1.0.0  (recommend JSR-231)&lt;br /&gt;The graphics of jV is based on OpenGL ([https://jogl.dev.java.net/ JOGL]), thereby producing fairly beautiful pictures.
** version 1.0 [[http://ef-site.hgc.jp/eF-site/jV/JOGL1.0_win32.zip Windows],[http://ef-site.hgc.jp/eF-site/jV/JOGL1.0_macosx.tar.gz Mac OS X],[http://ef-site.hgc.jp/eF-site/jV/JOGL1.0_linux.tar.gz Linux]]
** version 1.1.1 [[http://ef-site.hgc.jp/eF-site/jV/JOGL1.1.1_win32.zip Windows],[http://ef-site.hgc.jp/eF-site/jV/JOGL1.1.1_macosx.tar.gz Mac OS X], [http://ef-site.hgc.jp/eF-site/jV/JOGL1.1.1_linux.tar.gz Linux]]
** JSR-231 1.0.0 [[http://ef-site.hgc.jp/eF-site/jV/JOGL_JSR231_win32.zip Windows], [http://ef-site.hgc.jp/eF-site/jV/JOGL_JSR231_macosx_ppc.tar.gz Mac OS X ppc], [http://ef-site.hgc.jp/eF-site/jV/JOGL_JSR231_macosx_universal.tar.gz Mac OS X universal], [http://ef-site.hgc.jp/eF-site/jV/JOGL_JSR231_linux_i586.tar.gz Linux]]

&lt;font size="1"&gt;Note: &amp;nbsp; JOGL 1.0 and 1.1.1 are not available for Intel Mac.The latest version of JOGL, JSR-231 1.0.0, runs on Intel Mac.&lt;/font&gt;

== jV version 2 ==
jV version 2 is an advanced version of PDBjViewer, which can be used only as a stand-alone program. It enables to display more than one molecule images at the same time and their display models and transforms can be operated separately. An animation of molecules can be also performed. jV version 2 runs with .NET framework 1.1 on the Windows platform. Therefore the .NET framework must be installed on your computer.

== jV version 1 (PDBjViewer) ==
Visualization of structure and surface of molecules is performed by a Java applet program called 'PDBjViewer'.

Two image windows are opened. The structure of the molecule is shown in the left window and the molecular surface is displayed in the right window. The mouse control is as follows. 
&lt;br /&gt;
&lt;div align="center"&gt;
{| class="wikitable" cellspacing="0" border="1"
 ! action !! Windows 
 |-
 | rotate x, y || left
 |-
 | zoom || Alt + left
 |-
 | tranlate x, y || right
 |-
|}
&lt;br /&gt;
&lt;/div&gt;
&lt;br&gt;
In order to use PDBjViewer, [http://java.sun.com/products/plugin/ Java Plug-in] and
[http://java.sun.com/products/java-media/3D/ Java 3D API] must be installed on your computer.
The version requirements are as follows.&lt;br /&gt;
* JRE (includes Java Plug-in) 1.4.1 or later (recommend 1.4.2)
* Java 3D API (OpenGL) 1.2.1 or later (recommend 1.2.1_04)
Important notes
* You can select two kinds of implementation of Java 3D, OpenGL version and DirectX version. But, PDBjViewer only work with OpenGL version at present.
* PDBjViewer does not work with JRE from 1.4.1_03 to 1.4.1_06.&lt;br /&gt;
PDBjViewer can be used as a stand-alone program as well as an applet
with the same requirements as above.
In addition to mouse controls, a command line interface is provided.
&lt;br&gt;</text>
    <sha1>c3162246e7fe29a9055915d50138fa5c9b5c2d37</sha1>
  </revision>
  <revision>
    <id>48</id>
    <parentid>47</parentid>
    <timestamp>2009-03-03T09:35:31Z</timestamp>
    <contributor>
      <username>JVuser</username>
      <id>2</id>
    </contributor>
    <comment>/* jV version 1 (PDBjViewer) */</comment>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="5031" xml:space="preserve">&lt;big&gt;'''Welcome to jV wiki.'''&lt;/big&gt;
{| style="float:right"
 |__TOC__
 |}
jV(formerly known as PDBjViewer) is a program to display molecular graphics of protein and nucleic acids. 
jV can use as a stand-alone program and can operate on a web browser as an Java applet. jV is used by PDBj services([http://ef-site.hgc.jp/eF-site/index.jsp eF-site], [http://ef-site.hgc.jp/eF-seek/index.jsp eF-seek], the molecular structure surface database of the protein functional part).

jV supports the following features:
* jV can read and display PDBML files, the canonical XML format for the Protein Data Bank.
* Of course, jV can read and display the traditional PDB format files, too.
* RasMol-like usability.
* jV can process more than one molecules.
* jV can display polygons specified by XML. ([http://ef-site.hgc.jp/eF-site/schema/polygon12.xsd XML Schema for polygons] is available.)
* Multiple polygons can be processed simultaneously, and be superimposed onto molecular images.
* Animation can be realized.


The program 'jV' has been developed by [http://www.hgc.jp/~kinosita/TOP.html Kengo Kinoshita] ([http://www.hgc.jp/english/ Human Genome Center], [http://www.ims.u-tokyo.ac.jp/imsut/en/ Insutitute for Medical Science],[http://www.u-tokyo.ac.jp/index_e.html University of Tokyo]) and [http://www.protein.osaka-u.ac.jp/rcsfp/pi/ Haruki Nakamura] ([http://www.protein.osaka-u.ac.jp/index_e.php Institute for Protein Research], [http://www.osaka-u.ac.jp/eng/index.html Osaka Univeristy]), with the support from [http://www-bird.jst.go.jp/index_e.html JST-BIRD].

== jV version 3 ==
[[File:Download.png|right|link=http://ef-site.hgc.jp/eF-site/servlet/Registration|Download]] jV version 3 is now used to display molecules and their surfaces as a Java applet program.&lt;br /&gt;&lt;font size="1"&gt;Version 3.6 was released on 11, Aug, 2008.&lt;br /&gt;This version is fully compativle with [https://applet-launcher.dev.java.net/ applet-launcher].&lt;/font&gt;&lt;br /&gt;Go to [[jV version 3]].
&lt;br /&gt;
It requires the following softwares.&lt;br /&gt;
* JRE 1.4.2 or later  (recommend 1.4.2_12)&lt;br&gt;jV runs on the Java Runtime Environment ([http://java.sun.com/javase/index.jsp JRE]) so that it can work as a stand-alone application as well as an applet.
* JOGL 1.0, 1.1.1 or JSR-231 1.0.0  (recommend JSR-231)&lt;br /&gt;The graphics of jV is based on OpenGL ([https://jogl.dev.java.net/ JOGL]), thereby producing fairly beautiful pictures.
** version 1.0 [[http://ef-site.hgc.jp/eF-site/jV/JOGL1.0_win32.zip Windows],[http://ef-site.hgc.jp/eF-site/jV/JOGL1.0_macosx.tar.gz Mac OS X],[http://ef-site.hgc.jp/eF-site/jV/JOGL1.0_linux.tar.gz Linux]]
** version 1.1.1 [[http://ef-site.hgc.jp/eF-site/jV/JOGL1.1.1_win32.zip Windows],[http://ef-site.hgc.jp/eF-site/jV/JOGL1.1.1_macosx.tar.gz Mac OS X], [http://ef-site.hgc.jp/eF-site/jV/JOGL1.1.1_linux.tar.gz Linux]]
** JSR-231 1.0.0 [[http://ef-site.hgc.jp/eF-site/jV/JOGL_JSR231_win32.zip Windows], [http://ef-site.hgc.jp/eF-site/jV/JOGL_JSR231_macosx_ppc.tar.gz Mac OS X ppc], [http://ef-site.hgc.jp/eF-site/jV/JOGL_JSR231_macosx_universal.tar.gz Mac OS X universal], [http://ef-site.hgc.jp/eF-site/jV/JOGL_JSR231_linux_i586.tar.gz Linux]]

&lt;font size="1"&gt;Note: &amp;nbsp; JOGL 1.0 and 1.1.1 are not available for Intel Mac.The latest version of JOGL, JSR-231 1.0.0, runs on Intel Mac.&lt;/font&gt;

== jV version 2 ==
jV version 2 is an advanced version of PDBjViewer, which can be used only as a stand-alone program. It enables to display more than one molecule images at the same time and their display models and transforms can be operated separately. An animation of molecules can be also performed. jV version 2 runs with .NET framework 1.1 on the Windows platform. Therefore the .NET framework must be installed on your computer.

== jV version 1 (PDBjViewer) ==
Visualization of structure and surface of molecules is performed by a Java applet program called 'PDBjViewer'.

Two image windows are opened. The structure of the molecule is shown in the left window and the molecular surface is displayed in the right window. The mouse control is as follows. 
&lt;br /&gt;
&lt;div align="center"&gt;
{| class="wikitable" cellspacing="0" border="1"
 ! action !! Windows 
 |-
 | rotate x, y || left
 |-
 | zoom || Alt + left
 |-
 | tranlate x, y || right
 |-
|}
&lt;br /&gt;
&lt;/div&gt;
&lt;br&gt;
In order to use PDBjViewer, [http://java.sun.com/products/plugin/ Java Plug-in] and
[http://java.sun.com/products/java-media/3D/ Java 3D API] must be installed on your computer.
The version requirements are as follows.&lt;br /&gt;
* JRE (includes Java Plug-in) 1.4.1 or later (recommend 1.4.2)
* Java 3D API (OpenGL) 1.2.1 or later (recommend 1.2.1_04)
Important notes
- You can select two kinds of implementation of Java 3D, OpenGL version and DirectX version. But, PDBjViewer only work with OpenGL version at present.
- PDBjViewer does not work with JRE from 1.4.1_03 to 1.4.1_06.&lt;br /&gt;
PDBjViewer can be used as a stand-alone program as well as an applet
with the same requirements as above.
In addition to mouse controls, a command line interface is provided.
&lt;br&gt;</text>
    <sha1>7407de2e5e863324508e5fbf690035de459dda91</sha1>
  </revision>
  <revision>
    <id>49</id>
    <parentid>48</parentid>
    <timestamp>2009-03-03T09:36:56Z</timestamp>
    <contributor>
      <username>JVuser</username>
      <id>2</id>
    </contributor>
    <comment>/* jV version 1 (PDBjViewer) */</comment>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="5037" xml:space="preserve">&lt;big&gt;'''Welcome to jV wiki.'''&lt;/big&gt;
{| style="float:right"
 |__TOC__
 |}
jV(formerly known as PDBjViewer) is a program to display molecular graphics of protein and nucleic acids. 
jV can use as a stand-alone program and can operate on a web browser as an Java applet. jV is used by PDBj services([http://ef-site.hgc.jp/eF-site/index.jsp eF-site], [http://ef-site.hgc.jp/eF-seek/index.jsp eF-seek], the molecular structure surface database of the protein functional part).

jV supports the following features:
* jV can read and display PDBML files, the canonical XML format for the Protein Data Bank.
* Of course, jV can read and display the traditional PDB format files, too.
* RasMol-like usability.
* jV can process more than one molecules.
* jV can display polygons specified by XML. ([http://ef-site.hgc.jp/eF-site/schema/polygon12.xsd XML Schema for polygons] is available.)
* Multiple polygons can be processed simultaneously, and be superimposed onto molecular images.
* Animation can be realized.


The program 'jV' has been developed by [http://www.hgc.jp/~kinosita/TOP.html Kengo Kinoshita] ([http://www.hgc.jp/english/ Human Genome Center], [http://www.ims.u-tokyo.ac.jp/imsut/en/ Insutitute for Medical Science],[http://www.u-tokyo.ac.jp/index_e.html University of Tokyo]) and [http://www.protein.osaka-u.ac.jp/rcsfp/pi/ Haruki Nakamura] ([http://www.protein.osaka-u.ac.jp/index_e.php Institute for Protein Research], [http://www.osaka-u.ac.jp/eng/index.html Osaka Univeristy]), with the support from [http://www-bird.jst.go.jp/index_e.html JST-BIRD].

== jV version 3 ==
[[File:Download.png|right|link=http://ef-site.hgc.jp/eF-site/servlet/Registration|Download]] jV version 3 is now used to display molecules and their surfaces as a Java applet program.&lt;br /&gt;&lt;font size="1"&gt;Version 3.6 was released on 11, Aug, 2008.&lt;br /&gt;This version is fully compativle with [https://applet-launcher.dev.java.net/ applet-launcher].&lt;/font&gt;&lt;br /&gt;Go to [[jV version 3]].
&lt;br /&gt;
It requires the following softwares.&lt;br /&gt;
* JRE 1.4.2 or later  (recommend 1.4.2_12)&lt;br&gt;jV runs on the Java Runtime Environment ([http://java.sun.com/javase/index.jsp JRE]) so that it can work as a stand-alone application as well as an applet.
* JOGL 1.0, 1.1.1 or JSR-231 1.0.0  (recommend JSR-231)&lt;br /&gt;The graphics of jV is based on OpenGL ([https://jogl.dev.java.net/ JOGL]), thereby producing fairly beautiful pictures.
** version 1.0 [[http://ef-site.hgc.jp/eF-site/jV/JOGL1.0_win32.zip Windows],[http://ef-site.hgc.jp/eF-site/jV/JOGL1.0_macosx.tar.gz Mac OS X],[http://ef-site.hgc.jp/eF-site/jV/JOGL1.0_linux.tar.gz Linux]]
** version 1.1.1 [[http://ef-site.hgc.jp/eF-site/jV/JOGL1.1.1_win32.zip Windows],[http://ef-site.hgc.jp/eF-site/jV/JOGL1.1.1_macosx.tar.gz Mac OS X], [http://ef-site.hgc.jp/eF-site/jV/JOGL1.1.1_linux.tar.gz Linux]]
** JSR-231 1.0.0 [[http://ef-site.hgc.jp/eF-site/jV/JOGL_JSR231_win32.zip Windows], [http://ef-site.hgc.jp/eF-site/jV/JOGL_JSR231_macosx_ppc.tar.gz Mac OS X ppc], [http://ef-site.hgc.jp/eF-site/jV/JOGL_JSR231_macosx_universal.tar.gz Mac OS X universal], [http://ef-site.hgc.jp/eF-site/jV/JOGL_JSR231_linux_i586.tar.gz Linux]]

&lt;font size="1"&gt;Note: &amp;nbsp; JOGL 1.0 and 1.1.1 are not available for Intel Mac.The latest version of JOGL, JSR-231 1.0.0, runs on Intel Mac.&lt;/font&gt;

== jV version 2 ==
jV version 2 is an advanced version of PDBjViewer, which can be used only as a stand-alone program. It enables to display more than one molecule images at the same time and their display models and transforms can be operated separately. An animation of molecules can be also performed. jV version 2 runs with .NET framework 1.1 on the Windows platform. Therefore the .NET framework must be installed on your computer.

== jV version 1 (PDBjViewer) ==
Visualization of structure and surface of molecules is performed by a Java applet program called 'PDBjViewer'.

Two image windows are opened. The structure of the molecule is shown in the left window and the molecular surface is displayed in the right window. The mouse control is as follows. 
&lt;br /&gt;
&lt;div align="center"&gt;
{| class="wikitable" cellspacing="0" border="1"
 ! action !! Windows 
 |-
 | rotate x, y || left
 |-
 | zoom || Alt + left
 |-
 | tranlate x, y || right
 |-
|}
&lt;br /&gt;
&lt;/div&gt;
&lt;br&gt;
In order to use PDBjViewer, [http://java.sun.com/products/plugin/ Java Plug-in] and
[http://java.sun.com/products/java-media/3D/ Java 3D API] must be installed on your computer.
The version requirements are as follows.&lt;br /&gt;
* JRE (includes Java Plug-in) 1.4.1 or later (recommend 1.4.2)
* Java 3D API (OpenGL) 1.2.1 or later (recommend 1.2.1_04)
&lt;br /&gt;Important notes
# You can select two kinds of implementation of Java 3D, OpenGL version and DirectX version. But, PDBjViewer only work with OpenGL version at present.
# PDBjViewer does not work with JRE from 1.4.1_03 to 1.4.1_06.&lt;br /&gt;
PDBjViewer can be used as a stand-alone program as well as an applet
with the same requirements as above.
In addition to mouse controls, a command line interface is provided.
&lt;br&gt;</text>
    <sha1>794ff49e7b4736f7d80b2aeb7c647725ec567fc1</sha1>
  </revision>
</page>
<page arvcontinue="">
  <title>File:Download.png</title>
  <ns>6</ns>
  <id>2</id>
  <revision>
    <id>14</id>
    <timestamp>2009-03-03T07:10:42Z</timestamp>
    <contributor>
      <username>JVuser</username>
      <id>2</id>
    </contributor>
    <comment>{{Information|
|Description=Download.png
|Source=jV-Top
|Date=20090303
|Author=eF-site
|Permission=jV
}}</comment>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="104" xml:space="preserve">{{Information|
|Description=Download.png
|Source=jV-Top
|Date=20090303
|Author=eF-site
|Permission=jV
}}</text>
    <sha1>e06b71d0164a642671b71c5c6dcbd8ba7dd6db0a</sha1>
  </revision>
</page>
<page arvcontinue="">
  <title>XML Schema for polygons</title>
  <ns>0</ns>
  <id>3</id>
  <revision>
    <id>20</id>
    <timestamp>2009-03-03T07:32:32Z</timestamp>
    <contributor>
      <username>JVuser</username>
      <id>2</id>
    </contributor>
    <comment>Created page with 'This XML Schema for polygons can be used by jV.   &lt;?xml version="1.0" ?&gt;   - &lt;schema xmlns="http://www.w3.org/2001/XMLSchema" xmlns:pv="http://pdbj.protein.osaka-u.ac.jp/PDBjView...'</comment>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="5079" xml:space="preserve">This XML Schema for polygons can be used by jV.

 &lt;?xml version="1.0" ?&gt; 
 - &lt;schema xmlns="http://www.w3.org/2001/XMLSchema" xmlns:pv="http://pdbj.protein.osaka-u.ac.jp/PDBjViewer" targetNamespace="http://pdbj.protein.osaka-u.ac.jp/PDBjViewer" elementFormDefault="qualified"&gt;
  &lt;element name="polygon" type="pv:polygon_type" /&gt; 
 - &lt;complexType name="polygon_type"&gt;
 - &lt;sequence&gt;
  &lt;element ref="pv:vertices" /&gt; 
  &lt;element ref="pv:point_array" minOccurs="0" /&gt; 
  &lt;element ref="pv:line_array" minOccurs="0" /&gt; 
  &lt;element ref="pv:triangle_array" minOccurs="0" /&gt; 
  &lt;element ref="pv:quad_array" minOccurs="0" /&gt; 
  &lt;element ref="pv:polyline_array" minOccurs="0" /&gt; 
  &lt;/sequence&gt;
  &lt;/complexType&gt;
  &lt;element name="vertices" type="pv:vertices_type" /&gt; 
 - &lt;complexType name="vertices_type"&gt;
 - &lt;sequence&gt;
  &lt;element ref="pv:vertex" maxOccurs="unbounded" /&gt; 
  &lt;/sequence&gt;
  &lt;attribute name="count" use="required" type="integer" /&gt; 
  &lt;attribute name="id_numbers" use="required" type="string" /&gt; 
- &lt;!-- 
      id_numbers is "use" or "ignore".
      if set to be "ignore", id number of each vertex element is 
      automatically assigned sequential integer (starts from 1)
      in order of appearance.
    

  --&gt; 
  &lt;/complexType&gt;
  &lt;element name="vertex" type="pv:vertex_type" /&gt; 
- &lt;complexType name="vertex_type"&gt;
- &lt;sequence&gt;
  &lt;element name="user_data" type="anyType" minOccurs="0" /&gt; 
  &lt;/sequence&gt;
  &lt;attribute name="id" use="required" type="integer" /&gt; 
  &lt;attribute name="image" use="required" type="string" /&gt; 
- &lt;!-- 
      image has 9 values separated by a space in such an order as
      "coordinates_x coordinates_y coordinates_z 
       normal_vector_x normal_vector_y normal_vector_z
       color_R color_G color_B"
      where RGB values are from 0 to 255
    

  --&gt; 
  &lt;/complexType&gt;
  &lt;element name="point_array" type="pv:point_array_type" /&gt; 
- &lt;complexType name="point_array_type"&gt;
- &lt;sequence&gt;
  &lt;element ref="pv:point" maxOccurs="unbounded" /&gt; 
  &lt;/sequence&gt;
  &lt;attribute name="count" use="required" type="integer" /&gt; 
  &lt;attribute name="transparency" use="optional" type="float" /&gt; 
  &lt;attribute name="size" use="optional" type="float" /&gt; 
  &lt;/complexType&gt;
  &lt;element name="point" type="pv:point_type" /&gt; 
- &lt;complexType name="point_type"&gt;
  &lt;attribute name="id" use="required" type="integer" /&gt; 
  &lt;attribute name="vertex" use="required" type="string" /&gt; 
- &lt;!-- 
      vertex has a single vertex ID
    

  --&gt; 
  &lt;/complexType&gt;
  &lt;element name="line_array" type="pv:line_array_type" /&gt; 
- &lt;complexType name="line_array_type"&gt;
- &lt;sequence&gt;
  &lt;element ref="pv:line" maxOccurs="unbounded" /&gt; 
  &lt;/sequence&gt;
  &lt;attribute name="count" use="required" type="integer" /&gt; 
  &lt;attribute name="transparency" use="optional" type="float" /&gt; 
  &lt;attribute name="width" use="optional" type="float" /&gt; 
  &lt;/complexType&gt;
  &lt;element name="line" type="pv:line_type" /&gt; 
- &lt;complexType name="line_type"&gt;
  &lt;attribute name="id" use="required" type="integer" /&gt; 
  &lt;attribute name="vertex" use="required" type="string" /&gt; 
- &lt;!-- 
      vertex has two vertex IDs separated by a space
    

  --&gt; 
  &lt;/complexType&gt;
  &lt;element name="triangle_array" type="pv:triangle_array_type" /&gt; 
- &lt;complexType name="triangle_array_type"&gt;
- &lt;sequence&gt;
  &lt;element ref="pv:triangle" maxOccurs="unbounded" /&gt; 
  &lt;/sequence&gt;
  &lt;attribute name="count" use="required" type="integer" /&gt; 
  &lt;attribute name="transparency" use="optional" type="float" /&gt; 
  &lt;/complexType&gt;
  &lt;element name="triangle" type="pv:triangle_type" /&gt; 
- &lt;complexType name="triangle_type"&gt;
  &lt;attribute name="id" use="required" type="integer" /&gt; 
  &lt;attribute name="vertex" use="required" type="string" /&gt; 
- &lt;!-- 
      vertex has three vertex IDs separated by a space
    

  --&gt; 
  &lt;/complexType&gt;
  &lt;element name="quad_array" type="pv:quad_array_type" /&gt; 
- &lt;complexType name="quad_array_type"&gt;
- &lt;sequence&gt;
  &lt;element ref="pv:quad" maxOccurs="unbounded" /&gt; 
  &lt;/sequence&gt;
  &lt;attribute name="count" use="required" type="integer" /&gt; 
  &lt;attribute name="transparency" use="optional" type="float" /&gt; 
  &lt;/complexType&gt;
  &lt;element name="quad" type="pv:quad_type" /&gt; 
- &lt;complexType name="quad_type"&gt;
  &lt;attribute name="id" use="required" type="integer" /&gt; 
  &lt;attribute name="vertex" use="required" type="string" /&gt; 
- &lt;!-- 
      vertex has four vertex IDs separated by a space
    

  --&gt; 
  &lt;/complexType&gt;
  &lt;element name="polyline_array" type="pv:polyline_array_type" /&gt; 
- &lt;complexType name="polyline_array_type"&gt;
- &lt;sequence&gt;
  &lt;element ref="pv:polyline" maxOccurs="unbounded" /&gt; 
  &lt;/sequence&gt;
  &lt;attribute name="count" use="required" type="integer" /&gt; 
  &lt;attribute name="transparency" use="optional" type="float" /&gt; 
  &lt;attribute name="width" use="optional" type="float" /&gt; 
  &lt;/complexType&gt;
  &lt;element name="polyline" type="pv:polyline_type" /&gt; 
- &lt;complexType name="polyline_type"&gt;
  &lt;attribute name="id" use="required" type="integer" /&gt; 
  &lt;attribute name="vertex" use="required" type="string" /&gt; 
- &lt;!-- 
      vertex has more than one vertex IDs separated by a space
    

  --&gt; 
  &lt;/complexType&gt;
  &lt;/schema&gt;</text>
    <sha1>b2ad024fef3cc1862adda7e536dc5a76cc93501f</sha1>
  </revision>
  <revision>
    <id>21</id>
    <parentid>20</parentid>
    <timestamp>2009-03-03T07:33:34Z</timestamp>
    <contributor>
      <username>JVuser</username>
      <id>2</id>
    </contributor>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="5099" xml:space="preserve">This XML Schema for polygons can be used by jV.

 &lt;?xml version="1.0" ?&gt; 
 - &lt;schema xmlns="http://www.w3.org/2001/XMLSchema" xmlns:pv="http://pdbj.protein.osaka-u.ac.jp/PDBjViewer" targetNamespace="http://pdbj.protein.osaka-u.ac.jp/PDBjViewer" elementFormDefault="qualified"&gt;
  &lt;element name="polygon" type="pv:polygon_type" /&gt; 
 - &lt;complexType name="polygon_type"&gt;
 - &lt;sequence&gt;
  &lt;element ref="pv:vertices" /&gt; 
  &lt;element ref="pv:point_array" minOccurs="0" /&gt; 
  &lt;element ref="pv:line_array" minOccurs="0" /&gt; 
  &lt;element ref="pv:triangle_array" minOccurs="0" /&gt; 
  &lt;element ref="pv:quad_array" minOccurs="0" /&gt; 
  &lt;element ref="pv:polyline_array" minOccurs="0" /&gt; 
  &lt;/sequence&gt;
  &lt;/complexType&gt;
  &lt;element name="vertices" type="pv:vertices_type" /&gt; 
 - &lt;complexType name="vertices_type"&gt;
 - &lt;sequence&gt;
  &lt;element ref="pv:vertex" maxOccurs="unbounded" /&gt; 
  &lt;/sequence&gt;
  &lt;attribute name="count" use="required" type="integer" /&gt; 
  &lt;attribute name="id_numbers" use="required" type="string" /&gt; 
 - &lt;!-- 
      id_numbers is "use" or "ignore".
      if set to be "ignore", id number of each vertex element is 
      automatically assigned sequential integer (starts from 1)
      in order of appearance.
    

  --&gt; 
  &lt;/complexType&gt;
  &lt;element name="vertex" type="pv:vertex_type" /&gt; 
 - &lt;complexType name="vertex_type"&gt;
 - &lt;sequence&gt;
  &lt;element name="user_data" type="anyType" minOccurs="0" /&gt; 
  &lt;/sequence&gt;
  &lt;attribute name="id" use="required" type="integer" /&gt; 
  &lt;attribute name="image" use="required" type="string" /&gt; 
 - &lt;!-- 
      image has 9 values separated by a space in such an order as
      "coordinates_x coordinates_y coordinates_z 
       normal_vector_x normal_vector_y normal_vector_z
       color_R color_G color_B"
      where RGB values are from 0 to 255
    

  --&gt; 
  &lt;/complexType&gt;
  &lt;element name="point_array" type="pv:point_array_type" /&gt; 
 - &lt;complexType name="point_array_type"&gt;
 - &lt;sequence&gt;
  &lt;element ref="pv:point" maxOccurs="unbounded" /&gt; 
  &lt;/sequence&gt;
  &lt;attribute name="count" use="required" type="integer" /&gt; 
  &lt;attribute name="transparency" use="optional" type="float" /&gt; 
  &lt;attribute name="size" use="optional" type="float" /&gt; 
  &lt;/complexType&gt;
  &lt;element name="point" type="pv:point_type" /&gt; 
 - &lt;complexType name="point_type"&gt;
  &lt;attribute name="id" use="required" type="integer" /&gt; 
  &lt;attribute name="vertex" use="required" type="string" /&gt; 
 - &lt;!-- 
      vertex has a single vertex ID
    

  --&gt; 
  &lt;/complexType&gt;
  &lt;element name="line_array" type="pv:line_array_type" /&gt; 
 - &lt;complexType name="line_array_type"&gt;
 - &lt;sequence&gt;
  &lt;element ref="pv:line" maxOccurs="unbounded" /&gt; 
  &lt;/sequence&gt;
  &lt;attribute name="count" use="required" type="integer" /&gt; 
  &lt;attribute name="transparency" use="optional" type="float" /&gt; 
  &lt;attribute name="width" use="optional" type="float" /&gt; 
  &lt;/complexType&gt;
  &lt;element name="line" type="pv:line_type" /&gt; 
 - &lt;complexType name="line_type"&gt;
  &lt;attribute name="id" use="required" type="integer" /&gt; 
  &lt;attribute name="vertex" use="required" type="string" /&gt; 
 - &lt;!-- 
      vertex has two vertex IDs separated by a space
    

  --&gt; 
  &lt;/complexType&gt;
  &lt;element name="triangle_array" type="pv:triangle_array_type" /&gt; 
- &lt;complexType name="triangle_array_type"&gt;
- &lt;sequence&gt;
  &lt;element ref="pv:triangle" maxOccurs="unbounded" /&gt; 
  &lt;/sequence&gt;
  &lt;attribute name="count" use="required" type="integer" /&gt; 
  &lt;attribute name="transparency" use="optional" type="float" /&gt; 
  &lt;/complexType&gt;
  &lt;element name="triangle" type="pv:triangle_type" /&gt; 
- &lt;complexType name="triangle_type"&gt;
  &lt;attribute name="id" use="required" type="integer" /&gt; 
  &lt;attribute name="vertex" use="required" type="string" /&gt; 
- &lt;!-- 
      vertex has three vertex IDs separated by a space
    

  --&gt; 
  &lt;/complexType&gt;
  &lt;element name="quad_array" type="pv:quad_array_type" /&gt; 
 - &lt;complexType name="quad_array_type"&gt;
 - &lt;sequence&gt;
  &lt;element ref="pv:quad" maxOccurs="unbounded" /&gt; 
  &lt;/sequence&gt;
  &lt;attribute name="count" use="required" type="integer" /&gt; 
  &lt;attribute name="transparency" use="optional" type="float" /&gt; 
  &lt;/complexType&gt;
  &lt;element name="quad" type="pv:quad_type" /&gt; 
 - &lt;complexType name="quad_type"&gt;
  &lt;attribute name="id" use="required" type="integer" /&gt; 
  &lt;attribute name="vertex" use="required" type="string" /&gt; 
 - &lt;!-- 
      vertex has four vertex IDs separated by a space
    

  --&gt; 
  &lt;/complexType&gt;
  &lt;element name="polyline_array" type="pv:polyline_array_type" /&gt; 
 - &lt;complexType name="polyline_array_type"&gt;
 - &lt;sequence&gt;
  &lt;element ref="pv:polyline" maxOccurs="unbounded" /&gt; 
  &lt;/sequence&gt;
  &lt;attribute name="count" use="required" type="integer" /&gt; 
  &lt;attribute name="transparency" use="optional" type="float" /&gt; 
  &lt;attribute name="width" use="optional" type="float" /&gt; 
  &lt;/complexType&gt;
  &lt;element name="polyline" type="pv:polyline_type" /&gt; 
 - &lt;complexType name="polyline_type"&gt;
  &lt;attribute name="id" use="required" type="integer" /&gt; 
  &lt;attribute name="vertex" use="required" type="string" /&gt; 
 - &lt;!-- 
      vertex has more than one vertex IDs separated by a space
    

  --&gt; 
  &lt;/complexType&gt;
  &lt;/schema&gt;</text>
    <sha1>a8d624775042e94ca93a531dd3f80dda81d87367</sha1>
  </revision>
  <revision>
    <id>22</id>
    <parentid>21</parentid>
    <timestamp>2009-03-03T07:34:20Z</timestamp>
    <contributor>
      <username>JVuser</username>
      <id>2</id>
    </contributor>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="5118" xml:space="preserve">This XML Schema for polygons can be used by jV.

 &lt;?xml version="1.0" ?&gt; 
 - &lt;schema xmlns="http://www.w3.org/2001/XMLSchema" 
    xmlns:pv="http://pdbj.protein.osaka-u.ac.jp/PDBjViewer" 
    targetNamespace="http://pdbj.protein.osaka-u.ac.jp/PDBjViewer" 
    elementFormDefault="qualified"&gt;
  &lt;element name="polygon" type="pv:polygon_type" /&gt; 
 - &lt;complexType name="polygon_type"&gt;
 - &lt;sequence&gt;
  &lt;element ref="pv:vertices" /&gt; 
  &lt;element ref="pv:point_array" minOccurs="0" /&gt; 
  &lt;element ref="pv:line_array" minOccurs="0" /&gt; 
  &lt;element ref="pv:triangle_array" minOccurs="0" /&gt; 
  &lt;element ref="pv:quad_array" minOccurs="0" /&gt; 
  &lt;element ref="pv:polyline_array" minOccurs="0" /&gt; 
  &lt;/sequence&gt;
  &lt;/complexType&gt;
  &lt;element name="vertices" type="pv:vertices_type" /&gt; 
 - &lt;complexType name="vertices_type"&gt;
 - &lt;sequence&gt;
  &lt;element ref="pv:vertex" maxOccurs="unbounded" /&gt; 
  &lt;/sequence&gt;
  &lt;attribute name="count" use="required" type="integer" /&gt; 
  &lt;attribute name="id_numbers" use="required" type="string" /&gt; 
 - &lt;!-- 
      id_numbers is "use" or "ignore".
      if set to be "ignore", id number of each vertex element is 
      automatically assigned sequential integer (starts from 1)
      in order of appearance.
    

  --&gt; 
  &lt;/complexType&gt;
  &lt;element name="vertex" type="pv:vertex_type" /&gt; 
 - &lt;complexType name="vertex_type"&gt;
 - &lt;sequence&gt;
  &lt;element name="user_data" type="anyType" minOccurs="0" /&gt; 
  &lt;/sequence&gt;
  &lt;attribute name="id" use="required" type="integer" /&gt; 
  &lt;attribute name="image" use="required" type="string" /&gt; 
 - &lt;!-- 
      image has 9 values separated by a space in such an order as
      "coordinates_x coordinates_y coordinates_z 
       normal_vector_x normal_vector_y normal_vector_z
       color_R color_G color_B"
      where RGB values are from 0 to 255
    

  --&gt; 
  &lt;/complexType&gt;
  &lt;element name="point_array" type="pv:point_array_type" /&gt; 
 - &lt;complexType name="point_array_type"&gt;
 - &lt;sequence&gt;
  &lt;element ref="pv:point" maxOccurs="unbounded" /&gt; 
  &lt;/sequence&gt;
  &lt;attribute name="count" use="required" type="integer" /&gt; 
  &lt;attribute name="transparency" use="optional" type="float" /&gt; 
  &lt;attribute name="size" use="optional" type="float" /&gt; 
  &lt;/complexType&gt;
  &lt;element name="point" type="pv:point_type" /&gt; 
 - &lt;complexType name="point_type"&gt;
  &lt;attribute name="id" use="required" type="integer" /&gt; 
  &lt;attribute name="vertex" use="required" type="string" /&gt; 
 - &lt;!-- 
      vertex has a single vertex ID
    

  --&gt; 
  &lt;/complexType&gt;
  &lt;element name="line_array" type="pv:line_array_type" /&gt; 
 - &lt;complexType name="line_array_type"&gt;
 - &lt;sequence&gt;
  &lt;element ref="pv:line" maxOccurs="unbounded" /&gt; 
  &lt;/sequence&gt;
  &lt;attribute name="count" use="required" type="integer" /&gt; 
  &lt;attribute name="transparency" use="optional" type="float" /&gt; 
  &lt;attribute name="width" use="optional" type="float" /&gt; 
  &lt;/complexType&gt;
  &lt;element name="line" type="pv:line_type" /&gt; 
 - &lt;complexType name="line_type"&gt;
  &lt;attribute name="id" use="required" type="integer" /&gt; 
  &lt;attribute name="vertex" use="required" type="string" /&gt; 
 - &lt;!-- 
      vertex has two vertex IDs separated by a space
    

  --&gt; 
  &lt;/complexType&gt;
  &lt;element name="triangle_array" type="pv:triangle_array_type" /&gt; 
 - &lt;complexType name="triangle_array_type"&gt;
 - &lt;sequence&gt;
  &lt;element ref="pv:triangle" maxOccurs="unbounded" /&gt; 
  &lt;/sequence&gt;
  &lt;attribute name="count" use="required" type="integer" /&gt; 
  &lt;attribute name="transparency" use="optional" type="float" /&gt; 
  &lt;/complexType&gt;
  &lt;element name="triangle" type="pv:triangle_type" /&gt; 
 - &lt;complexType name="triangle_type"&gt;
  &lt;attribute name="id" use="required" type="integer" /&gt; 
  &lt;attribute name="vertex" use="required" type="string" /&gt; 
 - &lt;!-- 
      vertex has three vertex IDs separated by a space
    

  --&gt; 
  &lt;/complexType&gt;
  &lt;element name="quad_array" type="pv:quad_array_type" /&gt; 
 - &lt;complexType name="quad_array_type"&gt;
 - &lt;sequence&gt;
  &lt;element ref="pv:quad" maxOccurs="unbounded" /&gt; 
  &lt;/sequence&gt;
  &lt;attribute name="count" use="required" type="integer" /&gt; 
  &lt;attribute name="transparency" use="optional" type="float" /&gt; 
  &lt;/complexType&gt;
  &lt;element name="quad" type="pv:quad_type" /&gt; 
 - &lt;complexType name="quad_type"&gt;
  &lt;attribute name="id" use="required" type="integer" /&gt; 
  &lt;attribute name="vertex" use="required" type="string" /&gt; 
 - &lt;!-- 
      vertex has four vertex IDs separated by a space
    

  --&gt; 
  &lt;/complexType&gt;
  &lt;element name="polyline_array" type="pv:polyline_array_type" /&gt; 
 - &lt;complexType name="polyline_array_type"&gt;
 - &lt;sequence&gt;
  &lt;element ref="pv:polyline" maxOccurs="unbounded" /&gt; 
  &lt;/sequence&gt;
  &lt;attribute name="count" use="required" type="integer" /&gt; 
  &lt;attribute name="transparency" use="optional" type="float" /&gt; 
  &lt;attribute name="width" use="optional" type="float" /&gt; 
  &lt;/complexType&gt;
  &lt;element name="polyline" type="pv:polyline_type" /&gt; 
 - &lt;complexType name="polyline_type"&gt;
  &lt;attribute name="id" use="required" type="integer" /&gt; 
  &lt;attribute name="vertex" use="required" type="string" /&gt; 
 - &lt;!-- 
      vertex has more than one vertex IDs separated by a space
    

  --&gt; 
  &lt;/complexType&gt;
  &lt;/schema&gt;</text>
    <sha1>d4ac7064f0f49735cfd77465e91ce7bbac494060</sha1>
  </revision>
  <revision>
    <id>23</id>
    <parentid>22</parentid>
    <timestamp>2009-03-03T07:37:10Z</timestamp>
    <contributor>
      <username>JVuser</username>
      <id>2</id>
    </contributor>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="5170" xml:space="preserve">This XML Schema for polygons can be used by jV.
http://ef-site.hgc.jp/eF-site/schema/polygon12.xsd


 &lt;?xml version="1.0" ?&gt; 
 - &lt;schema xmlns="http://www.w3.org/2001/XMLSchema" 
    xmlns:pv="http://pdbj.protein.osaka-u.ac.jp/PDBjViewer" 
    targetNamespace="http://pdbj.protein.osaka-u.ac.jp/PDBjViewer" 
    elementFormDefault="qualified"&gt;
  &lt;element name="polygon" type="pv:polygon_type" /&gt; 
 - &lt;complexType name="polygon_type"&gt;
 - &lt;sequence&gt;
  &lt;element ref="pv:vertices" /&gt; 
  &lt;element ref="pv:point_array" minOccurs="0" /&gt; 
  &lt;element ref="pv:line_array" minOccurs="0" /&gt; 
  &lt;element ref="pv:triangle_array" minOccurs="0" /&gt; 
  &lt;element ref="pv:quad_array" minOccurs="0" /&gt; 
  &lt;element ref="pv:polyline_array" minOccurs="0" /&gt; 
  &lt;/sequence&gt;
  &lt;/complexType&gt;
  &lt;element name="vertices" type="pv:vertices_type" /&gt; 
 - &lt;complexType name="vertices_type"&gt;
 - &lt;sequence&gt;
  &lt;element ref="pv:vertex" maxOccurs="unbounded" /&gt; 
  &lt;/sequence&gt;
  &lt;attribute name="count" use="required" type="integer" /&gt; 
  &lt;attribute name="id_numbers" use="required" type="string" /&gt; 
 - &lt;!-- 
      id_numbers is "use" or "ignore".
      if set to be "ignore", id number of each vertex element is 
      automatically assigned sequential integer (starts from 1)
      in order of appearance.
    

  --&gt; 
  &lt;/complexType&gt;
  &lt;element name="vertex" type="pv:vertex_type" /&gt; 
 - &lt;complexType name="vertex_type"&gt;
 - &lt;sequence&gt;
  &lt;element name="user_data" type="anyType" minOccurs="0" /&gt; 
  &lt;/sequence&gt;
  &lt;attribute name="id" use="required" type="integer" /&gt; 
  &lt;attribute name="image" use="required" type="string" /&gt; 
 - &lt;!-- 
      image has 9 values separated by a space in such an order as
      "coordinates_x coordinates_y coordinates_z 
       normal_vector_x normal_vector_y normal_vector_z
       color_R color_G color_B"
      where RGB values are from 0 to 255
    

  --&gt; 
  &lt;/complexType&gt;
  &lt;element name="point_array" type="pv:point_array_type" /&gt; 
 - &lt;complexType name="point_array_type"&gt;
 - &lt;sequence&gt;
  &lt;element ref="pv:point" maxOccurs="unbounded" /&gt; 
  &lt;/sequence&gt;
  &lt;attribute name="count" use="required" type="integer" /&gt; 
  &lt;attribute name="transparency" use="optional" type="float" /&gt; 
  &lt;attribute name="size" use="optional" type="float" /&gt; 
  &lt;/complexType&gt;
  &lt;element name="point" type="pv:point_type" /&gt; 
 - &lt;complexType name="point_type"&gt;
  &lt;attribute name="id" use="required" type="integer" /&gt; 
  &lt;attribute name="vertex" use="required" type="string" /&gt; 
 - &lt;!-- 
      vertex has a single vertex ID
    

  --&gt; 
  &lt;/complexType&gt;
  &lt;element name="line_array" type="pv:line_array_type" /&gt; 
 - &lt;complexType name="line_array_type"&gt;
 - &lt;sequence&gt;
  &lt;element ref="pv:line" maxOccurs="unbounded" /&gt; 
  &lt;/sequence&gt;
  &lt;attribute name="count" use="required" type="integer" /&gt; 
  &lt;attribute name="transparency" use="optional" type="float" /&gt; 
  &lt;attribute name="width" use="optional" type="float" /&gt; 
  &lt;/complexType&gt;
  &lt;element name="line" type="pv:line_type" /&gt; 
 - &lt;complexType name="line_type"&gt;
  &lt;attribute name="id" use="required" type="integer" /&gt; 
  &lt;attribute name="vertex" use="required" type="string" /&gt; 
 - &lt;!-- 
      vertex has two vertex IDs separated by a space
    

  --&gt; 
  &lt;/complexType&gt;
  &lt;element name="triangle_array" type="pv:triangle_array_type" /&gt; 
 - &lt;complexType name="triangle_array_type"&gt;
 - &lt;sequence&gt;
  &lt;element ref="pv:triangle" maxOccurs="unbounded" /&gt; 
  &lt;/sequence&gt;
  &lt;attribute name="count" use="required" type="integer" /&gt; 
  &lt;attribute name="transparency" use="optional" type="float" /&gt; 
  &lt;/complexType&gt;
  &lt;element name="triangle" type="pv:triangle_type" /&gt; 
 - &lt;complexType name="triangle_type"&gt;
  &lt;attribute name="id" use="required" type="integer" /&gt; 
  &lt;attribute name="vertex" use="required" type="string" /&gt; 
 - &lt;!-- 
      vertex has three vertex IDs separated by a space
    

  --&gt; 
  &lt;/complexType&gt;
  &lt;element name="quad_array" type="pv:quad_array_type" /&gt; 
 - &lt;complexType name="quad_array_type"&gt;
 - &lt;sequence&gt;
  &lt;element ref="pv:quad" maxOccurs="unbounded" /&gt; 
  &lt;/sequence&gt;
  &lt;attribute name="count" use="required" type="integer" /&gt; 
  &lt;attribute name="transparency" use="optional" type="float" /&gt; 
  &lt;/complexType&gt;
  &lt;element name="quad" type="pv:quad_type" /&gt; 
 - &lt;complexType name="quad_type"&gt;
  &lt;attribute name="id" use="required" type="integer" /&gt; 
  &lt;attribute name="vertex" use="required" type="string" /&gt; 
 - &lt;!-- 
      vertex has four vertex IDs separated by a space
    

  --&gt; 
  &lt;/complexType&gt;
  &lt;element name="polyline_array" type="pv:polyline_array_type" /&gt; 
 - &lt;complexType name="polyline_array_type"&gt;
 - &lt;sequence&gt;
  &lt;element ref="pv:polyline" maxOccurs="unbounded" /&gt; 
  &lt;/sequence&gt;
  &lt;attribute name="count" use="required" type="integer" /&gt; 
  &lt;attribute name="transparency" use="optional" type="float" /&gt; 
  &lt;attribute name="width" use="optional" type="float" /&gt; 
  &lt;/complexType&gt;
  &lt;element name="polyline" type="pv:polyline_type" /&gt; 
 - &lt;complexType name="polyline_type"&gt;
  &lt;attribute name="id" use="required" type="integer" /&gt; 
  &lt;attribute name="vertex" use="required" type="string" /&gt; 
 - &lt;!-- 
      vertex has more than one vertex IDs separated by a space
    

  --&gt; 
  &lt;/complexType&gt;
  &lt;/schema&gt;</text>
    <sha1>5ca62e69cb170d5dde3c092ae67d4e20243875d9</sha1>
  </revision>
  <revision>
    <id>24</id>
    <parentid>23</parentid>
    <timestamp>2009-03-03T07:37:37Z</timestamp>
    <contributor>
      <username>JVuser</username>
      <id>2</id>
    </contributor>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="5176" xml:space="preserve">This XML Schema for polygons can be used by jV.&lt;br /&gt;
http://ef-site.hgc.jp/eF-site/schema/polygon12.xsd


 &lt;?xml version="1.0" ?&gt; 
 - &lt;schema xmlns="http://www.w3.org/2001/XMLSchema" 
    xmlns:pv="http://pdbj.protein.osaka-u.ac.jp/PDBjViewer" 
    targetNamespace="http://pdbj.protein.osaka-u.ac.jp/PDBjViewer" 
    elementFormDefault="qualified"&gt;
  &lt;element name="polygon" type="pv:polygon_type" /&gt; 
 - &lt;complexType name="polygon_type"&gt;
 - &lt;sequence&gt;
  &lt;element ref="pv:vertices" /&gt; 
  &lt;element ref="pv:point_array" minOccurs="0" /&gt; 
  &lt;element ref="pv:line_array" minOccurs="0" /&gt; 
  &lt;element ref="pv:triangle_array" minOccurs="0" /&gt; 
  &lt;element ref="pv:quad_array" minOccurs="0" /&gt; 
  &lt;element ref="pv:polyline_array" minOccurs="0" /&gt; 
  &lt;/sequence&gt;
  &lt;/complexType&gt;
  &lt;element name="vertices" type="pv:vertices_type" /&gt; 
 - &lt;complexType name="vertices_type"&gt;
 - &lt;sequence&gt;
  &lt;element ref="pv:vertex" maxOccurs="unbounded" /&gt; 
  &lt;/sequence&gt;
  &lt;attribute name="count" use="required" type="integer" /&gt; 
  &lt;attribute name="id_numbers" use="required" type="string" /&gt; 
 - &lt;!-- 
      id_numbers is "use" or "ignore".
      if set to be "ignore", id number of each vertex element is 
      automatically assigned sequential integer (starts from 1)
      in order of appearance.
    

  --&gt; 
  &lt;/complexType&gt;
  &lt;element name="vertex" type="pv:vertex_type" /&gt; 
 - &lt;complexType name="vertex_type"&gt;
 - &lt;sequence&gt;
  &lt;element name="user_data" type="anyType" minOccurs="0" /&gt; 
  &lt;/sequence&gt;
  &lt;attribute name="id" use="required" type="integer" /&gt; 
  &lt;attribute name="image" use="required" type="string" /&gt; 
 - &lt;!-- 
      image has 9 values separated by a space in such an order as
      "coordinates_x coordinates_y coordinates_z 
       normal_vector_x normal_vector_y normal_vector_z
       color_R color_G color_B"
      where RGB values are from 0 to 255
    

  --&gt; 
  &lt;/complexType&gt;
  &lt;element name="point_array" type="pv:point_array_type" /&gt; 
 - &lt;complexType name="point_array_type"&gt;
 - &lt;sequence&gt;
  &lt;element ref="pv:point" maxOccurs="unbounded" /&gt; 
  &lt;/sequence&gt;
  &lt;attribute name="count" use="required" type="integer" /&gt; 
  &lt;attribute name="transparency" use="optional" type="float" /&gt; 
  &lt;attribute name="size" use="optional" type="float" /&gt; 
  &lt;/complexType&gt;
  &lt;element name="point" type="pv:point_type" /&gt; 
 - &lt;complexType name="point_type"&gt;
  &lt;attribute name="id" use="required" type="integer" /&gt; 
  &lt;attribute name="vertex" use="required" type="string" /&gt; 
 - &lt;!-- 
      vertex has a single vertex ID
    

  --&gt; 
  &lt;/complexType&gt;
  &lt;element name="line_array" type="pv:line_array_type" /&gt; 
 - &lt;complexType name="line_array_type"&gt;
 - &lt;sequence&gt;
  &lt;element ref="pv:line" maxOccurs="unbounded" /&gt; 
  &lt;/sequence&gt;
  &lt;attribute name="count" use="required" type="integer" /&gt; 
  &lt;attribute name="transparency" use="optional" type="float" /&gt; 
  &lt;attribute name="width" use="optional" type="float" /&gt; 
  &lt;/complexType&gt;
  &lt;element name="line" type="pv:line_type" /&gt; 
 - &lt;complexType name="line_type"&gt;
  &lt;attribute name="id" use="required" type="integer" /&gt; 
  &lt;attribute name="vertex" use="required" type="string" /&gt; 
 - &lt;!-- 
      vertex has two vertex IDs separated by a space
    

  --&gt; 
  &lt;/complexType&gt;
  &lt;element name="triangle_array" type="pv:triangle_array_type" /&gt; 
 - &lt;complexType name="triangle_array_type"&gt;
 - &lt;sequence&gt;
  &lt;element ref="pv:triangle" maxOccurs="unbounded" /&gt; 
  &lt;/sequence&gt;
  &lt;attribute name="count" use="required" type="integer" /&gt; 
  &lt;attribute name="transparency" use="optional" type="float" /&gt; 
  &lt;/complexType&gt;
  &lt;element name="triangle" type="pv:triangle_type" /&gt; 
 - &lt;complexType name="triangle_type"&gt;
  &lt;attribute name="id" use="required" type="integer" /&gt; 
  &lt;attribute name="vertex" use="required" type="string" /&gt; 
 - &lt;!-- 
      vertex has three vertex IDs separated by a space
    

  --&gt; 
  &lt;/complexType&gt;
  &lt;element name="quad_array" type="pv:quad_array_type" /&gt; 
 - &lt;complexType name="quad_array_type"&gt;
 - &lt;sequence&gt;
  &lt;element ref="pv:quad" maxOccurs="unbounded" /&gt; 
  &lt;/sequence&gt;
  &lt;attribute name="count" use="required" type="integer" /&gt; 
  &lt;attribute name="transparency" use="optional" type="float" /&gt; 
  &lt;/complexType&gt;
  &lt;element name="quad" type="pv:quad_type" /&gt; 
 - &lt;complexType name="quad_type"&gt;
  &lt;attribute name="id" use="required" type="integer" /&gt; 
  &lt;attribute name="vertex" use="required" type="string" /&gt; 
 - &lt;!-- 
      vertex has four vertex IDs separated by a space
    

  --&gt; 
  &lt;/complexType&gt;
  &lt;element name="polyline_array" type="pv:polyline_array_type" /&gt; 
 - &lt;complexType name="polyline_array_type"&gt;
 - &lt;sequence&gt;
  &lt;element ref="pv:polyline" maxOccurs="unbounded" /&gt; 
  &lt;/sequence&gt;
  &lt;attribute name="count" use="required" type="integer" /&gt; 
  &lt;attribute name="transparency" use="optional" type="float" /&gt; 
  &lt;attribute name="width" use="optional" type="float" /&gt; 
  &lt;/complexType&gt;
  &lt;element name="polyline" type="pv:polyline_type" /&gt; 
 - &lt;complexType name="polyline_type"&gt;
  &lt;attribute name="id" use="required" type="integer" /&gt; 
  &lt;attribute name="vertex" use="required" type="string" /&gt; 
 - &lt;!-- 
      vertex has more than one vertex IDs separated by a space
    

  --&gt; 
  &lt;/complexType&gt;
  &lt;/schema&gt;</text>
    <sha1>4da6105f87b4e867eaa1c4a59a1bfebf629c836c</sha1>
  </revision>
  <revision>
    <id>25</id>
    <parentid>24</parentid>
    <timestamp>2009-03-03T07:39:07Z</timestamp>
    <contributor>
      <username>JVuser</username>
      <id>2</id>
    </contributor>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="5147" xml:space="preserve">This XML Schema for polygons can be used by jV.&lt;br /&gt;
http://ef-site.hgc.jp/eF-site/schema/polygon12.xsd


 &lt;?xml version="1.0" ?&gt; 
  &lt;schema xmlns="http://www.w3.org/2001/XMLSchema" 
    xmlns:pv="http://pdbj.protein.osaka-u.ac.jp/PDBjViewer" 
    targetNamespace="http://pdbj.protein.osaka-u.ac.jp/PDBjViewer" 
    elementFormDefault="qualified"&gt;
  &lt;element name="polygon" type="pv:polygon_type" /&gt; 
  &lt;complexType name="polygon_type"&gt;
  &lt;sequence&gt;
  &lt;element ref="pv:vertices" /&gt; 
  &lt;element ref="pv:point_array" minOccurs="0" /&gt; 
  &lt;element ref="pv:line_array" minOccurs="0" /&gt; 
  &lt;element ref="pv:triangle_array" minOccurs="0" /&gt; 
  &lt;element ref="pv:quad_array" minOccurs="0" /&gt; 
  &lt;element ref="pv:polyline_array" minOccurs="0" /&gt; 
  &lt;/sequence&gt;
  &lt;/complexType&gt;
  &lt;element name="vertices" type="pv:vertices_type" /&gt; 
  &lt;complexType name="vertices_type"&gt;
  &lt;sequence&gt;
  &lt;element ref="pv:vertex" maxOccurs="unbounded" /&gt; 
  &lt;/sequence&gt;
  &lt;attribute name="count" use="required" type="integer" /&gt; 
  &lt;attribute name="id_numbers" use="required" type="string" /&gt; 
  &lt;!-- 
      id_numbers is "use" or "ignore".
      if set to be "ignore", id number of each vertex element is 
      automatically assigned sequential integer (starts from 1)
      in order of appearance.
    

  --&gt; 
  &lt;/complexType&gt;
  &lt;element name="vertex" type="pv:vertex_type" /&gt; 
  &lt;complexType name="vertex_type"&gt;
  &lt;sequence&gt;
  &lt;element name="user_data" type="anyType" minOccurs="0" /&gt; 
  &lt;/sequence&gt;
  &lt;attribute name="id" use="required" type="integer" /&gt; 
  &lt;attribute name="image" use="required" type="string" /&gt; 
  &lt;!-- 
      image has 9 values separated by a space in such an order as
      "coordinates_x coordinates_y coordinates_z 
       normal_vector_x normal_vector_y normal_vector_z
       color_R color_G color_B"
      where RGB values are from 0 to 255
    

  --&gt; 
  &lt;/complexType&gt;
  &lt;element name="point_array" type="pv:point_array_type" /&gt; 
  &lt;complexType name="point_array_type"&gt;
  &lt;sequence&gt;
  &lt;element ref="pv:point" maxOccurs="unbounded" /&gt; 
  &lt;/sequence&gt;
  &lt;attribute name="count" use="required" type="integer" /&gt; 
  &lt;attribute name="transparency" use="optional" type="float" /&gt; 
  &lt;attribute name="size" use="optional" type="float" /&gt; 
  &lt;/complexType&gt;
  &lt;element name="point" type="pv:point_type" /&gt; 
  &lt;complexType name="point_type"&gt;
  &lt;attribute name="id" use="required" type="integer" /&gt; 
  &lt;attribute name="vertex" use="required" type="string" /&gt; 
  &lt;!-- 
      vertex has a single vertex ID
    

  --&gt; 
  &lt;/complexType&gt;
  &lt;element name="line_array" type="pv:line_array_type" /&gt; 
  &lt;complexType name="line_array_type"&gt;
  &lt;sequence&gt;
  &lt;element ref="pv:line" maxOccurs="unbounded" /&gt; 
  &lt;/sequence&gt;
  &lt;attribute name="count" use="required" type="integer" /&gt; 
  &lt;attribute name="transparency" use="optional" type="float" /&gt; 
  &lt;attribute name="width" use="optional" type="float" /&gt; 
  &lt;/complexType&gt;
  &lt;element name="line" type="pv:line_type" /&gt; 
  &lt;complexType name="line_type"&gt;
  &lt;attribute name="id" use="required" type="integer" /&gt; 
  &lt;attribute name="vertex" use="required" type="string" /&gt; 
  &lt;!-- 
      vertex has two vertex IDs separated by a space
    

  --&gt; 
  &lt;/complexType&gt;
  &lt;element name="triangle_array" type="pv:triangle_array_type" /&gt; 
  &lt;complexType name="triangle_array_type"&gt;
  &lt;sequence&gt;
  &lt;element ref="pv:triangle" maxOccurs="unbounded" /&gt; 
  &lt;/sequence&gt;
  &lt;attribute name="count" use="required" type="integer" /&gt; 
  &lt;attribute name="transparency" use="optional" type="float" /&gt; 
  &lt;/complexType&gt;
  &lt;element name="triangle" type="pv:triangle_type" /&gt; 
  &lt;complexType name="triangle_type"&gt;
  &lt;attribute name="id" use="required" type="integer" /&gt; 
  &lt;attribute name="vertex" use="required" type="string" /&gt; 
  &lt;!-- 
      vertex has three vertex IDs separated by a space
    

  --&gt; 
  &lt;/complexType&gt;
  &lt;element name="quad_array" type="pv:quad_array_type" /&gt; 
  &lt;complexType name="quad_array_type"&gt;
  &lt;sequence&gt;
  &lt;element ref="pv:quad" maxOccurs="unbounded" /&gt; 
  &lt;/sequence&gt;
  &lt;attribute name="count" use="required" type="integer" /&gt; 
  &lt;attribute name="transparency" use="optional" type="float" /&gt; 
  &lt;/complexType&gt;
  &lt;element name="quad" type="pv:quad_type" /&gt; 
  &lt;complexType name="quad_type"&gt;
  &lt;attribute name="id" use="required" type="integer" /&gt; 
  &lt;attribute name="vertex" use="required" type="string" /&gt; 
  &lt;!-- 
      vertex has four vertex IDs separated by a space
    

  --&gt; 
  &lt;/complexType&gt;
  &lt;element name="polyline_array" type="pv:polyline_array_type" /&gt; 
  &lt;complexType name="polyline_array_type"&gt;
  &lt;sequence&gt;
  &lt;element ref="pv:polyline" maxOccurs="unbounded" /&gt; 
  &lt;/sequence&gt;
  &lt;attribute name="count" use="required" type="integer" /&gt; 
  &lt;attribute name="transparency" use="optional" type="float" /&gt; 
  &lt;attribute name="width" use="optional" type="float" /&gt; 
  &lt;/complexType&gt;
  &lt;element name="polyline" type="pv:polyline_type" /&gt; 
  &lt;complexType name="polyline_type"&gt;
  &lt;attribute name="id" use="required" type="integer" /&gt; 
  &lt;attribute name="vertex" use="required" type="string" /&gt; 
  &lt;!-- 
      vertex has more than one vertex IDs separated by a space
    

  --&gt; 
  &lt;/complexType&gt;
  &lt;/schema&gt;</text>
    <sha1>92fdcf40c6b156c0873ad88e3a7dc8b6c63394eb</sha1>
  </revision>
</page>
<page arvcontinue="">
  <title>Links</title>
  <ns>0</ns>
  <id>4</id>
  <revision>
    <id>50</id>
    <timestamp>2009-03-03T09:51:31Z</timestamp>
    <contributor>
      <username>JVuser</username>
      <id>2</id>
    </contributor>
    <comment>Created page with '* [http://ef-site.hgc.jp/eF-site/ eF-site] (DB of electrostatic surface of functional site of proteins) * [http://ef-site.hgc.jp/eF-seek/ eF-seek] (Prediction of ligand binding s...'</comment>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="1037" xml:space="preserve">* [http://ef-site.hgc.jp/eF-site/ eF-site] (DB of electrostatic surface of functional site of proteins)
* [http://ef-site.hgc.jp/eF-seek/ eF-seek] (Prediction of ligand binding site of proteins)
* [http://ef-site.hgc.jp/eF-surf/ eF-surf] (Calculate the molecular surface and electrostatic potential of proteins)
* [http://pre-s.protein.osaka-u.ac.jp/~preds/ P&lt;i&gt;re&lt;/i&gt;D&lt;i&gt;s&lt;/i&gt;] (Prediction of DNA-binding site)
* [http://pre-s.protein.osaka-u.ac.jp/~prebi/ PreBI] (Prediction of biological interface of proteins homo-interface)
* [http://pre-s.protein.osaka-u.ac.jp/~preds classPPI] (Classification of homo protein-protein interfaces)
* [http://p-cats.hgc.jp/p-cats/ P-cats] (Prediction of Catalytic residues in proteins)
* [http://pdbjs3.protein.osaka-u.ac.jp/xPSSS/index.html xPSSS] (xml-based protein structure search service)
* [http://eprots.protein.osaka-u.ac.jp/eProtS/Top_e.jsp eProtS] (Encyclopedia of protein structures)
* [http://cube.socs.waseda.ac.jp:80/pages/jsp/index.jsp ProMode] (DB of normal mode analysis of proteins)</text>
    <sha1>05e47afced59e933795bdab4415946dd3b892301</sha1>
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<page arvcontinue="20090303095249|51">
  <title>Links</title>
  <ns>0</ns>
  <id>4</id>
  <revision>
    <id>51</id>
    <parentid>50</parentid>
    <timestamp>2009-03-03T09:52:49Z</timestamp>
    <contributor>
      <username>JVuser</username>
      <id>2</id>
    </contributor>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="1037" xml:space="preserve">* [http://ef-site.hgc.jp/eF-site/ eF-site] (DB of electrostatic surface of functional site of proteins)
* [http://ef-site.hgc.jp/eF-seek/ eF-seek] (Prediction of ligand binding site of proteins)
* [http://ef-site.hgc.jp/eF-surf/ eF-surf] (Calculate the molecular surface and electrostatic potential of proteins)

* [http://pre-s.protein.osaka-u.ac.jp/~preds/ P&lt;i&gt;re&lt;/i&gt;D&lt;i&gt;s&lt;/i&gt;] (Prediction of DNA-binding site)
* [http://pre-s.protein.osaka-u.ac.jp/~prebi/ PreBI] (Prediction of biological interface of proteins homo-interface)
* [http://pre-s.protein.osaka-u.ac.jp/~preds classPPI] (Classification of homo protein-protein interfaces)

* [http://p-cats.hgc.jp/p-cats/ P-cats] (Prediction of Catalytic residues in proteins)

* [http://pdbjs3.protein.osaka-u.ac.jp/xPSSS/index.html xPSSS] (xml-based protein structure search service)
* [http://eprots.protein.osaka-u.ac.jp/eProtS/Top_e.jsp eProtS] (Encyclopedia of protein structures)
* [http://cube.socs.waseda.ac.jp/pages/jsp/index.jsp ProMode] (DB of normal mode analysis of proteins)</text>
    <sha1>ef6bc22da4d82540e14a71bab76b146db57e6402</sha1>
  </revision>
  <revision>
    <id>52</id>
    <parentid>51</parentid>
    <timestamp>2009-03-03T09:53:07Z</timestamp>
    <contributor>
      <username>JVuser</username>
      <id>2</id>
    </contributor>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="1055" xml:space="preserve">* [http://ef-site.hgc.jp/eF-site/ eF-site] (DB of electrostatic surface of functional site of proteins)
* [http://ef-site.hgc.jp/eF-seek/ eF-seek] (Prediction of ligand binding site of proteins)
* [http://ef-site.hgc.jp/eF-surf/ eF-surf] (Calculate the molecular surface and electrostatic potential of proteins)
&lt;br /&gt;
* [http://pre-s.protein.osaka-u.ac.jp/~preds/ P&lt;i&gt;re&lt;/i&gt;D&lt;i&gt;s&lt;/i&gt;] (Prediction of DNA-binding site)
* [http://pre-s.protein.osaka-u.ac.jp/~prebi/ PreBI] (Prediction of biological interface of proteins homo-interface)
* [http://pre-s.protein.osaka-u.ac.jp/~preds classPPI] (Classification of homo protein-protein interfaces)
&lt;br /&gt;
* [http://p-cats.hgc.jp/p-cats/ P-cats] (Prediction of Catalytic residues in proteins)
&lt;br /&gt;
* [http://pdbjs3.protein.osaka-u.ac.jp/xPSSS/index.html xPSSS] (xml-based protein structure search service)
* [http://eprots.protein.osaka-u.ac.jp/eProtS/Top_e.jsp eProtS] (Encyclopedia of protein structures)
* [http://cube.socs.waseda.ac.jp/pages/jsp/index.jsp ProMode] (DB of normal mode analysis of proteins)</text>
    <sha1>382fbf5f5e6522a582a966c71caaa09d370b4d6f</sha1>
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  <revision>
    <id>55</id>
    <parentid>52</parentid>
    <timestamp>2009-03-03T10:07:02Z</timestamp>
    <contributor>
      <username>WikiSysop</username>
      <id>1</id>
    </contributor>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="1276" xml:space="preserve">== Organization ==
* [http://www-bird.jst.go.jp/index_e.html JST-BIRD]
* [http://www.hgc.jp/english/ Human Genome Center]
* [http://www.protein.osaka-u.ac.jp/home_e/index_e.html Institute for Protein Research]

== DBs ==
* [http://ef-site.hgc.jp/eF-site/ eF-site] (DB of electrostatic surface of functional site of proteins)
* [http://ef-site.hgc.jp/eF-seek/ eF-seek] (Prediction of ligand binding site of proteins)
* [http://ef-site.hgc.jp/eF-surf/ eF-surf] (Calculate the molecular surface and electrostatic potential of proteins)
&lt;br /&gt;
* [http://pre-s.protein.osaka-u.ac.jp/~preds/ P&lt;i&gt;re&lt;/i&gt;D&lt;i&gt;s&lt;/i&gt;] (Prediction of DNA-binding site)
* [http://pre-s.protein.osaka-u.ac.jp/~prebi/ PreBI] (Prediction of biological interface of proteins homo-interface)
* [http://pre-s.protein.osaka-u.ac.jp/~preds classPPI] (Classification of homo protein-protein interfaces)
&lt;br /&gt;
* [http://p-cats.hgc.jp/p-cats/ P-cats] (Prediction of Catalytic residues in proteins)
&lt;br /&gt;
* [http://pdbjs3.protein.osaka-u.ac.jp/xPSSS/index.html xPSSS] (xml-based protein structure search service)
* [http://eprots.protein.osaka-u.ac.jp/eProtS/Top_e.jsp eProtS] (Encyclopedia of protein structures)
* [http://cube.socs.waseda.ac.jp/pages/jsp/index.jsp ProMode] (DB of normal mode analysis of proteins)</text>
    <sha1>36b61d11bdff8922233853e201a070e51505ea04</sha1>
  </revision>
  <revision>
    <id>56</id>
    <parentid>55</parentid>
    <timestamp>2009-03-03T10:07:20Z</timestamp>
    <contributor>
      <username>WikiSysop</username>
      <id>1</id>
    </contributor>
    <comment>/* Organization */</comment>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="1283" xml:space="preserve">== Organization ==
* [http://www-bird.jst.go.jp/index_e.html JST-BIRD]
* [http://www.hgc.jp/english/ Human Genome Center]
* [http://www.protein.osaka-u.ac.jp/home_e/index_e.html Institute for Protein Research]
&lt;br /&gt;

== DBs ==
* [http://ef-site.hgc.jp/eF-site/ eF-site] (DB of electrostatic surface of functional site of proteins)
* [http://ef-site.hgc.jp/eF-seek/ eF-seek] (Prediction of ligand binding site of proteins)
* [http://ef-site.hgc.jp/eF-surf/ eF-surf] (Calculate the molecular surface and electrostatic potential of proteins)
&lt;br /&gt;
* [http://pre-s.protein.osaka-u.ac.jp/~preds/ P&lt;i&gt;re&lt;/i&gt;D&lt;i&gt;s&lt;/i&gt;] (Prediction of DNA-binding site)
* [http://pre-s.protein.osaka-u.ac.jp/~prebi/ PreBI] (Prediction of biological interface of proteins homo-interface)
* [http://pre-s.protein.osaka-u.ac.jp/~preds classPPI] (Classification of homo protein-protein interfaces)
&lt;br /&gt;
* [http://p-cats.hgc.jp/p-cats/ P-cats] (Prediction of Catalytic residues in proteins)
&lt;br /&gt;
* [http://pdbjs3.protein.osaka-u.ac.jp/xPSSS/index.html xPSSS] (xml-based protein structure search service)
* [http://eprots.protein.osaka-u.ac.jp/eProtS/Top_e.jsp eProtS] (Encyclopedia of protein structures)
* [http://cube.socs.waseda.ac.jp/pages/jsp/index.jsp ProMode] (DB of normal mode analysis of proteins)</text>
    <sha1>872316597216663b94529335fe7ce359cc9ef569</sha1>
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</page>
<page arvcontinue="20090303095249|51">
  <title>MediaWiki:Sidebar</title>
  <ns>8</ns>
  <id>5</id>
  <revision>
    <id>53</id>
    <timestamp>2009-03-03T10:01:52Z</timestamp>
    <contributor>
      <username>WikiSysop</username>
      <id>1</id>
    </contributor>
    <comment>Created page with '* navigation ** mainpage|mainpage-description ** portal-url|portal ** currentevents-url|currentevents ** recentchanges-url|recentchanges ** randompage-url|randompage ** helppage|...'</comment>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="228" xml:space="preserve">* navigation
** mainpage|mainpage-description
** portal-url|portal
** currentevents-url|currentevents
** recentchanges-url|recentchanges
** randompage-url|randompage
** helppage|help
** links|links
* SEARCH
* TOOLBOX
* LANGUAGES</text>
    <sha1>6140878409e85e58e5743ae62d1dc1134ef44d23</sha1>
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    <contributor>
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      <id>1</id>
    </contributor>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="228" xml:space="preserve">* navigation
** mainpage|mainpage-description
** portal-url|portal
** currentevents-url|currentevents
** recentchanges-url|recentchanges
** randompage-url|randompage
** helppage|help
** Links|Links
* SEARCH
* TOOLBOX
* LANGUAGES</text>
    <sha1>07809774f0950cfd14f9d6204af7c401fb576159</sha1>
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</page>
<page arvcontinue="20090303095249|51">
  <title>Main Page</title>
  <ns>0</ns>
  <id>1</id>
  <revision>
    <id>57</id>
    <parentid>49</parentid>
    <timestamp>2009-03-09T02:46:40Z</timestamp>
    <contributor>
      <username>127.0.0.1</username>
      <id>0</id>
    </contributor>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="5056" xml:space="preserve">&lt;big&gt;'''Welcome to jV wiki.'''&lt;/big&gt;
{| style="float:right"
 |__TOC__
 |}
jV(formerly known as PDBjViewer) is a program to display molecular graphics of protein and nucleic acids. 
jV can use as a stand-alone program and can operate on a web browser as an Java applet. jV is used by PDBj services([http://ef-site.hgc.jp/eF-site/index.jsp eF-site], [http://ef-site.hgc.jp/eF-seek/index.jsp eF-seek], the molecular structure surface database of the protein functional part).

jV supports the following features:
* jV can read and display PDBML files, the canonical XML format for the Protein Data Bank.
* Of course, jV can read and display the traditional PDB format files, too.
* RasMol-like usability.
* jV can process more than one molecules.
* jV can display polygons specified by XML. ([http://ef-site.hgc.jp/eF-site/schema/polygon12.xsd XML Schema for polygons] is available.)
* Multiple polygons can be processed simultaneously, and be superimposed onto molecular images.
* Animation can be realized.


The program 'jV' has been developed by [http://www.hgc.jp/~kinosita/TOP.html Kengo Kinoshita] ([http://www.hgc.jp/english/ Human Genome Center], [http://www.ims.u-tokyo.ac.jp/imsut/en/ Insutitute for Medical Science],[http://www.u-tokyo.ac.jp/index_e.html University of Tokyo]) and [http://www.protein.osaka-u.ac.jp/rcsfp/pi/ Haruki Nakamura] ([http://www.protein.osaka-u.ac.jp/index_e.php Institute for Protein Research], [http://www.osaka-u.ac.jp/eng/index.html Osaka Univeristy]), with the support from [http://www-bird.jst.go.jp/index_e.html JST-BIRD].


[[old version]]


== jV version 3 ==
[[File:Download.png|right|link=http://ef-site.hgc.jp/eF-site/servlet/Registration|Download]] jV version 3 is now used to display molecules and their surfaces as a Java applet program.&lt;br /&gt;&lt;font size="1"&gt;Version 3.6 was released on 11, Aug, 2008.&lt;br /&gt;This version is fully compativle with [https://applet-launcher.dev.java.net/ applet-launcher].&lt;/font&gt;&lt;br /&gt;Go to [[jV version 3]].
&lt;br /&gt;
It requires the following softwares.&lt;br /&gt;
* JRE 1.4.2 or later  (recommend 1.4.2_12)&lt;br&gt;jV runs on the Java Runtime Environment ([http://java.sun.com/javase/index.jsp JRE]) so that it can work as a stand-alone application as well as an applet.
* JOGL 1.0, 1.1.1 or JSR-231 1.0.0  (recommend JSR-231)&lt;br /&gt;The graphics of jV is based on OpenGL ([https://jogl.dev.java.net/ JOGL]), thereby producing fairly beautiful pictures.
** version 1.0 [[http://ef-site.hgc.jp/eF-site/jV/JOGL1.0_win32.zip Windows],[http://ef-site.hgc.jp/eF-site/jV/JOGL1.0_macosx.tar.gz Mac OS X],[http://ef-site.hgc.jp/eF-site/jV/JOGL1.0_linux.tar.gz Linux]]
** version 1.1.1 [[http://ef-site.hgc.jp/eF-site/jV/JOGL1.1.1_win32.zip Windows],[http://ef-site.hgc.jp/eF-site/jV/JOGL1.1.1_macosx.tar.gz Mac OS X], [http://ef-site.hgc.jp/eF-site/jV/JOGL1.1.1_linux.tar.gz Linux]]
** JSR-231 1.0.0 [[http://ef-site.hgc.jp/eF-site/jV/JOGL_JSR231_win32.zip Windows], [http://ef-site.hgc.jp/eF-site/jV/JOGL_JSR231_macosx_ppc.tar.gz Mac OS X ppc], [http://ef-site.hgc.jp/eF-site/jV/JOGL_JSR231_macosx_universal.tar.gz Mac OS X universal], [http://ef-site.hgc.jp/eF-site/jV/JOGL_JSR231_linux_i586.tar.gz Linux]]

&lt;font size="1"&gt;Note: &amp;nbsp; JOGL 1.0 and 1.1.1 are not available for Intel Mac.The latest version of JOGL, JSR-231 1.0.0, runs on Intel Mac.&lt;/font&gt;

== jV version 2 ==
jV version 2 is an advanced version of PDBjViewer, which can be used only as a stand-alone program. It enables to display more than one molecule images at the same time and their display models and transforms can be operated separately. An animation of molecules can be also performed. jV version 2 runs with .NET framework 1.1 on the Windows platform. Therefore the .NET framework must be installed on your computer.

== jV version 1 (PDBjViewer) ==
Visualization of structure and surface of molecules is performed by a Java applet program called 'PDBjViewer'.

Two image windows are opened. The structure of the molecule is shown in the left window and the molecular surface is displayed in the right window. The mouse control is as follows. 
&lt;br /&gt;
&lt;div align="center"&gt;
{| class="wikitable" cellspacing="0" border="1"
 ! action !! Windows 
 |-
 | rotate x, y || left
 |-
 | zoom || Alt + left
 |-
 | tranlate x, y || right
 |-
|}
&lt;br /&gt;
&lt;/div&gt;
&lt;br&gt;
In order to use PDBjViewer, [http://java.sun.com/products/plugin/ Java Plug-in] and
[http://java.sun.com/products/java-media/3D/ Java 3D API] must be installed on your computer.
The version requirements are as follows.&lt;br /&gt;
* JRE (includes Java Plug-in) 1.4.1 or later (recommend 1.4.2)
* Java 3D API (OpenGL) 1.2.1 or later (recommend 1.2.1_04)
&lt;br /&gt;Important notes
# You can select two kinds of implementation of Java 3D, OpenGL version and DirectX version. But, PDBjViewer only work with OpenGL version at present.
# PDBjViewer does not work with JRE from 1.4.1_03 to 1.4.1_06.&lt;br /&gt;
PDBjViewer can be used as a stand-alone program as well as an applet
with the same requirements as above.
In addition to mouse controls, a command line interface is provided.
&lt;br&gt;</text>
    <sha1>bd507306e3548fbc5d3c537367411d79a8b1ec40</sha1>
  </revision>
  <revision>
    <id>58</id>
    <parentid>57</parentid>
    <timestamp>2009-03-09T02:48:41Z</timestamp>
    <contributor>
      <username>127.0.0.1</username>
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    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="3325" xml:space="preserve">&lt;big&gt;'''Welcome to jV wiki.'''&lt;/big&gt;
{| style="float:right"
 |__TOC__
 |}
jV version3 (formerly known as PDBjViewer) is a program to display molecular graphics of protein and nucleic acids. 
jV can use as a stand-alone program and can operate on a web browser as an Java applet. jV is used by PDBj services([http://ef-site.hgc.jp/eF-site/index.jsp eF-site], [http://ef-site.hgc.jp/eF-seek/index.jsp eF-seek], the molecular structure surface database of the protein functional part).

jV supports the following features:
* jV can read and display PDBML files, the canonical XML format for the Protein Data Bank.
* Of course, jV can read and display the traditional PDB format files, too.
* RasMol-like usability.
* jV can process more than one molecules.
* jV can display polygons specified by XML. ([http://ef-site.hgc.jp/eF-site/schema/polygon12.xsd XML Schema for polygons] is available.)
* Multiple polygons can be processed simultaneously, and be superimposed onto molecular images.
* Animation can be realized.


The program 'jV' has been developed by [http://www.hgc.jp/~kinosita/TOP.html Kengo Kinoshita] ([http://www.hgc.jp/english/ Human Genome Center], [http://www.ims.u-tokyo.ac.jp/imsut/en/ Insutitute for Medical Science],[http://www.u-tokyo.ac.jp/index_e.html University of Tokyo]) and [http://www.protein.osaka-u.ac.jp/rcsfp/pi/ Haruki Nakamura] ([http://www.protein.osaka-u.ac.jp/index_e.php Institute for Protein Research], [http://www.osaka-u.ac.jp/eng/index.html Osaka Univeristy]), with the support from [http://www-bird.jst.go.jp/index_e.html JST-BIRD].


[[old version]]


== jV version 3 ==
[[File:Download.png|right|link=http://ef-site.hgc.jp/eF-site/servlet/Registration|Download]] jV version 3 is now used to display molecules and their surfaces as a Java applet program.&lt;br /&gt;&lt;font size="1"&gt;Version 3.6 was released on 11, Aug, 2008.&lt;br /&gt;This version is fully compativle with [https://applet-launcher.dev.java.net/ applet-launcher].&lt;/font&gt;&lt;br /&gt;Go to [[jV version 3]].
&lt;br /&gt;
It requires the following softwares.&lt;br /&gt;
* JRE 1.4.2 or later  (recommend 1.4.2_12)&lt;br&gt;jV runs on the Java Runtime Environment ([http://java.sun.com/javase/index.jsp JRE]) so that it can work as a stand-alone application as well as an applet.
* JOGL 1.0, 1.1.1 or JSR-231 1.0.0  (recommend JSR-231)&lt;br /&gt;The graphics of jV is based on OpenGL ([https://jogl.dev.java.net/ JOGL]), thereby producing fairly beautiful pictures.
** version 1.0 [[http://ef-site.hgc.jp/eF-site/jV/JOGL1.0_win32.zip Windows],[http://ef-site.hgc.jp/eF-site/jV/JOGL1.0_macosx.tar.gz Mac OS X],[http://ef-site.hgc.jp/eF-site/jV/JOGL1.0_linux.tar.gz Linux]]
** version 1.1.1 [[http://ef-site.hgc.jp/eF-site/jV/JOGL1.1.1_win32.zip Windows],[http://ef-site.hgc.jp/eF-site/jV/JOGL1.1.1_macosx.tar.gz Mac OS X], [http://ef-site.hgc.jp/eF-site/jV/JOGL1.1.1_linux.tar.gz Linux]]
** JSR-231 1.0.0 [[http://ef-site.hgc.jp/eF-site/jV/JOGL_JSR231_win32.zip Windows], [http://ef-site.hgc.jp/eF-site/jV/JOGL_JSR231_macosx_ppc.tar.gz Mac OS X ppc], [http://ef-site.hgc.jp/eF-site/jV/JOGL_JSR231_macosx_universal.tar.gz Mac OS X universal], [http://ef-site.hgc.jp/eF-site/jV/JOGL_JSR231_linux_i586.tar.gz Linux]]

&lt;font size="1"&gt;Note: &amp;nbsp; JOGL 1.0 and 1.1.1 are not available for Intel Mac.The latest version of JOGL, JSR-231 1.0.0, runs on Intel Mac.&lt;/font&gt;</text>
    <sha1>af5c9817c973dcaa7a03f34836a23c7ed9bae621</sha1>
  </revision>
  <revision>
    <id>61</id>
    <parentid>58</parentid>
    <timestamp>2009-03-09T02:51:26Z</timestamp>
    <contributor>
      <username>127.0.0.1</username>
      <id>0</id>
    </contributor>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="3366" xml:space="preserve">&lt;big&gt;'''Welcome to jV wiki.'''&lt;/big&gt;
{| style="float:right"
 |__TOC__
 |}
jV version3 (formerly known as PDBjViewer) is a program to display molecular graphics of protein and nucleic acids. 
jV can use as a stand-alone program and can operate on a web browser as an Java applet. jV is used by PDBj services([http://ef-site.hgc.jp/eF-site/index.jsp eF-site], [http://ef-site.hgc.jp/eF-seek/index.jsp eF-seek], the molecular structure surface database of the protein functional part).

jV supports the following features:
* jV can read and display PDBML files, the canonical XML format for the Protein Data Bank.
* Of course, jV can read and display the traditional PDB format files, too.
* RasMol-like usability.
* jV can process more than one molecules.
* jV can display polygons specified by XML. ([http://ef-site.hgc.jp/eF-site/schema/polygon12.xsd XML Schema for polygons] is available.)
* Multiple polygons can be processed simultaneously, and be superimposed onto molecular images.
* Animation can be realized.


The program 'jV' has been developed by [http://www.hgc.jp/~kinosita/TOP.html Kengo Kinoshita] ([http://www.hgc.jp/english/ Human Genome Center], [http://www.ims.u-tokyo.ac.jp/imsut/en/ Insutitute for Medical Science],[http://www.u-tokyo.ac.jp/index_e.html University of Tokyo]) and [http://www.protein.osaka-u.ac.jp/rcsfp/pi/ Haruki Nakamura] ([http://www.protein.osaka-u.ac.jp/index_e.php Institute for Protein Research], [http://www.osaka-u.ac.jp/eng/index.html Osaka Univeristy]), with the support from [http://www-bird.jst.go.jp/index_e.html JST-BIRD].


Please refer to here about jV2 &amp; jV1 an [[old version]].


== jV version 3 ==
[[File:Download.png|right|link=http://ef-site.hgc.jp/eF-site/servlet/Registration|Download]] jV version 3 is now used to display molecules and their surfaces as a Java applet program.&lt;br /&gt;&lt;font size="1"&gt;Version 3.6 was released on 11, Aug, 2008.&lt;br /&gt;This version is fully compativle with [https://applet-launcher.dev.java.net/ applet-launcher].&lt;/font&gt;&lt;br /&gt;Go to [[jV version 3]].
&lt;br /&gt;
It requires the following softwares.&lt;br /&gt;
* JRE 1.4.2 or later  (recommend 1.4.2_12)&lt;br&gt;jV runs on the Java Runtime Environment ([http://java.sun.com/javase/index.jsp JRE]) so that it can work as a stand-alone application as well as an applet.
* JOGL 1.0, 1.1.1 or JSR-231 1.0.0  (recommend JSR-231)&lt;br /&gt;The graphics of jV is based on OpenGL ([https://jogl.dev.java.net/ JOGL]), thereby producing fairly beautiful pictures.
** version 1.0 [[http://ef-site.hgc.jp/eF-site/jV/JOGL1.0_win32.zip Windows],[http://ef-site.hgc.jp/eF-site/jV/JOGL1.0_macosx.tar.gz Mac OS X],[http://ef-site.hgc.jp/eF-site/jV/JOGL1.0_linux.tar.gz Linux]]
** version 1.1.1 [[http://ef-site.hgc.jp/eF-site/jV/JOGL1.1.1_win32.zip Windows],[http://ef-site.hgc.jp/eF-site/jV/JOGL1.1.1_macosx.tar.gz Mac OS X], [http://ef-site.hgc.jp/eF-site/jV/JOGL1.1.1_linux.tar.gz Linux]]
** JSR-231 1.0.0 [[http://ef-site.hgc.jp/eF-site/jV/JOGL_JSR231_win32.zip Windows], [http://ef-site.hgc.jp/eF-site/jV/JOGL_JSR231_macosx_ppc.tar.gz Mac OS X ppc], [http://ef-site.hgc.jp/eF-site/jV/JOGL_JSR231_macosx_universal.tar.gz Mac OS X universal], [http://ef-site.hgc.jp/eF-site/jV/JOGL_JSR231_linux_i586.tar.gz Linux]]

&lt;font size="1"&gt;Note: &amp;nbsp; JOGL 1.0 and 1.1.1 are not available for Intel Mac.The latest version of JOGL, JSR-231 1.0.0, runs on Intel Mac.&lt;/font&gt;</text>
    <sha1>d01b9b697c1514a6eda30ac7d6073bc080051195</sha1>
  </revision>
  <revision>
    <id>62</id>
    <parentid>61</parentid>
    <timestamp>2009-03-09T02:52:32Z</timestamp>
    <contributor>
      <username>127.0.0.1</username>
      <id>0</id>
    </contributor>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="3380" xml:space="preserve">&lt;big&gt;'''Welcome to jV wiki.'''&lt;/big&gt;
{| style="float:right"
 |__TOC__
 |}
jV version3 (formerly known as PDBjViewer) is a program to display molecular graphics of protein and nucleic acids. 
jV can use as a stand-alone program and can operate on a web browser as an Java applet. jV is used by PDBj services([http://ef-site.hgc.jp/eF-site/index.jsp eF-site], [http://ef-site.hgc.jp/eF-seek/index.jsp eF-seek], the molecular structure surface database of the protein functional part).

jV supports the following features:
* jV can read and display PDBML files, the canonical XML format for the Protein Data Bank.
* Of course, jV can read and display the traditional PDB format files, too.
* RasMol-like usability.
* jV can process more than one molecules.
* jV can display polygons specified by XML. ([http://ef-site.hgc.jp/eF-site/schema/polygon12.xsd XML Schema for polygons] is available.)
* Multiple polygons can be processed simultaneously, and be superimposed onto molecular images.
* Animation can be realized.


The program 'jV' has been developed by [http://www.hgc.jp/~kinosita/TOP.html Kengo Kinoshita] ([http://www.hgc.jp/english/ Human Genome Center], [http://www.ims.u-tokyo.ac.jp/imsut/en/ Insutitute for Medical Science],[http://www.u-tokyo.ac.jp/index_e.html University of Tokyo]) and [http://www.protein.osaka-u.ac.jp/rcsfp/pi/ Haruki Nakamura] ([http://www.protein.osaka-u.ac.jp/index_e.php Institute for Protein Research], [http://www.osaka-u.ac.jp/eng/index.html Osaka Univeristy]), with the support from [http://www-bird.jst.go.jp/index_e.html JST-BIRD].


Please refer to here about [[old version]](jV version1 &amp; jV version2).


== jV version 3 ==
[[File:Download.png|right|link=http://ef-site.hgc.jp/eF-site/servlet/Registration|Download]] jV version 3 is now used to display molecules and their surfaces as a Java applet program.&lt;br /&gt;&lt;font size="1"&gt;Version 3.6 was released on 11, Aug, 2008.&lt;br /&gt;This version is fully compativle with [https://applet-launcher.dev.java.net/ applet-launcher].&lt;/font&gt;&lt;br /&gt;Go to [[jV version 3]].
&lt;br /&gt;
It requires the following softwares.&lt;br /&gt;
* JRE 1.4.2 or later  (recommend 1.4.2_12)&lt;br&gt;jV runs on the Java Runtime Environment ([http://java.sun.com/javase/index.jsp JRE]) so that it can work as a stand-alone application as well as an applet.
* JOGL 1.0, 1.1.1 or JSR-231 1.0.0  (recommend JSR-231)&lt;br /&gt;The graphics of jV is based on OpenGL ([https://jogl.dev.java.net/ JOGL]), thereby producing fairly beautiful pictures.
** version 1.0 [[http://ef-site.hgc.jp/eF-site/jV/JOGL1.0_win32.zip Windows],[http://ef-site.hgc.jp/eF-site/jV/JOGL1.0_macosx.tar.gz Mac OS X],[http://ef-site.hgc.jp/eF-site/jV/JOGL1.0_linux.tar.gz Linux]]
** version 1.1.1 [[http://ef-site.hgc.jp/eF-site/jV/JOGL1.1.1_win32.zip Windows],[http://ef-site.hgc.jp/eF-site/jV/JOGL1.1.1_macosx.tar.gz Mac OS X], [http://ef-site.hgc.jp/eF-site/jV/JOGL1.1.1_linux.tar.gz Linux]]
** JSR-231 1.0.0 [[http://ef-site.hgc.jp/eF-site/jV/JOGL_JSR231_win32.zip Windows], [http://ef-site.hgc.jp/eF-site/jV/JOGL_JSR231_macosx_ppc.tar.gz Mac OS X ppc], [http://ef-site.hgc.jp/eF-site/jV/JOGL_JSR231_macosx_universal.tar.gz Mac OS X universal], [http://ef-site.hgc.jp/eF-site/jV/JOGL_JSR231_linux_i586.tar.gz Linux]]

&lt;font size="1"&gt;Note: &amp;nbsp; JOGL 1.0 and 1.1.1 are not available for Intel Mac.The latest version of JOGL, JSR-231 1.0.0, runs on Intel Mac.&lt;/font&gt;</text>
    <sha1>247dae772979f925c0d4a0abeee3f8ba335b5530</sha1>
  </revision>
  <revision>
    <id>63</id>
    <parentid>62</parentid>
    <timestamp>2009-03-09T02:55:49Z</timestamp>
    <contributor>
      <username>127.0.0.1</username>
      <id>0</id>
    </contributor>
    <comment>/* jV version 3 */</comment>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="3375" xml:space="preserve">&lt;big&gt;'''Welcome to jV wiki.'''&lt;/big&gt;
{| style="float:right"
 |__TOC__
 |}
jV version3 (formerly known as PDBjViewer) is a program to display molecular graphics of protein and nucleic acids. 
jV can use as a stand-alone program and can operate on a web browser as an Java applet. jV is used by PDBj services([http://ef-site.hgc.jp/eF-site/index.jsp eF-site], [http://ef-site.hgc.jp/eF-seek/index.jsp eF-seek], the molecular structure surface database of the protein functional part).

jV supports the following features:
* jV can read and display PDBML files, the canonical XML format for the Protein Data Bank.
* Of course, jV can read and display the traditional PDB format files, too.
* RasMol-like usability.
* jV can process more than one molecules.
* jV can display polygons specified by XML. ([http://ef-site.hgc.jp/eF-site/schema/polygon12.xsd XML Schema for polygons] is available.)
* Multiple polygons can be processed simultaneously, and be superimposed onto molecular images.
* Animation can be realized.


The program 'jV' has been developed by [http://www.hgc.jp/~kinosita/TOP.html Kengo Kinoshita] ([http://www.hgc.jp/english/ Human Genome Center], [http://www.ims.u-tokyo.ac.jp/imsut/en/ Insutitute for Medical Science],[http://www.u-tokyo.ac.jp/index_e.html University of Tokyo]) and [http://www.protein.osaka-u.ac.jp/rcsfp/pi/ Haruki Nakamura] ([http://www.protein.osaka-u.ac.jp/index_e.php Institute for Protein Research], [http://www.osaka-u.ac.jp/eng/index.html Osaka Univeristy]), with the support from [http://www-bird.jst.go.jp/index_e.html JST-BIRD].


Please refer to here about [[old version]](jV version1 &amp; jV version2).


== Outline ==
[[File:Download.png|right|link=http://ef-site.hgc.jp/eF-site/servlet/Registration|Download]] jV version 3 is now used to display molecules and their surfaces as a Java applet program.&lt;br /&gt;&lt;font size="1"&gt;Version 3.6 was released on 11, Aug, 2008.&lt;br /&gt;This version is fully compativle with [https://applet-launcher.dev.java.net/ applet-launcher].&lt;/font&gt;&lt;br /&gt;Go to [[jV version 3]].
&lt;br /&gt;
It requires the following softwares.&lt;br /&gt;
* JRE 1.4.2 or later  (recommend 1.4.2_12)&lt;br&gt;jV runs on the Java Runtime Environment ([http://java.sun.com/javase/index.jsp JRE]) so that it can work as a stand-alone application as well as an applet.
* JOGL 1.0, 1.1.1 or JSR-231 1.0.0  (recommend JSR-231)&lt;br /&gt;The graphics of jV is based on OpenGL ([https://jogl.dev.java.net/ JOGL]), thereby producing fairly beautiful pictures.
** version 1.0 [[http://ef-site.hgc.jp/eF-site/jV/JOGL1.0_win32.zip Windows],[http://ef-site.hgc.jp/eF-site/jV/JOGL1.0_macosx.tar.gz Mac OS X],[http://ef-site.hgc.jp/eF-site/jV/JOGL1.0_linux.tar.gz Linux]]
** version 1.1.1 [[http://ef-site.hgc.jp/eF-site/jV/JOGL1.1.1_win32.zip Windows],[http://ef-site.hgc.jp/eF-site/jV/JOGL1.1.1_macosx.tar.gz Mac OS X], [http://ef-site.hgc.jp/eF-site/jV/JOGL1.1.1_linux.tar.gz Linux]]
** JSR-231 1.0.0 [[http://ef-site.hgc.jp/eF-site/jV/JOGL_JSR231_win32.zip Windows], [http://ef-site.hgc.jp/eF-site/jV/JOGL_JSR231_macosx_ppc.tar.gz Mac OS X ppc], [http://ef-site.hgc.jp/eF-site/jV/JOGL_JSR231_macosx_universal.tar.gz Mac OS X universal], [http://ef-site.hgc.jp/eF-site/jV/JOGL_JSR231_linux_i586.tar.gz Linux]]

&lt;font size="1"&gt;Note: &amp;nbsp; JOGL 1.0 and 1.1.1 are not available for Intel Mac.The latest version of JOGL, JSR-231 1.0.0, runs on Intel Mac.&lt;/font&gt;</text>
    <sha1>edf32bfb80503b63c85a1eb531f1ca294923cab6</sha1>
  </revision>
  <revision>
    <id>64</id>
    <parentid>63</parentid>
    <timestamp>2009-03-09T02:56:08Z</timestamp>
    <contributor>
      <username>127.0.0.1</username>
      <id>0</id>
    </contributor>
    <comment>/* Outline */</comment>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="3381" xml:space="preserve">&lt;big&gt;'''Welcome to jV wiki.'''&lt;/big&gt;
{| style="float:right"
 |__TOC__
 |}
jV version3 (formerly known as PDBjViewer) is a program to display molecular graphics of protein and nucleic acids. 
jV can use as a stand-alone program and can operate on a web browser as an Java applet. jV is used by PDBj services([http://ef-site.hgc.jp/eF-site/index.jsp eF-site], [http://ef-site.hgc.jp/eF-seek/index.jsp eF-seek], the molecular structure surface database of the protein functional part).

jV supports the following features:
* jV can read and display PDBML files, the canonical XML format for the Protein Data Bank.
* Of course, jV can read and display the traditional PDB format files, too.
* RasMol-like usability.
* jV can process more than one molecules.
* jV can display polygons specified by XML. ([http://ef-site.hgc.jp/eF-site/schema/polygon12.xsd XML Schema for polygons] is available.)
* Multiple polygons can be processed simultaneously, and be superimposed onto molecular images.
* Animation can be realized.


The program 'jV' has been developed by [http://www.hgc.jp/~kinosita/TOP.html Kengo Kinoshita] ([http://www.hgc.jp/english/ Human Genome Center], [http://www.ims.u-tokyo.ac.jp/imsut/en/ Insutitute for Medical Science],[http://www.u-tokyo.ac.jp/index_e.html University of Tokyo]) and [http://www.protein.osaka-u.ac.jp/rcsfp/pi/ Haruki Nakamura] ([http://www.protein.osaka-u.ac.jp/index_e.php Institute for Protein Research], [http://www.osaka-u.ac.jp/eng/index.html Osaka Univeristy]), with the support from [http://www-bird.jst.go.jp/index_e.html JST-BIRD].


Please refer to here about [[old version]](jV version1 &amp; jV version2).


== ｊV3 Outline ==
[[File:Download.png|right|link=http://ef-site.hgc.jp/eF-site/servlet/Registration|Download]] jV version 3 is now used to display molecules and their surfaces as a Java applet program.&lt;br /&gt;&lt;font size="1"&gt;Version 3.6 was released on 11, Aug, 2008.&lt;br /&gt;This version is fully compativle with [https://applet-launcher.dev.java.net/ applet-launcher].&lt;/font&gt;&lt;br /&gt;Go to [[jV version 3]].
&lt;br /&gt;
It requires the following softwares.&lt;br /&gt;
* JRE 1.4.2 or later  (recommend 1.4.2_12)&lt;br&gt;jV runs on the Java Runtime Environment ([http://java.sun.com/javase/index.jsp JRE]) so that it can work as a stand-alone application as well as an applet.
* JOGL 1.0, 1.1.1 or JSR-231 1.0.0  (recommend JSR-231)&lt;br /&gt;The graphics of jV is based on OpenGL ([https://jogl.dev.java.net/ JOGL]), thereby producing fairly beautiful pictures.
** version 1.0 [[http://ef-site.hgc.jp/eF-site/jV/JOGL1.0_win32.zip Windows],[http://ef-site.hgc.jp/eF-site/jV/JOGL1.0_macosx.tar.gz Mac OS X],[http://ef-site.hgc.jp/eF-site/jV/JOGL1.0_linux.tar.gz Linux]]
** version 1.1.1 [[http://ef-site.hgc.jp/eF-site/jV/JOGL1.1.1_win32.zip Windows],[http://ef-site.hgc.jp/eF-site/jV/JOGL1.1.1_macosx.tar.gz Mac OS X], [http://ef-site.hgc.jp/eF-site/jV/JOGL1.1.1_linux.tar.gz Linux]]
** JSR-231 1.0.0 [[http://ef-site.hgc.jp/eF-site/jV/JOGL_JSR231_win32.zip Windows], [http://ef-site.hgc.jp/eF-site/jV/JOGL_JSR231_macosx_ppc.tar.gz Mac OS X ppc], [http://ef-site.hgc.jp/eF-site/jV/JOGL_JSR231_macosx_universal.tar.gz Mac OS X universal], [http://ef-site.hgc.jp/eF-site/jV/JOGL_JSR231_linux_i586.tar.gz Linux]]

&lt;font size="1"&gt;Note: &amp;nbsp; JOGL 1.0 and 1.1.1 are not available for Intel Mac.The latest version of JOGL, JSR-231 1.0.0, runs on Intel Mac.&lt;/font&gt;</text>
    <sha1>b8ca2be16e4cf9645358241c0e17a8c4ff7d473f</sha1>
  </revision>
  <revision>
    <id>65</id>
    <parentid>64</parentid>
    <timestamp>2009-03-09T02:56:26Z</timestamp>
    <contributor>
      <username>127.0.0.1</username>
      <id>0</id>
    </contributor>
    <comment>/* ｊV3 Outline */</comment>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="3379" xml:space="preserve">&lt;big&gt;'''Welcome to jV wiki.'''&lt;/big&gt;
{| style="float:right"
 |__TOC__
 |}
jV version3 (formerly known as PDBjViewer) is a program to display molecular graphics of protein and nucleic acids. 
jV can use as a stand-alone program and can operate on a web browser as an Java applet. jV is used by PDBj services([http://ef-site.hgc.jp/eF-site/index.jsp eF-site], [http://ef-site.hgc.jp/eF-seek/index.jsp eF-seek], the molecular structure surface database of the protein functional part).

jV supports the following features:
* jV can read and display PDBML files, the canonical XML format for the Protein Data Bank.
* Of course, jV can read and display the traditional PDB format files, too.
* RasMol-like usability.
* jV can process more than one molecules.
* jV can display polygons specified by XML. ([http://ef-site.hgc.jp/eF-site/schema/polygon12.xsd XML Schema for polygons] is available.)
* Multiple polygons can be processed simultaneously, and be superimposed onto molecular images.
* Animation can be realized.


The program 'jV' has been developed by [http://www.hgc.jp/~kinosita/TOP.html Kengo Kinoshita] ([http://www.hgc.jp/english/ Human Genome Center], [http://www.ims.u-tokyo.ac.jp/imsut/en/ Insutitute for Medical Science],[http://www.u-tokyo.ac.jp/index_e.html University of Tokyo]) and [http://www.protein.osaka-u.ac.jp/rcsfp/pi/ Haruki Nakamura] ([http://www.protein.osaka-u.ac.jp/index_e.php Institute for Protein Research], [http://www.osaka-u.ac.jp/eng/index.html Osaka Univeristy]), with the support from [http://www-bird.jst.go.jp/index_e.html JST-BIRD].


Please refer to here about [[old version]](jV version1 &amp; jV version2).


== jV3 Outline ==
[[File:Download.png|right|link=http://ef-site.hgc.jp/eF-site/servlet/Registration|Download]] jV version 3 is now used to display molecules and their surfaces as a Java applet program.&lt;br /&gt;&lt;font size="1"&gt;Version 3.6 was released on 11, Aug, 2008.&lt;br /&gt;This version is fully compativle with [https://applet-launcher.dev.java.net/ applet-launcher].&lt;/font&gt;&lt;br /&gt;Go to [[jV version 3]].
&lt;br /&gt;
It requires the following softwares.&lt;br /&gt;
* JRE 1.4.2 or later  (recommend 1.4.2_12)&lt;br&gt;jV runs on the Java Runtime Environment ([http://java.sun.com/javase/index.jsp JRE]) so that it can work as a stand-alone application as well as an applet.
* JOGL 1.0, 1.1.1 or JSR-231 1.0.0  (recommend JSR-231)&lt;br /&gt;The graphics of jV is based on OpenGL ([https://jogl.dev.java.net/ JOGL]), thereby producing fairly beautiful pictures.
** version 1.0 [[http://ef-site.hgc.jp/eF-site/jV/JOGL1.0_win32.zip Windows],[http://ef-site.hgc.jp/eF-site/jV/JOGL1.0_macosx.tar.gz Mac OS X],[http://ef-site.hgc.jp/eF-site/jV/JOGL1.0_linux.tar.gz Linux]]
** version 1.1.1 [[http://ef-site.hgc.jp/eF-site/jV/JOGL1.1.1_win32.zip Windows],[http://ef-site.hgc.jp/eF-site/jV/JOGL1.1.1_macosx.tar.gz Mac OS X], [http://ef-site.hgc.jp/eF-site/jV/JOGL1.1.1_linux.tar.gz Linux]]
** JSR-231 1.0.0 [[http://ef-site.hgc.jp/eF-site/jV/JOGL_JSR231_win32.zip Windows], [http://ef-site.hgc.jp/eF-site/jV/JOGL_JSR231_macosx_ppc.tar.gz Mac OS X ppc], [http://ef-site.hgc.jp/eF-site/jV/JOGL_JSR231_macosx_universal.tar.gz Mac OS X universal], [http://ef-site.hgc.jp/eF-site/jV/JOGL_JSR231_linux_i586.tar.gz Linux]]

&lt;font size="1"&gt;Note: &amp;nbsp; JOGL 1.0 and 1.1.1 are not available for Intel Mac.The latest version of JOGL, JSR-231 1.0.0, runs on Intel Mac.&lt;/font&gt;</text>
    <sha1>da21d011c3ed2f0f5d09a1f77b13a1a865a77567</sha1>
  </revision>
  <revision>
    <id>67</id>
    <parentid>65</parentid>
    <timestamp>2009-03-09T03:01:07Z</timestamp>
    <contributor>
      <username>127.0.0.1</username>
      <id>0</id>
    </contributor>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="3373" xml:space="preserve">&lt;big&gt;'''Welcome to jV wiki.'''&lt;/big&gt;
{| style="float:right"
 |__TOC__
 |}
jV version3 (formerly known as PDBjViewer) is a program to display molecular graphics of protein and nucleic acids. 
jV can use as a stand-alone program and can operate on a web browser as an Java applet. jV is used by PDBj services([http://ef-site.hgc.jp/eF-site/index.jsp eF-site], [http://ef-site.hgc.jp/eF-seek/index.jsp eF-seek], the molecular structure surface database of the protein functional part).

jV supports the following features:
* jV can read and display PDBML files, the canonical XML format for the Protein Data Bank.
* Of course, jV can read and display the traditional PDB format files, too.
* RasMol-like usability.
* jV can process more than one molecules.
* jV can display polygons specified by XML. ([http://ef-site.hgc.jp/eF-site/schema/polygon12.xsd XML Schema for polygons] is available.)
* Multiple polygons can be processed simultaneously, and be superimposed onto molecular images.
* Animation can be realized.
* The graphics of jV is based on OpenGL [https://jogl.dev.java.net/ JOGL]), thereby producing fairly beautiful pictures.
* jV runs on the Java Runtime Environment ([http://java.sun.com/javase/index.jsp JRE]) so that it can work as a stand-alone application as well as an applet.

The program 'jV' has been developed by [http://www.hgc.jp/~kinosita/TOP.html Kengo Kinoshita] ([http://www.hgc.jp/english/ Human Genome Center], [http://www.ims.u-tokyo.ac.jp/imsut/en/ Insutitute for Medical Science],[http://www.u-tokyo.ac.jp/index_e.html University of Tokyo]) and [http://www.protein.osaka-u.ac.jp/rcsfp/pi/ Haruki Nakamura] ([http://www.protein.osaka-u.ac.jp/index_e.php Institute for Protein Research], [http://www.osaka-u.ac.jp/eng/index.html Osaka Univeristy]), with the support from [http://www-bird.jst.go.jp/index_e.html JST-BIRD].


Please refer to here about [[old version]](jV version1 &amp; jV version2).


== jV3 Outline ==
[[File:Download.png|right|link=http://ef-site.hgc.jp/eF-site/servlet/Registration|Download]] jV version 3 is now used to display molecules and their surfaces as a Java applet program.&lt;br /&gt;&lt;font size="1"&gt;Version 3.6 was released on 11, Aug, 2008.&lt;br /&gt;This version is fully compativle with [https://applet-launcher.dev.java.net/ applet-launcher].&lt;/font&gt;&lt;br /&gt;Go to [[jV version 3]].
&lt;br /&gt;
It requires the following softwares.
* JRE 1.4.2 or later  (recommend 1.4.2_12)
* JOGL 1.0, 1.1.1 or JSR-231 1.0.0  (recommend JSR-231)&lt;br /&gt;
** version 1.0 [[http://ef-site.hgc.jp/eF-site/jV/JOGL1.0_win32.zip Windows],[http://ef-site.hgc.jp/eF-site/jV/JOGL1.0_macosx.tar.gz Mac OS X],[http://ef-site.hgc.jp/eF-site/jV/JOGL1.0_linux.tar.gz Linux]]
** version 1.1.1 [[http://ef-site.hgc.jp/eF-site/jV/JOGL1.1.1_win32.zip Windows],[http://ef-site.hgc.jp/eF-site/jV/JOGL1.1.1_macosx.tar.gz Mac OS X], [http://ef-site.hgc.jp/eF-site/jV/JOGL1.1.1_linux.tar.gz Linux]]
** JSR-231 1.0.0 [[http://ef-site.hgc.jp/eF-site/jV/JOGL_JSR231_win32.zip Windows], [http://ef-site.hgc.jp/eF-site/jV/JOGL_JSR231_macosx_ppc.tar.gz Mac OS X ppc], [http://ef-site.hgc.jp/eF-site/jV/JOGL_JSR231_macosx_universal.tar.gz Mac OS X universal], [http://ef-site.hgc.jp/eF-site/jV/JOGL_JSR231_linux_i586.tar.gz Linux]]

&lt;font size="1"&gt;Note: &amp;nbsp; JOGL 1.0 and 1.1.1 are not available for Intel Mac.The latest version of JOGL, JSR-231 1.0.0, runs on Intel Mac.&lt;/font&gt;</text>
    <sha1>d92464a9b73b05d2e4889290be93e65e51ae6505</sha1>
  </revision>
  <revision>
    <id>68</id>
    <parentid>67</parentid>
    <timestamp>2009-03-09T03:14:05Z</timestamp>
    <contributor>
      <username>127.0.0.1</username>
      <id>0</id>
    </contributor>
    <comment>/* jV3 Outline */</comment>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="3405" xml:space="preserve">&lt;big&gt;'''Welcome to jV wiki.'''&lt;/big&gt;
{| style="float:right"
 |__TOC__
 |}
jV version3 (formerly known as PDBjViewer) is a program to display molecular graphics of protein and nucleic acids. 
jV can use as a stand-alone program and can operate on a web browser as an Java applet. jV is used by PDBj services([http://ef-site.hgc.jp/eF-site/index.jsp eF-site], [http://ef-site.hgc.jp/eF-seek/index.jsp eF-seek], the molecular structure surface database of the protein functional part).

jV supports the following features:
* jV can read and display PDBML files, the canonical XML format for the Protein Data Bank.
* Of course, jV can read and display the traditional PDB format files, too.
* RasMol-like usability.
* jV can process more than one molecules.
* jV can display polygons specified by XML. ([http://ef-site.hgc.jp/eF-site/schema/polygon12.xsd XML Schema for polygons] is available.)
* Multiple polygons can be processed simultaneously, and be superimposed onto molecular images.
* Animation can be realized.
* The graphics of jV is based on OpenGL [https://jogl.dev.java.net/ JOGL]), thereby producing fairly beautiful pictures.
* jV runs on the Java Runtime Environment ([http://java.sun.com/javase/index.jsp JRE]) so that it can work as a stand-alone application as well as an applet.

The program 'jV' has been developed by [http://www.hgc.jp/~kinosita/TOP.html Kengo Kinoshita] ([http://www.hgc.jp/english/ Human Genome Center], [http://www.ims.u-tokyo.ac.jp/imsut/en/ Insutitute for Medical Science],[http://www.u-tokyo.ac.jp/index_e.html University of Tokyo]) and [http://www.protein.osaka-u.ac.jp/rcsfp/pi/ Haruki Nakamura] ([http://www.protein.osaka-u.ac.jp/index_e.php Institute for Protein Research], [http://www.osaka-u.ac.jp/eng/index.html Osaka Univeristy]), with the support from [http://www-bird.jst.go.jp/index_e.html JST-BIRD].


Please refer to here about [[old version]](jV version1 &amp; jV version2).


== jV3 Outline ==
[[File:Download.png|right|link=http://ef-site.hgc.jp/eF-site/servlet/Registration|Download]] jV version 3 is now used to display molecules and their surfaces as a Java applet program.&lt;br /&gt;&lt;font size="1"&gt;Version 3.6 was released on 11, Aug, 2008.&lt;br /&gt;This version is fully compativle with [https://applet-launcher.dev.java.net/ applet-launcher].&lt;/font&gt;&lt;br /&gt;Go to [[jV version 3]].
&lt;br /&gt;
It requires the following softwares.
* [ JRE] 1.4.2 or later  (recommend 1.4.2_12)
* [https://jogl.dev.java.net/ JOGL] 1.0, 1.1.1 or JSR-231 1.0.0  (recommend JSR-231)&lt;br /&gt;
** version 1.0 [[http://ef-site.hgc.jp/eF-site/jV/JOGL1.0_win32.zip Windows],[http://ef-site.hgc.jp/eF-site/jV/JOGL1.0_macosx.tar.gz Mac OS X],[http://ef-site.hgc.jp/eF-site/jV/JOGL1.0_linux.tar.gz Linux]]
** version 1.1.1 [[http://ef-site.hgc.jp/eF-site/jV/JOGL1.1.1_win32.zip Windows],[http://ef-site.hgc.jp/eF-site/jV/JOGL1.1.1_macosx.tar.gz Mac OS X], [http://ef-site.hgc.jp/eF-site/jV/JOGL1.1.1_linux.tar.gz Linux]]
** JSR-231 1.0.0 [[http://ef-site.hgc.jp/eF-site/jV/JOGL_JSR231_win32.zip Windows], [http://ef-site.hgc.jp/eF-site/jV/JOGL_JSR231_macosx_ppc.tar.gz Mac OS X ppc], [http://ef-site.hgc.jp/eF-site/jV/JOGL_JSR231_macosx_universal.tar.gz Mac OS X universal], [http://ef-site.hgc.jp/eF-site/jV/JOGL_JSR231_linux_i586.tar.gz Linux]]

&lt;font size="1"&gt;Note: &amp;nbsp; JOGL 1.0 and 1.1.1 are not available for Intel Mac.The latest version of JOGL, JSR-231 1.0.0, runs on Intel Mac.&lt;/font&gt;</text>
    <sha1>12bdc8988e19b15db11c3e1d00082cb175c82c04</sha1>
  </revision>
  <revision>
    <id>69</id>
    <parentid>68</parentid>
    <timestamp>2009-03-09T03:17:11Z</timestamp>
    <contributor>
      <username>127.0.0.1</username>
      <id>0</id>
    </contributor>
    <comment>/* jV3 Outline */</comment>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="3455" xml:space="preserve">&lt;big&gt;'''Welcome to jV wiki.'''&lt;/big&gt;
{| style="float:right"
 |__TOC__
 |}
jV version3 (formerly known as PDBjViewer) is a program to display molecular graphics of protein and nucleic acids. 
jV can use as a stand-alone program and can operate on a web browser as an Java applet. jV is used by PDBj services([http://ef-site.hgc.jp/eF-site/index.jsp eF-site], [http://ef-site.hgc.jp/eF-seek/index.jsp eF-seek], the molecular structure surface database of the protein functional part).

jV supports the following features:
* jV can read and display PDBML files, the canonical XML format for the Protein Data Bank.
* Of course, jV can read and display the traditional PDB format files, too.
* RasMol-like usability.
* jV can process more than one molecules.
* jV can display polygons specified by XML. ([http://ef-site.hgc.jp/eF-site/schema/polygon12.xsd XML Schema for polygons] is available.)
* Multiple polygons can be processed simultaneously, and be superimposed onto molecular images.
* Animation can be realized.
* The graphics of jV is based on OpenGL [https://jogl.dev.java.net/ JOGL]), thereby producing fairly beautiful pictures.
* jV runs on the Java Runtime Environment ([http://java.sun.com/javase/index.jsp JRE]) so that it can work as a stand-alone application as well as an applet.

The program 'jV' has been developed by [http://www.hgc.jp/~kinosita/TOP.html Kengo Kinoshita] ([http://www.hgc.jp/english/ Human Genome Center], [http://www.ims.u-tokyo.ac.jp/imsut/en/ Insutitute for Medical Science],[http://www.u-tokyo.ac.jp/index_e.html University of Tokyo]) and [http://www.protein.osaka-u.ac.jp/rcsfp/pi/ Haruki Nakamura] ([http://www.protein.osaka-u.ac.jp/index_e.php Institute for Protein Research], [http://www.osaka-u.ac.jp/eng/index.html Osaka Univeristy]), with the support from [http://www-bird.jst.go.jp/index_e.html JST-BIRD].


Please refer to here about [[old version]](jV version1 &amp; jV version2).


== jV3 Outline ==
[[File:Download.png|right|link=http://ef-site.hgc.jp/eF-site/servlet/Registration|Download]] jV version 3 is now used to display molecules and their surfaces as a Java applet program.&lt;br /&gt;&lt;font size="1"&gt;Version 3.6 was released on 11, Aug, 2008.&lt;br /&gt;This version is fully compativle with [https://applet-launcher.dev.java.net/ applet-launcher].&lt;/font&gt;&lt;br /&gt;Go to [[jV version 3]].
&lt;br /&gt;
It requires the following softwares.
* [http://java.sun.com/products/plugin/index-1.4.html JRE] 1.4.2 or later  (recommend 1.4.2_12)
* [https://jogl.dev.java.net/ JOGL] 1.0, 1.1.1 or JSR-231 1.0.0  (recommend JSR-231)&lt;br /&gt;
** version 1.0 [[http://ef-site.hgc.jp/eF-site/jV/JOGL1.0_win32.zip Windows],[http://ef-site.hgc.jp/eF-site/jV/JOGL1.0_macosx.tar.gz Mac OS X],[http://ef-site.hgc.jp/eF-site/jV/JOGL1.0_linux.tar.gz Linux]]
** version 1.1.1 [[http://ef-site.hgc.jp/eF-site/jV/JOGL1.1.1_win32.zip Windows],[http://ef-site.hgc.jp/eF-site/jV/JOGL1.1.1_macosx.tar.gz Mac OS X], [http://ef-site.hgc.jp/eF-site/jV/JOGL1.1.1_linux.tar.gz Linux]]
** JSR-231 1.0.0 [[http://ef-site.hgc.jp/eF-site/jV/JOGL_JSR231_win32.zip Windows], [http://ef-site.hgc.jp/eF-site/jV/JOGL_JSR231_macosx_ppc.tar.gz Mac OS X ppc], [http://ef-site.hgc.jp/eF-site/jV/JOGL_JSR231_macosx_universal.tar.gz Mac OS X universal], [http://ef-site.hgc.jp/eF-site/jV/JOGL_JSR231_linux_i586.tar.gz Linux]]

&lt;font size="1"&gt;Note: &amp;nbsp; JOGL 1.0 and 1.1.1 are not available for Intel Mac.The latest version of JOGL, JSR-231 1.0.0, runs on Intel Mac.&lt;/font&gt;</text>
    <sha1>bf39911c66c03d431b6d6a984d934692a5b8adf6</sha1>
  </revision>
  <revision>
    <id>70</id>
    <parentid>69</parentid>
    <timestamp>2009-03-09T03:20:52Z</timestamp>
    <contributor>
      <username>127.0.0.1</username>
      <id>0</id>
    </contributor>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="3532" xml:space="preserve">&lt;big&gt;'''Welcome to jV wiki.'''&lt;/big&gt;
{| style="float:right"
 |__TOC__
 |}
jV version3 (formerly known as PDBjViewer) is a program to display molecular graphics of protein and nucleic acids. 
jV can use as a stand-alone program and can operate on a web browser as an Java applet. jV is used by PDBj services([http://ef-site.hgc.jp/eF-site/index.jsp eF-site], [http://ef-site.hgc.jp/eF-seek/index.jsp eF-seek], the molecular structure surface database of the protein functional part).

jV supports the following features:
* jV can read and display PDBML files, the canonical XML format for the Protein Data Bank.
* Of course, jV can read and display the traditional PDB format files, too.
* RasMol-like usability.
* jV can process more than one molecules.
* jV can display polygons specified by XML. ([http://ef-site.hgc.jp/eF-site/schema/polygon12.xsd XML Schema for polygons] is available.)
* Multiple polygons can be processed simultaneously, and be superimposed onto molecular images.
* Animation can be realized.
* The graphics of jV is based on OpenGL [https://jogl.dev.java.net/ JOGL]), thereby producing fairly beautiful pictures.
* jV runs on the Java Runtime Environment ([http://java.sun.com/javase/index.jsp JRE]) so that it can work as a stand-alone application as well as an applet.

The program 'jV' has been developed by [http://www.hgc.jp/~kinosita/TOP.html Kengo Kinoshita] ([http://www.hgc.jp/english/ Human Genome Center], [http://www.ims.u-tokyo.ac.jp/imsut/en/ Insutitute for Medical Science],[http://www.u-tokyo.ac.jp/index_e.html University of Tokyo]) and [http://www.protein.osaka-u.ac.jp/rcsfp/pi/ Haruki Nakamura] ([http://www.protein.osaka-u.ac.jp/index_e.php Institute for Protein Research], [http://www.osaka-u.ac.jp/eng/index.html Osaka Univeristy]), with the support from [http://www-bird.jst.go.jp/index_e.html JST-BIRD].

About installation of jV3 [[Install jV3]]
About how to use jV3 [[jV3 Manual]]
Please refer to here about [[old version]](jV version1 &amp; jV version2).


== jV3 Outline ==
[[File:Download.png|right|link=http://ef-site.hgc.jp/eF-site/servlet/Registration|Download]] jV version 3 is now used to display molecules and their surfaces as a Java applet program.&lt;br /&gt;&lt;font size="1"&gt;Version 3.6 was released on 11, Aug, 2008.&lt;br /&gt;This version is fully compativle with [https://applet-launcher.dev.java.net/ applet-launcher].&lt;/font&gt;&lt;br /&gt;Go to [[jV version 3]].
&lt;br /&gt;
It requires the following softwares.
* [http://java.sun.com/products/plugin/index-1.4.html JRE] 1.4.2 or later  (recommend 1.4.2_12)
* [https://jogl.dev.java.net/ JOGL] 1.0, 1.1.1 or JSR-231 1.0.0  (recommend JSR-231)&lt;br /&gt;
** version 1.0 [[http://ef-site.hgc.jp/eF-site/jV/JOGL1.0_win32.zip Windows],[http://ef-site.hgc.jp/eF-site/jV/JOGL1.0_macosx.tar.gz Mac OS X],[http://ef-site.hgc.jp/eF-site/jV/JOGL1.0_linux.tar.gz Linux]]
** version 1.1.1 [[http://ef-site.hgc.jp/eF-site/jV/JOGL1.1.1_win32.zip Windows],[http://ef-site.hgc.jp/eF-site/jV/JOGL1.1.1_macosx.tar.gz Mac OS X], [http://ef-site.hgc.jp/eF-site/jV/JOGL1.1.1_linux.tar.gz Linux]]
** JSR-231 1.0.0 [[http://ef-site.hgc.jp/eF-site/jV/JOGL_JSR231_win32.zip Windows], [http://ef-site.hgc.jp/eF-site/jV/JOGL_JSR231_macosx_ppc.tar.gz Mac OS X ppc], [http://ef-site.hgc.jp/eF-site/jV/JOGL_JSR231_macosx_universal.tar.gz Mac OS X universal], [http://ef-site.hgc.jp/eF-site/jV/JOGL_JSR231_linux_i586.tar.gz Linux]]

&lt;font size="1"&gt;Note: &amp;nbsp; JOGL 1.0 and 1.1.1 are not available for Intel Mac.The latest version of JOGL, JSR-231 1.0.0, runs on Intel Mac.&lt;/font&gt;</text>
    <sha1>f79411ba8f31b0a21bd81c17c793bb5ac54e917e</sha1>
  </revision>
  <revision>
    <id>71</id>
    <parentid>70</parentid>
    <timestamp>2009-03-09T03:21:29Z</timestamp>
    <contributor>
      <username>127.0.0.1</username>
      <id>0</id>
    </contributor>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="3552" xml:space="preserve">&lt;big&gt;'''Welcome to jV wiki.'''&lt;/big&gt;
{| style="float:right"
 |__TOC__
 |}
jV version3 (formerly known as PDBjViewer) is a program to display molecular graphics of protein and nucleic acids. 
jV can use as a stand-alone program and can operate on a web browser as an Java applet. jV is used by PDBj services([http://ef-site.hgc.jp/eF-site/index.jsp eF-site], [http://ef-site.hgc.jp/eF-seek/index.jsp eF-seek], the molecular structure surface database of the protein functional part).

jV supports the following features:
* jV can read and display PDBML files, the canonical XML format for the Protein Data Bank.
* Of course, jV can read and display the traditional PDB format files, too.
* RasMol-like usability.
* jV can process more than one molecules.
* jV can display polygons specified by XML. ([http://ef-site.hgc.jp/eF-site/schema/polygon12.xsd XML Schema for polygons] is available.)
* Multiple polygons can be processed simultaneously, and be superimposed onto molecular images.
* Animation can be realized.
* The graphics of jV is based on OpenGL [https://jogl.dev.java.net/ JOGL]), thereby producing fairly beautiful pictures.
* jV runs on the Java Runtime Environment ([http://java.sun.com/javase/index.jsp JRE]) so that it can work as a stand-alone application as well as an applet.

The program 'jV' has been developed by [http://www.hgc.jp/~kinosita/TOP.html Kengo Kinoshita] ([http://www.hgc.jp/english/ Human Genome Center], [http://www.ims.u-tokyo.ac.jp/imsut/en/ Insutitute for Medical Science],[http://www.u-tokyo.ac.jp/index_e.html University of Tokyo]) and [http://www.protein.osaka-u.ac.jp/rcsfp/pi/ Haruki Nakamura] ([http://www.protein.osaka-u.ac.jp/index_e.php Institute for Protein Research], [http://www.osaka-u.ac.jp/eng/index.html Osaka Univeristy]), with the support from [http://www-bird.jst.go.jp/index_e.html JST-BIRD].

About installation of jV3 [[Install jV3]].&lt;br /&gt;
About how to use jV3 [[jV3 Manual]].&lt;br /&gt;&lt;br /&gt;
Please refer to here about [[old version]](jV version1 &amp; jV version2).


== jV3 Outline ==
[[File:Download.png|right|link=http://ef-site.hgc.jp/eF-site/servlet/Registration|Download]] jV version 3 is now used to display molecules and their surfaces as a Java applet program.&lt;br /&gt;&lt;font size="1"&gt;Version 3.6 was released on 11, Aug, 2008.&lt;br /&gt;This version is fully compativle with [https://applet-launcher.dev.java.net/ applet-launcher].&lt;/font&gt;&lt;br /&gt;Go to [[jV version 3]].
&lt;br /&gt;
It requires the following softwares.
* [http://java.sun.com/products/plugin/index-1.4.html JRE] 1.4.2 or later  (recommend 1.4.2_12)
* [https://jogl.dev.java.net/ JOGL] 1.0, 1.1.1 or JSR-231 1.0.0  (recommend JSR-231)&lt;br /&gt;
** version 1.0 [[http://ef-site.hgc.jp/eF-site/jV/JOGL1.0_win32.zip Windows],[http://ef-site.hgc.jp/eF-site/jV/JOGL1.0_macosx.tar.gz Mac OS X],[http://ef-site.hgc.jp/eF-site/jV/JOGL1.0_linux.tar.gz Linux]]
** version 1.1.1 [[http://ef-site.hgc.jp/eF-site/jV/JOGL1.1.1_win32.zip Windows],[http://ef-site.hgc.jp/eF-site/jV/JOGL1.1.1_macosx.tar.gz Mac OS X], [http://ef-site.hgc.jp/eF-site/jV/JOGL1.1.1_linux.tar.gz Linux]]
** JSR-231 1.0.0 [[http://ef-site.hgc.jp/eF-site/jV/JOGL_JSR231_win32.zip Windows], [http://ef-site.hgc.jp/eF-site/jV/JOGL_JSR231_macosx_ppc.tar.gz Mac OS X ppc], [http://ef-site.hgc.jp/eF-site/jV/JOGL_JSR231_macosx_universal.tar.gz Mac OS X universal], [http://ef-site.hgc.jp/eF-site/jV/JOGL_JSR231_linux_i586.tar.gz Linux]]

&lt;font size="1"&gt;Note: &amp;nbsp; JOGL 1.0 and 1.1.1 are not available for Intel Mac.The latest version of JOGL, JSR-231 1.0.0, runs on Intel Mac.&lt;/font&gt;</text>
    <sha1>04600a277a4588de57fcd0a81e1f79a395c06c4b</sha1>
  </revision>
  <revision>
    <id>72</id>
    <parentid>71</parentid>
    <timestamp>2009-03-09T03:28:52Z</timestamp>
    <contributor>
      <username>127.0.0.1</username>
      <id>0</id>
    </contributor>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="3579" xml:space="preserve">&lt;big&gt;'''Welcome to jV wiki.'''&lt;/big&gt;
{| style="float:right"
 |__TOC__
 |}
jV version3 (formerly known as PDBjViewer) is a program to display molecular graphics of protein and nucleic acids. 
jV can use as a stand-alone program and can operate on a web browser as an Java applet. jV is used by PDBj services([http://ef-site.hgc.jp/eF-site/index.jsp eF-site], [http://ef-site.hgc.jp/eF-seek/index.jsp eF-seek], the molecular structure surface database of the protein functional part).

jV supports the following features:
* jV can read and display PDBML files, the canonical XML format for the Protein Data Bank.
* Of course, jV can read and display the traditional PDB format files, too.
* RasMol-like usability.
* jV can process more than one molecules.
* jV can display polygons specified by XML. ([http://ef-site.hgc.jp/eF-site/schema/polygon12.xsd XML Schema for polygons] is available.)
* Multiple polygons can be processed simultaneously, and be superimposed onto molecular images.
* Animation can be realized.
* The graphics of jV is based on OpenGL [https://jogl.dev.java.net/ JOGL]), thereby producing fairly beautiful pictures.
* jV runs on the Java Runtime Environment ([http://java.sun.com/javase/index.jsp JRE]) so that it can work as a stand-alone application as well as an applet.

The program 'jV' has been developed by [http://www.hgc.jp/~kinosita/TOP.html Kengo Kinoshita] ([http://www.hgc.jp/english/ Human Genome Center], [http://www.ims.u-tokyo.ac.jp/imsut/en/ Insutitute for Medical Science],[http://www.u-tokyo.ac.jp/index_e.html University of Tokyo]) and [http://www.protein.osaka-u.ac.jp/rcsfp/pi/ Haruki Nakamura] ([http://www.protein.osaka-u.ac.jp/index_e.php Institute for Protein Research], [http://www.osaka-u.ac.jp/eng/index.html Osaka Univeristy]), with the support from [http://www-bird.jst.go.jp/index_e.html JST-BIRD].

[[Installation of jV3]] is a procedure installed in a local machine.&lt;br /&gt;
[[jV3 Manual]]　is　how to use jV3.&lt;br /&gt;&lt;br /&gt;
Please refer to here about [[old version]](jV version1 &amp; jV version2).


== jV3 Outline ==
[[File:Download.png|right|link=http://ef-site.hgc.jp/eF-site/servlet/Registration|Download]] jV version 3 is now used to display molecules and their surfaces as a Java applet program.&lt;br /&gt;&lt;font size="1"&gt;Version 3.6 was released on 11, Aug, 2008.&lt;br /&gt;This version is fully compativle with [https://applet-launcher.dev.java.net/ applet-launcher].&lt;/font&gt;&lt;br /&gt;Go to [[jV version 3]].
&lt;br /&gt;
It requires the following softwares.
* [http://java.sun.com/products/plugin/index-1.4.html JRE] 1.4.2 or later  (recommend 1.4.2_12)
* [https://jogl.dev.java.net/ JOGL] 1.0, 1.1.1 or JSR-231 1.0.0  (recommend JSR-231)&lt;br /&gt;
** version 1.0 [[http://ef-site.hgc.jp/eF-site/jV/JOGL1.0_win32.zip Windows],[http://ef-site.hgc.jp/eF-site/jV/JOGL1.0_macosx.tar.gz Mac OS X],[http://ef-site.hgc.jp/eF-site/jV/JOGL1.0_linux.tar.gz Linux]]
** version 1.1.1 [[http://ef-site.hgc.jp/eF-site/jV/JOGL1.1.1_win32.zip Windows],[http://ef-site.hgc.jp/eF-site/jV/JOGL1.1.1_macosx.tar.gz Mac OS X], [http://ef-site.hgc.jp/eF-site/jV/JOGL1.1.1_linux.tar.gz Linux]]
** JSR-231 1.0.0 [[http://ef-site.hgc.jp/eF-site/jV/JOGL_JSR231_win32.zip Windows], [http://ef-site.hgc.jp/eF-site/jV/JOGL_JSR231_macosx_ppc.tar.gz Mac OS X ppc], [http://ef-site.hgc.jp/eF-site/jV/JOGL_JSR231_macosx_universal.tar.gz Mac OS X universal], [http://ef-site.hgc.jp/eF-site/jV/JOGL_JSR231_linux_i586.tar.gz Linux]]

&lt;font size="1"&gt;Note: &amp;nbsp; JOGL 1.0 and 1.1.1 are not available for Intel Mac.The latest version of JOGL, JSR-231 1.0.0, runs on Intel Mac.&lt;/font&gt;</text>
    <sha1>173066c71ef7500e3cf4ee2e848cc7b97c975b8a</sha1>
  </revision>
  <revision>
    <id>73</id>
    <parentid>72</parentid>
    <timestamp>2009-03-09T05:14:50Z</timestamp>
    <contributor>
      <username>127.0.0.1</username>
      <id>0</id>
    </contributor>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="3595" xml:space="preserve">&lt;big&gt;'''Welcome to jV wiki.'''&lt;/big&gt;
{| style="float:right"
 |__TOC__
 |}
jV version3 (formerly known as PDBjViewer) is a program to display molecular graphics of protein and nucleic acids. 
jV can use as a stand-alone program and can operate on a web browser as an Java applet. jV is used by PDBj services([http://ef-site.hgc.jp/eF-site/index.jsp eF-site], [http://ef-site.hgc.jp/eF-seek/index.jsp eF-seek], the molecular structure surface database of the protein functional part).

jV supports the following features:
* jV can read and display PDBML files, the canonical XML format for the Protein Data Bank.
* Of course, jV can read and display the traditional PDB format files, too.
* RasMol-like usability.
* jV can process more than one molecules.
* jV can display polygons specified by XML. ([http://ef-site.hgc.jp/eF-site/schema/polygon12.xsd XML Schema for polygons] is available.)
* Multiple polygons can be processed simultaneously, and be superimposed onto molecular images.
* Animation can be realized.
* The graphics of jV is based on OpenGL [https://jogl.dev.java.net/ JOGL]), thereby producing fairly beautiful pictures.
* jV runs on the Java Runtime Environment ([http://java.sun.com/javase/index.jsp JRE]) so that it can work as a stand-alone application as well as an applet.

The program 'jV' has been developed by [http://www.hgc.jp/~kinosita/TOP.html Kengo Kinoshita] ([http://www.hgc.jp/english/ Human Genome Center], [http://www.ims.u-tokyo.ac.jp/imsut/en/ Insutitute for Medical Science],[http://www.u-tokyo.ac.jp/index_e.html University of Tokyo]) and [http://www.protein.osaka-u.ac.jp/rcsfp/pi/ Haruki Nakamura] ([http://www.protein.osaka-u.ac.jp/index_e.php Institute for Protein Research], [http://www.osaka-u.ac.jp/eng/index.html Osaka Univeristy]), with the support from [http://www-bird.jst.go.jp/index_e.html JST-BIRD].

[[Installation of jV3]] is a procedure installed in a local machine.&lt;br /&gt;
[[jV3 Manual]]　is　how to use jV3.&lt;br /&gt;&lt;br /&gt;
The [[old version]](jV version1 &amp; jV version2) has not carried out use recommendation.


== jV3 Outline ==
[[File:Download.png|right|link=http://ef-site.hgc.jp/eF-site/servlet/Registration|Download]] jV version 3 is now used to display molecules and their surfaces as a Java applet program.&lt;br /&gt;&lt;font size="1"&gt;Version 3.6 was released on 11, Aug, 2008.&lt;br /&gt;This version is fully compativle with [https://applet-launcher.dev.java.net/ applet-launcher].&lt;/font&gt;&lt;br /&gt;Go to [[jV version 3]].
&lt;br /&gt;
It requires the following softwares.
* [http://java.sun.com/products/plugin/index-1.4.html JRE] 1.4.2 or later  (recommend 1.4.2_12)
* [https://jogl.dev.java.net/ JOGL] 1.0, 1.1.1 or JSR-231 1.0.0  (recommend JSR-231)&lt;br /&gt;
** version 1.0 [[http://ef-site.hgc.jp/eF-site/jV/JOGL1.0_win32.zip Windows],[http://ef-site.hgc.jp/eF-site/jV/JOGL1.0_macosx.tar.gz Mac OS X],[http://ef-site.hgc.jp/eF-site/jV/JOGL1.0_linux.tar.gz Linux]]
** version 1.1.1 [[http://ef-site.hgc.jp/eF-site/jV/JOGL1.1.1_win32.zip Windows],[http://ef-site.hgc.jp/eF-site/jV/JOGL1.1.1_macosx.tar.gz Mac OS X], [http://ef-site.hgc.jp/eF-site/jV/JOGL1.1.1_linux.tar.gz Linux]]
** JSR-231 1.0.0 [[http://ef-site.hgc.jp/eF-site/jV/JOGL_JSR231_win32.zip Windows], [http://ef-site.hgc.jp/eF-site/jV/JOGL_JSR231_macosx_ppc.tar.gz Mac OS X ppc], [http://ef-site.hgc.jp/eF-site/jV/JOGL_JSR231_macosx_universal.tar.gz Mac OS X universal], [http://ef-site.hgc.jp/eF-site/jV/JOGL_JSR231_linux_i586.tar.gz Linux]]

&lt;font size="1"&gt;Note: &amp;nbsp; JOGL 1.0 and 1.1.1 are not available for Intel Mac.The latest version of JOGL, JSR-231 1.0.0, runs on Intel Mac.&lt;/font&gt;</text>
    <sha1>648109b11741a39b7314b9f16d7fd28cada0990a</sha1>
  </revision>
  <revision>
    <id>81</id>
    <parentid>73</parentid>
    <timestamp>2009-03-09T05:27:48Z</timestamp>
    <contributor>
      <username>JVuser</username>
      <id>2</id>
    </contributor>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="3684" xml:space="preserve">&lt;big&gt;'''Welcome to jV wiki.'''&lt;/big&gt;
{| style="float:right"
 |__TOC__
 |}
jV version3 (formerly known as PDBjViewer) is a program to display molecular graphics of protein and nucleic acids. 
jV can use as a stand-alone program and can operate on a web browser as an Java applet. jV is used by PDBj services([http://ef-site.hgc.jp/eF-site/index.jsp eF-site], [http://ef-site.hgc.jp/eF-seek/index.jsp eF-seek], the molecular structure surface database of the protein functional part).

jV supports the following features:
* jV can read and display PDBML files, the canonical XML format for the Protein Data Bank.
* Of course, jV can read and display the traditional PDB format files, too.
* RasMol-like usability.
* jV can process more than one molecules.
* jV can display polygons specified by XML. ([http://ef-site.hgc.jp/eF-site/schema/polygon12.xsd XML Schema for polygons] is available.)
* Multiple polygons can be processed simultaneously, and be superimposed onto molecular images.
* Animation can be realized.
* The graphics of jV is based on OpenGL [https://jogl.dev.java.net/ JOGL]), thereby producing fairly beautiful pictures.
* jV runs on the Java Runtime Environment ([http://java.sun.com/javase/index.jsp JRE]) so that it can work as a stand-alone application as well as an applet.

The program 'jV' has been developed by [http://www.hgc.jp/~kinosita/TOP.html Kengo Kinoshita] ([http://www.hgc.jp/english/ Human Genome Center], [http://www.ims.u-tokyo.ac.jp/imsut/en/ Insutitute for Medical Science],[http://www.u-tokyo.ac.jp/index_e.html University of Tokyo]) and [http://www.protein.osaka-u.ac.jp/rcsfp/pi/ Haruki Nakamura] ([http://www.protein.osaka-u.ac.jp/index_e.php Institute for Protein Research], [http://www.osaka-u.ac.jp/eng/index.html Osaka Univeristy]), with the support from [http://www-bird.jst.go.jp/index_e.html JST-BIRD].

[[Installation of jV3]] is a procedure installed in a local machine.&lt;br /&gt;
[[jV3 Manual]]　is　how to use jV3.&lt;br /&gt;&lt;br /&gt;
The [[old version]](jV version1 &amp; jV version2) has not carried out use recommendation.

&lt;gallery&gt;
File:Spacefill.jpg
File:Cartoon.jpg
File:Surface.jpg
File:edmap.jpg
&lt;/gallery&gt;

== jV3 Outline ==
[[File:Download.png|right|link=http://ef-site.hgc.jp/eF-site/servlet/Registration|Download]] jV version 3 is now used to display molecules and their surfaces as a Java applet program.&lt;br /&gt;&lt;font size="1"&gt;Version 3.6 was released on 11, Aug, 2008.&lt;br /&gt;This version is fully compativle with [https://applet-launcher.dev.java.net/ applet-launcher].&lt;/font&gt;&lt;br /&gt;Go to [[jV version 3]].
&lt;br /&gt;
It requires the following softwares.
* [http://java.sun.com/products/plugin/index-1.4.html JRE] 1.4.2 or later  (recommend 1.4.2_12)
* [https://jogl.dev.java.net/ JOGL] 1.0, 1.1.1 or JSR-231 1.0.0  (recommend JSR-231)&lt;br /&gt;
** version 1.0 [[http://ef-site.hgc.jp/eF-site/jV/JOGL1.0_win32.zip Windows],[http://ef-site.hgc.jp/eF-site/jV/JOGL1.0_macosx.tar.gz Mac OS X],[http://ef-site.hgc.jp/eF-site/jV/JOGL1.0_linux.tar.gz Linux]]
** version 1.1.1 [[http://ef-site.hgc.jp/eF-site/jV/JOGL1.1.1_win32.zip Windows],[http://ef-site.hgc.jp/eF-site/jV/JOGL1.1.1_macosx.tar.gz Mac OS X], [http://ef-site.hgc.jp/eF-site/jV/JOGL1.1.1_linux.tar.gz Linux]]
** JSR-231 1.0.0 [[http://ef-site.hgc.jp/eF-site/jV/JOGL_JSR231_win32.zip Windows], [http://ef-site.hgc.jp/eF-site/jV/JOGL_JSR231_macosx_ppc.tar.gz Mac OS X ppc], [http://ef-site.hgc.jp/eF-site/jV/JOGL_JSR231_macosx_universal.tar.gz Mac OS X universal], [http://ef-site.hgc.jp/eF-site/jV/JOGL_JSR231_linux_i586.tar.gz Linux]]

&lt;font size="1"&gt;Note: &amp;nbsp; JOGL 1.0 and 1.1.1 are not available for Intel Mac.The latest version of JOGL, JSR-231 1.0.0, runs on Intel Mac.&lt;/font&gt;</text>
    <sha1>c25ccbee44d31be57ba101c5ec21d4cdbe8c2f06</sha1>
  </revision>
  <revision>
    <id>82</id>
    <parentid>81</parentid>
    <timestamp>2009-03-09T05:29:29Z</timestamp>
    <contributor>
      <username>JVuser</username>
      <id>2</id>
    </contributor>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="3700" xml:space="preserve">&lt;big&gt;'''Welcome to jV wiki.'''&lt;/big&gt;
{| style="float:right"
 |__TOC__
 |}
jV version3 (formerly known as PDBjViewer) is a program to display molecular graphics of protein and nucleic acids. 
jV can use as a stand-alone program and can operate on a web browser as an Java applet. jV is used by PDBj services([http://ef-site.hgc.jp/eF-site/index.jsp eF-site], [http://ef-site.hgc.jp/eF-seek/index.jsp eF-seek], the molecular structure surface database of the protein functional part).

jV supports the following features:
* jV can read and display PDBML files, the canonical XML format for the Protein Data Bank.
* Of course, jV can read and display the traditional PDB format files, too.
* RasMol-like usability.
* jV can process more than one molecules.
* jV can display polygons specified by XML. ([http://ef-site.hgc.jp/eF-site/schema/polygon12.xsd XML Schema for polygons] is available.)
* Multiple polygons can be processed simultaneously, and be superimposed onto molecular images.
* Animation can be realized.
* The graphics of jV is based on OpenGL [https://jogl.dev.java.net/ JOGL]), thereby producing fairly beautiful pictures.
* jV runs on the Java Runtime Environment ([http://java.sun.com/javase/index.jsp JRE]) so that it can work as a stand-alone application as well as an applet.

The program 'jV' has been developed by [http://www.hgc.jp/~kinosita/TOP.html Kengo Kinoshita] ([http://www.hgc.jp/english/ Human Genome Center], [http://www.ims.u-tokyo.ac.jp/imsut/en/ Insutitute for Medical Science],[http://www.u-tokyo.ac.jp/index_e.html University of Tokyo]) and [http://www.protein.osaka-u.ac.jp/rcsfp/pi/ Haruki Nakamura] ([http://www.protein.osaka-u.ac.jp/index_e.php Institute for Protein Research], [http://www.osaka-u.ac.jp/eng/index.html Osaka Univeristy]), with the support from [http://www-bird.jst.go.jp/index_e.html JST-BIRD].

[[Installation of jV3]] is a procedure installed in a local machine.&lt;br /&gt;
[[jV3 Manual]]　is　how to use jV3.&lt;br /&gt;
&lt;font size="1"&gt;The [[old version]](jV version1 &amp; jV version2) has not carried out use recommendation.&lt;/font&gt;

&lt;gallery&gt;
File:Spacefill.jpg
File:Cartoon.jpg
File:Surface.jpg
File:edmap.jpg
&lt;/gallery&gt;

== jV3 Outline ==
[[File:Download.png|right|link=http://ef-site.hgc.jp/eF-site/servlet/Registration|Download]] jV version 3 is now used to display molecules and their surfaces as a Java applet program.&lt;br /&gt;&lt;font size="1"&gt;Version 3.6 was released on 11, Aug, 2008.&lt;br /&gt;This version is fully compativle with [https://applet-launcher.dev.java.net/ applet-launcher].&lt;/font&gt;&lt;br /&gt;Go to [[jV version 3]].
&lt;br /&gt;
It requires the following softwares.
* [http://java.sun.com/products/plugin/index-1.4.html JRE] 1.4.2 or later  (recommend 1.4.2_12)
* [https://jogl.dev.java.net/ JOGL] 1.0, 1.1.1 or JSR-231 1.0.0  (recommend JSR-231)&lt;br /&gt;
** version 1.0 [[http://ef-site.hgc.jp/eF-site/jV/JOGL1.0_win32.zip Windows],[http://ef-site.hgc.jp/eF-site/jV/JOGL1.0_macosx.tar.gz Mac OS X],[http://ef-site.hgc.jp/eF-site/jV/JOGL1.0_linux.tar.gz Linux]]
** version 1.1.1 [[http://ef-site.hgc.jp/eF-site/jV/JOGL1.1.1_win32.zip Windows],[http://ef-site.hgc.jp/eF-site/jV/JOGL1.1.1_macosx.tar.gz Mac OS X], [http://ef-site.hgc.jp/eF-site/jV/JOGL1.1.1_linux.tar.gz Linux]]
** JSR-231 1.0.0 [[http://ef-site.hgc.jp/eF-site/jV/JOGL_JSR231_win32.zip Windows], [http://ef-site.hgc.jp/eF-site/jV/JOGL_JSR231_macosx_ppc.tar.gz Mac OS X ppc], [http://ef-site.hgc.jp/eF-site/jV/JOGL_JSR231_macosx_universal.tar.gz Mac OS X universal], [http://ef-site.hgc.jp/eF-site/jV/JOGL_JSR231_linux_i586.tar.gz Linux]]

&lt;font size="1"&gt;Note: &amp;nbsp; JOGL 1.0 and 1.1.1 are not available for Intel Mac.The latest version of JOGL, JSR-231 1.0.0, runs on Intel Mac.&lt;/font&gt;</text>
    <sha1>496ac1ab52f0511b55e1983793f9dd0522e37dc7</sha1>
  </revision>
  <revision>
    <id>83</id>
    <parentid>82</parentid>
    <timestamp>2009-03-09T05:38:14Z</timestamp>
    <contributor>
      <username>127.0.0.1</username>
      <id>0</id>
    </contributor>
    <comment>/* jV3 Outline */</comment>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="3708" xml:space="preserve">&lt;big&gt;'''Welcome to jV wiki.'''&lt;/big&gt;
{| style="float:right"
 |__TOC__
 |}
jV version3 (formerly known as PDBjViewer) is a program to display molecular graphics of protein and nucleic acids. 
jV can use as a stand-alone program and can operate on a web browser as an Java applet. jV is used by PDBj services([http://ef-site.hgc.jp/eF-site/index.jsp eF-site], [http://ef-site.hgc.jp/eF-seek/index.jsp eF-seek], the molecular structure surface database of the protein functional part).

jV supports the following features:
* jV can read and display PDBML files, the canonical XML format for the Protein Data Bank.
* Of course, jV can read and display the traditional PDB format files, too.
* RasMol-like usability.
* jV can process more than one molecules.
* jV can display polygons specified by XML. ([http://ef-site.hgc.jp/eF-site/schema/polygon12.xsd XML Schema for polygons] is available.)
* Multiple polygons can be processed simultaneously, and be superimposed onto molecular images.
* Animation can be realized.
* The graphics of jV is based on OpenGL [https://jogl.dev.java.net/ JOGL]), thereby producing fairly beautiful pictures.
* jV runs on the Java Runtime Environment ([http://java.sun.com/javase/index.jsp JRE]) so that it can work as a stand-alone application as well as an applet.

The program 'jV' has been developed by [http://www.hgc.jp/~kinosita/TOP.html Kengo Kinoshita] ([http://www.hgc.jp/english/ Human Genome Center], [http://www.ims.u-tokyo.ac.jp/imsut/en/ Insutitute for Medical Science],[http://www.u-tokyo.ac.jp/index_e.html University of Tokyo]) and [http://www.protein.osaka-u.ac.jp/rcsfp/pi/ Haruki Nakamura] ([http://www.protein.osaka-u.ac.jp/index_e.php Institute for Protein Research], [http://www.osaka-u.ac.jp/eng/index.html Osaka Univeristy]), with the support from [http://www-bird.jst.go.jp/index_e.html JST-BIRD].

[[Installation of jV3]] is a procedure installed in a local machine.&lt;br /&gt;
[[jV3 Manual]]　is　how to use jV3.&lt;br /&gt;
&lt;font size="1"&gt;The [[old version]](jV version1 &amp; jV version2) has not carried out use recommendation.&lt;/font&gt;

&lt;gallery&gt;
File:Spacefill.jpg
File:Cartoon.jpg
File:Surface.jpg
File:edmap.jpg
&lt;/gallery&gt;

== jV3 Outline ==
[[File:Download.png|right|link=http://ef-site.hgc.jp/eF-site/servlet/DownloadViewerBinary|Download]] jV version 3 is now used to display molecules and their surfaces as a Java applet program.&lt;br /&gt;&lt;font size="1"&gt;Version 3.6 was released on 11, Aug, 2008.&lt;br /&gt;This version is fully compativle with [https://applet-launcher.dev.java.net/ applet-launcher].&lt;/font&gt;&lt;br /&gt;Go to [[jV version 3]].
&lt;br /&gt;
It requires the following softwares.
* [http://java.sun.com/products/plugin/index-1.4.html JRE] 1.4.2 or later  (recommend 1.4.2_12)
* [https://jogl.dev.java.net/ JOGL] 1.0, 1.1.1 or JSR-231 1.0.0  (recommend JSR-231)&lt;br /&gt;
** version 1.0 [[http://ef-site.hgc.jp/eF-site/jV/JOGL1.0_win32.zip Windows],[http://ef-site.hgc.jp/eF-site/jV/JOGL1.0_macosx.tar.gz Mac OS X],[http://ef-site.hgc.jp/eF-site/jV/JOGL1.0_linux.tar.gz Linux]]
** version 1.1.1 [[http://ef-site.hgc.jp/eF-site/jV/JOGL1.1.1_win32.zip Windows],[http://ef-site.hgc.jp/eF-site/jV/JOGL1.1.1_macosx.tar.gz Mac OS X], [http://ef-site.hgc.jp/eF-site/jV/JOGL1.1.1_linux.tar.gz Linux]]
** JSR-231 1.0.0 [[http://ef-site.hgc.jp/eF-site/jV/JOGL_JSR231_win32.zip Windows], [http://ef-site.hgc.jp/eF-site/jV/JOGL_JSR231_macosx_ppc.tar.gz Mac OS X ppc], [http://ef-site.hgc.jp/eF-site/jV/JOGL_JSR231_macosx_universal.tar.gz Mac OS X universal], [http://ef-site.hgc.jp/eF-site/jV/JOGL_JSR231_linux_i586.tar.gz Linux]]

&lt;font size="1"&gt;Note: &amp;nbsp; JOGL 1.0 and 1.1.1 are not available for Intel Mac.The latest version of JOGL, JSR-231 1.0.0, runs on Intel Mac.&lt;/font&gt;</text>
    <sha1>c093bb6b6910ada8b99c77abdf5a569ca30cf27c</sha1>
  </revision>
  <revision>
    <id>84</id>
    <parentid>83</parentid>
    <timestamp>2009-03-09T05:41:38Z</timestamp>
    <contributor>
      <username>127.0.0.1</username>
      <id>0</id>
    </contributor>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="3766" xml:space="preserve">&lt;big&gt;'''Welcome to jV wiki.'''&lt;/big&gt;
{| style="float:right"
 |__TOC__
 |}
jV version3 (formerly known as PDBjViewer) is a program to display molecular graphics of protein and nucleic acids. 
jV can use as a stand-alone program and can operate on a web browser as an Java applet. jV is used by PDBj services([http://ef-site.hgc.jp/eF-site/index.jsp eF-site], [http://ef-site.hgc.jp/eF-seek/index.jsp eF-seek], the molecular structure surface database of the protein functional part).

jV supports the following features:
* jV can read and display PDBML files, the canonical XML format for the Protein Data Bank.
* Of course, jV can read and display the traditional PDB format files, too.
* RasMol-like usability.
* jV can process more than one molecules.
* jV can display polygons specified by XML. ([http://ef-site.hgc.jp/eF-site/schema/polygon12.xsd XML Schema for polygons] is available.)
* Multiple polygons can be processed simultaneously, and be superimposed onto molecular images.
* Animation can be realized.
* The graphics of jV is based on OpenGL [https://jogl.dev.java.net/ JOGL]), thereby producing fairly beautiful pictures.
* jV runs on the Java Runtime Environment ([http://java.sun.com/javase/index.jsp JRE]) so that it can work as a stand-alone application as well as an applet.

The program 'jV' has been developed by [http://www.hgc.jp/~kinosita/TOP.html Kengo Kinoshita] ([http://www.hgc.jp/english/ Human Genome Center], [http://www.ims.u-tokyo.ac.jp/imsut/en/ Insutitute for Medical Science],[http://www.u-tokyo.ac.jp/index_e.html University of Tokyo]) and [http://www.protein.osaka-u.ac.jp/rcsfp/pi/ Haruki Nakamura] ([http://www.protein.osaka-u.ac.jp/index_e.php Institute for Protein Research], [http://www.osaka-u.ac.jp/eng/index.html Osaka Univeristy]), with the support from [http://www-bird.jst.go.jp/index_e.html JST-BIRD].

[[jV version 3]] has indicated more detailed explanation.
[[Installation of jV3]] is a procedure installed in a local machine.&lt;br /&gt;
[[jV3 Manual]]　is　how to use jV3.&lt;br /&gt;
&lt;font size="1"&gt;The [[old version]](jV version1 &amp; jV version2) has not carried out use recommendation.&lt;/font&gt;

&lt;gallery&gt;
File:Spacefill.jpg
File:Cartoon.jpg
File:Surface.jpg
File:edmap.jpg
&lt;/gallery&gt;

== jV3 Outline ==
[[File:Download.png|right|link=http://ef-site.hgc.jp/eF-site/servlet/DownloadViewerBinary|Download]] jV version 3 is now used to display molecules and their surfaces as a Java applet program.&lt;br /&gt;&lt;font size="1"&gt;Version 3.6 was released on 11, Aug, 2008.&lt;br /&gt;This version is fully compativle with [https://applet-launcher.dev.java.net/ applet-launcher].&lt;/font&gt;&lt;br /&gt;Go to [[jV version 3]].
&lt;br /&gt;
It requires the following softwares.
* [http://java.sun.com/products/plugin/index-1.4.html JRE] 1.4.2 or later  (recommend 1.4.2_12)
* [https://jogl.dev.java.net/ JOGL] 1.0, 1.1.1 or JSR-231 1.0.0  (recommend JSR-231)&lt;br /&gt;
** version 1.0 [[http://ef-site.hgc.jp/eF-site/jV/JOGL1.0_win32.zip Windows],[http://ef-site.hgc.jp/eF-site/jV/JOGL1.0_macosx.tar.gz Mac OS X],[http://ef-site.hgc.jp/eF-site/jV/JOGL1.0_linux.tar.gz Linux]]
** version 1.1.1 [[http://ef-site.hgc.jp/eF-site/jV/JOGL1.1.1_win32.zip Windows],[http://ef-site.hgc.jp/eF-site/jV/JOGL1.1.1_macosx.tar.gz Mac OS X], [http://ef-site.hgc.jp/eF-site/jV/JOGL1.1.1_linux.tar.gz Linux]]
** JSR-231 1.0.0 [[http://ef-site.hgc.jp/eF-site/jV/JOGL_JSR231_win32.zip Windows], [http://ef-site.hgc.jp/eF-site/jV/JOGL_JSR231_macosx_ppc.tar.gz Mac OS X ppc], [http://ef-site.hgc.jp/eF-site/jV/JOGL_JSR231_macosx_universal.tar.gz Mac OS X universal], [http://ef-site.hgc.jp/eF-site/jV/JOGL_JSR231_linux_i586.tar.gz Linux]]

&lt;font size="1"&gt;Note: &amp;nbsp; JOGL 1.0 and 1.1.1 are not available for Intel Mac.The latest version of JOGL, JSR-231 1.0.0, runs on Intel Mac.&lt;/font&gt;</text>
    <sha1>18de1c31c73073b6fdb7d25ce3671aafe05b19bc</sha1>
  </revision>
  <revision>
    <id>85</id>
    <parentid>84</parentid>
    <timestamp>2009-03-09T05:42:03Z</timestamp>
    <contributor>
      <username>127.0.0.1</username>
      <id>0</id>
    </contributor>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="3757" xml:space="preserve">&lt;big&gt;'''Welcome to jV wiki.'''&lt;/big&gt;
{| style="float:right"
 |__TOC__
 |}
jV version3 (formerly known as PDBjViewer) is a program to display molecular graphics of protein and nucleic acids. 
jV can use as a stand-alone program and can operate on a web browser as an Java applet. jV is used by PDBj services([http://ef-site.hgc.jp/eF-site/index.jsp eF-site], [http://ef-site.hgc.jp/eF-seek/index.jsp eF-seek], the molecular structure surface database of the protein functional part).

jV supports the following features:
* jV can read and display PDBML files, the canonical XML format for the Protein Data Bank.
* Of course, jV can read and display the traditional PDB format files, too.
* RasMol-like usability.
* jV can process more than one molecules.
* jV can display polygons specified by XML. ([http://ef-site.hgc.jp/eF-site/schema/polygon12.xsd XML Schema for polygons] is available.)
* Multiple polygons can be processed simultaneously, and be superimposed onto molecular images.
* Animation can be realized.
* The graphics of jV is based on OpenGL [https://jogl.dev.java.net/ JOGL]), thereby producing fairly beautiful pictures.
* jV runs on the Java Runtime Environment ([http://java.sun.com/javase/index.jsp JRE]) so that it can work as a stand-alone application as well as an applet.

The program 'jV' has been developed by [http://www.hgc.jp/~kinosita/TOP.html Kengo Kinoshita] ([http://www.hgc.jp/english/ Human Genome Center], [http://www.ims.u-tokyo.ac.jp/imsut/en/ Insutitute for Medical Science],[http://www.u-tokyo.ac.jp/index_e.html University of Tokyo]) and [http://www.protein.osaka-u.ac.jp/rcsfp/pi/ Haruki Nakamura] ([http://www.protein.osaka-u.ac.jp/index_e.php Institute for Protein Research], [http://www.osaka-u.ac.jp/eng/index.html Osaka Univeristy]), with the support from [http://www-bird.jst.go.jp/index_e.html JST-BIRD].

[[jV version 3]] has indicated more detailed explanation.

[[Installation of jV3]] is a procedure installed in a local machine.

[[jV3 Manual]]　is　how to use jV3.

&lt;font size="1"&gt;The [[old version]](jV version1 &amp; jV version2) has not carried out use recommendation.&lt;/font&gt;

&lt;gallery&gt;
File:Spacefill.jpg
File:Cartoon.jpg
File:Surface.jpg
File:edmap.jpg
&lt;/gallery&gt;

== jV3 Outline ==
[[File:Download.png|right|link=http://ef-site.hgc.jp/eF-site/servlet/DownloadViewerBinary|Download]] jV version 3 is now used to display molecules and their surfaces as a Java applet program.&lt;br /&gt;&lt;font size="1"&gt;Version 3.6 was released on 11, Aug, 2008.&lt;br /&gt;This version is fully compativle with [https://applet-launcher.dev.java.net/ applet-launcher].&lt;/font&gt;&lt;br /&gt;Go to [[jV version 3]].
&lt;br /&gt;
It requires the following softwares.
* [http://java.sun.com/products/plugin/index-1.4.html JRE] 1.4.2 or later  (recommend 1.4.2_12)
* [https://jogl.dev.java.net/ JOGL] 1.0, 1.1.1 or JSR-231 1.0.0  (recommend JSR-231)&lt;br /&gt;
** version 1.0 [[http://ef-site.hgc.jp/eF-site/jV/JOGL1.0_win32.zip Windows],[http://ef-site.hgc.jp/eF-site/jV/JOGL1.0_macosx.tar.gz Mac OS X],[http://ef-site.hgc.jp/eF-site/jV/JOGL1.0_linux.tar.gz Linux]]
** version 1.1.1 [[http://ef-site.hgc.jp/eF-site/jV/JOGL1.1.1_win32.zip Windows],[http://ef-site.hgc.jp/eF-site/jV/JOGL1.1.1_macosx.tar.gz Mac OS X], [http://ef-site.hgc.jp/eF-site/jV/JOGL1.1.1_linux.tar.gz Linux]]
** JSR-231 1.0.0 [[http://ef-site.hgc.jp/eF-site/jV/JOGL_JSR231_win32.zip Windows], [http://ef-site.hgc.jp/eF-site/jV/JOGL_JSR231_macosx_ppc.tar.gz Mac OS X ppc], [http://ef-site.hgc.jp/eF-site/jV/JOGL_JSR231_macosx_universal.tar.gz Mac OS X universal], [http://ef-site.hgc.jp/eF-site/jV/JOGL_JSR231_linux_i586.tar.gz Linux]]

&lt;font size="1"&gt;Note: &amp;nbsp; JOGL 1.0 and 1.1.1 are not available for Intel Mac.The latest version of JOGL, JSR-231 1.0.0, runs on Intel Mac.&lt;/font&gt;</text>
    <sha1>76afb2d1af7057c4daaadd9f5e58ad3be4561a3c</sha1>
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  <revision>
    <id>86</id>
    <parentid>85</parentid>
    <timestamp>2009-03-09T05:42:51Z</timestamp>
    <contributor>
      <username>127.0.0.1</username>
      <id>0</id>
    </contributor>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="3776" xml:space="preserve">&lt;big&gt;'''Welcome to jV wiki.'''&lt;/big&gt;
{| style="float:right"
 |__TOC__
 |}
jV version3 (formerly known as PDBjViewer) is a program to display molecular graphics of protein and nucleic acids. 
jV can use as a stand-alone program and can operate on a web browser as an Java applet. jV is used by PDBj services([http://ef-site.hgc.jp/eF-site/index.jsp eF-site], [http://ef-site.hgc.jp/eF-seek/index.jsp eF-seek], the molecular structure surface database of the protein functional part).

jV supports the following features:
* jV can read and display PDBML files, the canonical XML format for the Protein Data Bank.
* Of course, jV can read and display the traditional PDB format files, too.
* RasMol-like usability.
* jV can process more than one molecules.
* jV can display polygons specified by XML. ([http://ef-site.hgc.jp/eF-site/schema/polygon12.xsd XML Schema for polygons] is available.)
* Multiple polygons can be processed simultaneously, and be superimposed onto molecular images.
* Animation can be realized.
* The graphics of jV is based on OpenGL [https://jogl.dev.java.net/ JOGL]), thereby producing fairly beautiful pictures.
* jV runs on the Java Runtime Environment ([http://java.sun.com/javase/index.jsp JRE]) so that it can work as a stand-alone application as well as an applet.

The program 'jV' has been developed by [http://www.hgc.jp/~kinosita/TOP.html Kengo Kinoshita] ([http://www.hgc.jp/english/ Human Genome Center], [http://www.ims.u-tokyo.ac.jp/imsut/en/ Insutitute for Medical Science],[http://www.u-tokyo.ac.jp/index_e.html University of Tokyo]) and [http://www.protein.osaka-u.ac.jp/rcsfp/pi/ Haruki Nakamura] ([http://www.protein.osaka-u.ac.jp/index_e.php Institute for Protein Research], [http://www.osaka-u.ac.jp/eng/index.html Osaka Univeristy]), with the support from [http://www-bird.jst.go.jp/index_e.html JST-BIRD].

-[[jV version 3]] has indicated more detailed explanation.&lt;br /&gt;
-[[Installation of jV3]] is a procedure installed in a local machine.&lt;br /&gt;
-[[jV3 Manual]]　is　how to use jV3.&lt;br /&gt;

&lt;font size="1"&gt;The [[old version]](jV version1 &amp; jV version2) has not carried out use recommendation.&lt;/font&gt;

&lt;gallery&gt;
File:Spacefill.jpg
File:Cartoon.jpg
File:Surface.jpg
File:edmap.jpg
&lt;/gallery&gt;

== jV3 Outline ==
[[File:Download.png|right|link=http://ef-site.hgc.jp/eF-site/servlet/DownloadViewerBinary|Download]] jV version 3 is now used to display molecules and their surfaces as a Java applet program.&lt;br /&gt;&lt;font size="1"&gt;Version 3.6 was released on 11, Aug, 2008.&lt;br /&gt;This version is fully compativle with [https://applet-launcher.dev.java.net/ applet-launcher].&lt;/font&gt;&lt;br /&gt;Go to [[jV version 3]].
&lt;br /&gt;
It requires the following softwares.
* [http://java.sun.com/products/plugin/index-1.4.html JRE] 1.4.2 or later  (recommend 1.4.2_12)
* [https://jogl.dev.java.net/ JOGL] 1.0, 1.1.1 or JSR-231 1.0.0  (recommend JSR-231)&lt;br /&gt;
** version 1.0 [[http://ef-site.hgc.jp/eF-site/jV/JOGL1.0_win32.zip Windows],[http://ef-site.hgc.jp/eF-site/jV/JOGL1.0_macosx.tar.gz Mac OS X],[http://ef-site.hgc.jp/eF-site/jV/JOGL1.0_linux.tar.gz Linux]]
** version 1.1.1 [[http://ef-site.hgc.jp/eF-site/jV/JOGL1.1.1_win32.zip Windows],[http://ef-site.hgc.jp/eF-site/jV/JOGL1.1.1_macosx.tar.gz Mac OS X], [http://ef-site.hgc.jp/eF-site/jV/JOGL1.1.1_linux.tar.gz Linux]]
** JSR-231 1.0.0 [[http://ef-site.hgc.jp/eF-site/jV/JOGL_JSR231_win32.zip Windows], [http://ef-site.hgc.jp/eF-site/jV/JOGL_JSR231_macosx_ppc.tar.gz Mac OS X ppc], [http://ef-site.hgc.jp/eF-site/jV/JOGL_JSR231_macosx_universal.tar.gz Mac OS X universal], [http://ef-site.hgc.jp/eF-site/jV/JOGL_JSR231_linux_i586.tar.gz Linux]]

&lt;font size="1"&gt;Note: &amp;nbsp; JOGL 1.0 and 1.1.1 are not available for Intel Mac.The latest version of JOGL, JSR-231 1.0.0, runs on Intel Mac.&lt;/font&gt;</text>
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<page arvcontinue="20090303095249|51">
  <title>Old version</title>
  <ns>0</ns>
  <id>6</id>
  <revision>
    <id>59</id>
    <timestamp>2009-03-09T02:48:58Z</timestamp>
    <contributor>
      <username>127.0.0.1</username>
      <id>0</id>
    </contributor>
    <comment>Created page with '== jV version 2 == jV version 2 is an advanced version of PDBjViewer, which can be used only as a stand-alone program. It enables to display more than one molecule images at the ...'</comment>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="1739" xml:space="preserve">== jV version 2 ==
jV version 2 is an advanced version of PDBjViewer, which can be used only as a stand-alone program. It enables to display more than one molecule images at the same time and their display models and transforms can be operated separately. An animation of molecules can be also performed. jV version 2 runs with .NET framework 1.1 on the Windows platform. Therefore the .NET framework must be installed on your computer.

== jV version 1 (PDBjViewer) ==
Visualization of structure and surface of molecules is performed by a Java applet program called 'PDBjViewer'.

Two image windows are opened. The structure of the molecule is shown in the left window and the molecular surface is displayed in the right window. The mouse control is as follows. 
&lt;br /&gt;
&lt;div align="center"&gt;
{| class="wikitable" cellspacing="0" border="1"
 ! action !! Windows 
 |-
 | rotate x, y || left
 |-
 | zoom || Alt + left
 |-
 | tranlate x, y || right
 |-
|}
&lt;br /&gt;
&lt;/div&gt;
&lt;br&gt;
In order to use PDBjViewer, [http://java.sun.com/products/plugin/ Java Plug-in] and
[http://java.sun.com/products/java-media/3D/ Java 3D API] must be installed on your computer.
The version requirements are as follows.&lt;br /&gt;
* JRE (includes Java Plug-in) 1.4.1 or later (recommend 1.4.2)
* Java 3D API (OpenGL) 1.2.1 or later (recommend 1.2.1_04)
&lt;br /&gt;Important notes
# You can select two kinds of implementation of Java 3D, OpenGL version and DirectX version. But, PDBjViewer only work with OpenGL version at present.
# PDBjViewer does not work with JRE from 1.4.1_03 to 1.4.1_06.&lt;br /&gt;
PDBjViewer can be used as a stand-alone program as well as an applet
with the same requirements as above.
In addition to mouse controls, a command line interface is provided.
&lt;br&gt;</text>
    <sha1>c8144128e1e174ab5e7f227544aebd43fca099f1</sha1>
  </revision>
  <revision>
    <id>60</id>
    <parentid>59</parentid>
    <timestamp>2009-03-09T02:49:23Z</timestamp>
    <contributor>
      <username>127.0.0.1</username>
      <id>0</id>
    </contributor>
    <comment>/* jV version 1 (PDBjViewer) */</comment>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="1351" xml:space="preserve">== jV version 2 ==
jV version 2 is an advanced version of PDBjViewer, which can be used only as a stand-alone program. It enables to display more than one molecule images at the same time and their display models and transforms can be operated separately. An animation of molecules can be also performed. jV version 2 runs with .NET framework 1.1 on the Windows platform. Therefore the .NET framework must be installed on your computer.

== jV version 1 (PDBjViewer) ==
Visualization of structure and surface of molecules is performed by a Java applet program called 'PDBjViewer'.


In order to use PDBjViewer, [http://java.sun.com/products/plugin/ Java Plug-in] and
[http://java.sun.com/products/java-media/3D/ Java 3D API] must be installed on your computer.
The version requirements are as follows.&lt;br /&gt;
* JRE (includes Java Plug-in) 1.4.1 or later (recommend 1.4.2)
* Java 3D API (OpenGL) 1.2.1 or later (recommend 1.2.1_04)
&lt;br /&gt;Important notes
# You can select two kinds of implementation of Java 3D, OpenGL version and DirectX version. But, PDBjViewer only work with OpenGL version at present.
# PDBjViewer does not work with JRE from 1.4.1_03 to 1.4.1_06.&lt;br /&gt;
PDBjViewer can be used as a stand-alone program as well as an applet
with the same requirements as above.
In addition to mouse controls, a command line interface is provided.
&lt;br&gt;</text>
    <sha1>9852f9f35ec2d387ba8aef161d8a6a8bc78dca56</sha1>
  </revision>
  <revision>
    <id>66</id>
    <parentid>60</parentid>
    <timestamp>2009-03-09T02:57:08Z</timestamp>
    <contributor>
      <username>127.0.0.1</username>
      <id>0</id>
    </contributor>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="1351" xml:space="preserve">== jV version 1 (PDBjViewer) ==
Visualization of structure and surface of molecules is performed by a Java applet program called 'PDBjViewer'.


In order to use PDBjViewer, [http://java.sun.com/products/plugin/ Java Plug-in] and
[http://java.sun.com/products/java-media/3D/ Java 3D API] must be installed on your computer.
The version requirements are as follows.&lt;br /&gt;
* JRE (includes Java Plug-in) 1.4.1 or later (recommend 1.4.2)
* Java 3D API (OpenGL) 1.2.1 or later (recommend 1.2.1_04)
&lt;br /&gt;Important notes
# You can select two kinds of implementation of Java 3D, OpenGL version and DirectX version. But, PDBjViewer only work with OpenGL version at present.
# PDBjViewer does not work with JRE from 1.4.1_03 to 1.4.1_06.&lt;br /&gt;
PDBjViewer can be used as a stand-alone program as well as an applet
with the same requirements as above.
In addition to mouse controls, a command line interface is provided.
&lt;br&gt;

== jV version 2 ==
jV version 2 is an advanced version of PDBjViewer, which can be used only as a stand-alone program. It enables to display more than one molecule images at the same time and their display models and transforms can be operated separately. An animation of molecules can be also performed. jV version 2 runs with .NET framework 1.1 on the Windows platform. Therefore the .NET framework must be installed on your computer.</text>
    <sha1>7179d429b3750b0cc4365f77241129b35daa7ac5</sha1>
  </revision>
  <revision>
    <id>74</id>
    <parentid>66</parentid>
    <timestamp>2009-03-09T05:16:10Z</timestamp>
    <contributor>
      <username>127.0.0.1</username>
      <id>0</id>
    </contributor>
    <comment>/* jV version 1 (PDBjViewer) */</comment>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="1350" xml:space="preserve">== jV version 1 (PDBjViewer) ==
Visualization of structure and surface of molecules is performed by a Java applet program called 'PDBjViewer'.

In order to use PDBjViewer, [http://java.sun.com/products/plugin/ Java Plug-in] and
[http://java.sun.com/products/java-media/3D/ Java 3D API] must be installed on your computer.
The version requirements are as follows.&lt;br /&gt;
* JRE (includes Java Plug-in) 1.4.1 or later (recommend 1.4.2)
* Java 3D API (OpenGL) 1.2.1 or later (recommend 1.2.1_04)
&lt;br /&gt;Important notes
# You can select two kinds of implementation of Java 3D, OpenGL version and DirectX version. But, PDBjViewer only work with OpenGL version at present.
# PDBjViewer does not work with JRE from 1.4.1_03 to 1.4.1_06.&lt;br /&gt;
PDBjViewer can be used as a stand-alone program as well as an applet
with the same requirements as above.
In addition to mouse controls, a command line interface is provided.
&lt;br&gt;

== jV version 2 ==
jV version 2 is an advanced version of PDBjViewer, which can be used only as a stand-alone program. It enables to display more than one molecule images at the same time and their display models and transforms can be operated separately. An animation of molecules can be also performed. jV version 2 runs with .NET framework 1.1 on the Windows platform. Therefore the .NET framework must be installed on your computer.</text>
    <sha1>a265c4ec98f8f729093ce3fbdf2fd3d214236b8a</sha1>
  </revision>
  <revision>
    <id>75</id>
    <parentid>74</parentid>
    <timestamp>2009-03-09T05:16:28Z</timestamp>
    <contributor>
      <username>127.0.0.1</username>
      <id>0</id>
    </contributor>
    <comment>/* jV version 1 (PDBjViewer) */</comment>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="1344" xml:space="preserve">== jV version 1 (PDBjViewer) ==
Visualization of structure and surface of molecules is performed by a Java applet program called 'PDBjViewer'.

In order to use PDBjViewer, [http://java.sun.com/products/plugin/ Java Plug-in] and
[http://java.sun.com/products/java-media/3D/ Java 3D API] must be installed on your computer.
The version requirements are as follows.&lt;br /&gt;
* JRE (includes Java Plug-in) 1.4.1 or later (recommend 1.4.2)
* Java 3D API (OpenGL) 1.2.1 or later (recommend 1.2.1_04)
Important notes
# You can select two kinds of implementation of Java 3D, OpenGL version and DirectX version. But, PDBjViewer only work with OpenGL version at present.
# PDBjViewer does not work with JRE from 1.4.1_03 to 1.4.1_06.&lt;br /&gt;
PDBjViewer can be used as a stand-alone program as well as an applet
with the same requirements as above.
In addition to mouse controls, a command line interface is provided.
&lt;br&gt;

== jV version 2 ==
jV version 2 is an advanced version of PDBjViewer, which can be used only as a stand-alone program. It enables to display more than one molecule images at the same time and their display models and transforms can be operated separately. An animation of molecules can be also performed. jV version 2 runs with .NET framework 1.1 on the Windows platform. Therefore the .NET framework must be installed on your computer.</text>
    <sha1>4c70c50b5501a5807887e4a97221b46df797b574</sha1>
  </revision>
  <revision>
    <id>76</id>
    <parentid>75</parentid>
    <timestamp>2009-03-09T05:17:22Z</timestamp>
    <contributor>
      <username>127.0.0.1</username>
      <id>0</id>
    </contributor>
    <comment>/* jV version 1 (PDBjViewer) */</comment>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="1164" xml:space="preserve">== jV version 1 (PDBjViewer) ==
Visualization of structure and surface of molecules is performed by a Java applet program called 'PDBjViewer'.

In order to use PDBjViewer, [http://java.sun.com/products/plugin/ Java Plug-in] and
[http://java.sun.com/products/java-media/3D/ Java 3D API] must be installed on your computer.
The version requirements are as follows.&lt;br /&gt;
* JRE (includes Java Plug-in) 1.4.1 or later (recommend 1.4.2)
* Java 3D API (OpenGL) 1.2.1 or later (recommend 1.2.1_04)
Important notes
# You can select two kinds of implementation of Java 3D, OpenGL version and DirectX version. But, PDBjViewer only work with OpenGL version at present.
# PDBjViewer does not work with JRE from 1.4.1_03 to 1.4.1_06.&lt;br /&gt;

== jV version 2 ==
jV version 2 is an advanced version of PDBjViewer, which can be used only as a stand-alone program. It enables to display more than one molecule images at the same time and their display models and transforms can be operated separately. An animation of molecules can be also performed. jV version 2 runs with .NET framework 1.1 on the Windows platform. Therefore the .NET framework must be installed on your computer.</text>
    <sha1>044548772230aed8deb495ac2474f0efaf170d74</sha1>
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    <comment>{{Information|
 |Description=Spacefill
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  <title>File:Cartoon.jpg</title>
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    <timestamp>2009-03-09T05:23:44Z</timestamp>
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  <title>How to use</title>
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    <comment>Created page with 'jV is an interactive 3D viewer program to visualize protein and nucleic acid molecules. The program reads in a PDBML file that is an XML format for PDB. Usual PDB format files ar...'</comment>
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    <text bytes="3333" xml:space="preserve">jV is an interactive 3D viewer program to visualize protein and nucleic acid molecules. The program reads in a PDBML file that is an XML format for PDB. Usual PDB format files are also accepted. More than one molecule files can be opened and displayed at the same time and their display models and transforms can be operated separately. In addition to molecule files, a polygon file written in XML can be read and displayed. More than one polygon files can be opened at the same time and superposed on molecule images. The XML schema of the polygon file is available. jV can perform an animation of molecules. The animation file is a PDB format file in which each frame is separated by a MODEL line.

jV runs on Java Runtime Environment (JRE) and can be used both as a standalone program and an applet. The 3D rendering is performed with the use of JOGL API. The version requirements are as follows.

* JRE (includes Java Plug-in) 1.4.2 or later
* JOGL 1.1.1 or JSR-231

Here, Java Plug-in is required in order to use the program as an applet.

The program allows an interactive mouse control and command execution. The commnad syntax follows that of Rasmol with some modifications. In order to handle the transform of each molecule and polygon separately, every files are set to be either selected or not selected. The transform operation commands, such as rotate or translate, act only on selected files. On the other hand, every atoms in a molecule are also set to be either selected or not selected independently of whether the molecule itself is selected or not selected. Only selected atoms are the target of display model operations, such as wireframe or spacefill commands, and coloring operations.

Release note:
Changes and improvements have been made as follows.

* version 3.1
** The following commands have been added; 'animrange', 'set adjustview', 'show godata', and 'show xps3'.
** The xPSSS expression has been added in order to select a group of atoms.
** Several public methods have been added to the applet so as to append molecule or polygon files after the applet started.
** The applet can send information about mouse-picked atoms to JavaScript.
* version 3.1.1
** Some problems in GUI menu [Options]-[Hetero Atoms] and [Hydrogens] have been fixed.
** Some problems in 'trace' command have been fixed.
* version 3.1.2
** eF-site ID has been changed to a new format.
* version 3.1.3
** Some problems in xps3 atom selection have been fixed.
* version 3.1.4
** Some problems in finalization process of openGL rendering have been fixed.
* version 3.1.5
** The output of 'show xps3' command has been modified.
** Some problems in 'save png/jpeg' command have been fixed.
* version 3.1.6
** Some problems in loading an empty polygon file have been fixed.
* version 3.1.7
** Some problems in initialization process of the applet have been fixed.
* version 3.2
** 'show site' command has been added.
* version 3.3 beta 1
** Availabe JOGL version is restricted to JSR-231 beta 5 only.
* version 3.3
** Both the previous JOGL (version 1.1.1) and JSR-231 are available.
** The following commands have been added; 'set viewpoint', 'show viewpoint', 'set imagesize', and 'show imagesize'.
* version 3.3.1
** Some problems in reading a pdbMLplus file have been fixed.
* version 3.4
** PDB format version 3 can be processed.</text>
    <sha1>9c04b88c8e0fb243e9f958ce63198bc1e4d3969f</sha1>
  </revision>
  <revision>
    <id>88</id>
    <parentid>87</parentid>
    <timestamp>2009-03-09T05:55:09Z</timestamp>
    <contributor>
      <username>127.0.0.1</username>
      <id>0</id>
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    <text bytes="3523" xml:space="preserve">jV is an interactive 3D viewer program to visualize protein and nucleic acid molecules. The program reads in a PDBML file that is an XML format for PDB. Usual PDB format files are also accepted. More than one molecule files can be opened and displayed at the same time and their display models and transforms can be operated separately. In addition to molecule files, a polygon file written in XML can be read and displayed. More than one polygon files can be opened at the same time and superposed on molecule images. The [http://ef-site.hgc.jp/eF-site/schema/polygon12.xsd XML schema] of the polygon file is available. jV can perform an animation of molecules. The animation file is a PDB format file in which each frame is separated by a MODEL line.

jV runs on Java Runtime Environment ([http://java.sun.com/javase/index.jsp JRE]) and can be used both as a standalone program and an applet. The 3D rendering is performed with the use of [https://jogl.dev.java.net/ JOGL] API. The version requirements are as follows.

* JRE (includes Java Plug-in) 1.4.2 or later
* JOGL 1.1.1 or JSR-231

Here, [http://java.sun.com/products/plugin/ Java Plug-in] is required in order to use the program as an applet.

The program allows an interactive mouse control and command execution. The commnad syntax follows that of [http://www.rasmol.org/ Rasmol] with some modifications. In order to handle the transform of each molecule and polygon separately, every files are set to be either selected or not selected. The transform operation commands, such as rotate or translate, act only on selected files. On the other hand, every atoms in a molecule are also set to be either selected or not selected independently of whether the molecule itself is selected or not selected. Only selected atoms are the target of display model operations, such as wireframe or spacefill commands, and coloring operations.

== Release note ==
Changes and improvements have been made as follows.

* version 3.1
** The following commands have been added; 'animrange', 'set adjustview', 'show godata', and 'show xps3'.
** The xPSSS expression has been added in order to select a group of atoms.
** Several public methods have been added to the applet so as to append molecule or polygon files after the applet started.
** The applet can send information about mouse-picked atoms to JavaScript.
* version 3.1.1
** Some problems in GUI menu [Options]-[Hetero Atoms] and [Hydrogens] have been fixed.
** Some problems in 'trace' command have been fixed.
* version 3.1.2
** eF-site ID has been changed to a new format.
* version 3.1.3
** Some problems in xps3 atom selection have been fixed.
* version 3.1.4
** Some problems in finalization process of openGL rendering have been fixed.
* version 3.1.5
** The output of 'show xps3' command has been modified.
** Some problems in 'save png/jpeg' command have been fixed.
* version 3.1.6
** Some problems in loading an empty polygon file have been fixed.
* version 3.1.7
** Some problems in initialization process of the applet have been fixed.
* version 3.2
** 'show site' command has been added.
* version 3.3 beta 1
** Availabe JOGL version is restricted to JSR-231 beta 5 only.
* version 3.3
** Both the previous JOGL (version 1.1.1) and JSR-231 are available.
** The following commands have been added; 'set viewpoint', 'show viewpoint', 'set imagesize', and 'show imagesize'.
* version 3.3.1
** Some problems in reading a pdbMLplus file have been fixed.
* version 3.4
** PDB format version 3 can be processed.</text>
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  </revision>
  <revision>
    <id>89</id>
    <parentid>88</parentid>
    <timestamp>2009-03-09T06:09:09Z</timestamp>
    <contributor>
      <username>127.0.0.1</username>
      <id>0</id>
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    <text bytes="4146" xml:space="preserve">jV is an interactive 3D viewer program to visualize protein and nucleic acid molecules. The program reads in a PDBML file that is an XML format for PDB. Usual PDB format files are also accepted. More than one molecule files can be opened and displayed at the same time and their display models and transforms can be operated separately. In addition to molecule files, a polygon file written in XML can be read and displayed. More than one polygon files can be opened at the same time and superposed on molecule images. The [http://ef-site.hgc.jp/eF-site/schema/polygon12.xsd XML schema] of the polygon file is available. jV can perform an animation of molecules. The animation file is a PDB format file in which each frame is separated by a MODEL line.

jV runs on Java Runtime Environment ([http://java.sun.com/javase/index.jsp JRE]) and can be used both as a standalone program and an applet. The 3D rendering is performed with the use of [https://jogl.dev.java.net/ JOGL] API. The version requirements are as follows.

* JRE (includes Java Plug-in) 1.4.2 or later
* JOGL 1.1.1 or JSR-231

Here, [http://java.sun.com/products/plugin/ Java Plug-in] is required in order to use the program as an applet.

The program allows an interactive mouse control and command execution. The commnad syntax follows that of [http://www.rasmol.org/ Rasmol] with some modifications. In order to handle the transform of each molecule and polygon separately, every files are set to be either selected or not selected. The transform operation commands, such as rotate or translate, act only on selected files. On the other hand, every atoms in a molecule are also set to be either selected or not selected independently of whether the molecule itself is selected or not selected. Only selected atoms are the target of display model operations, such as wireframe or spacefill commands, and coloring operations.

== How to use the minimum things ==
The following table shows hot to do the minimum things with jV.&lt;br /&gt;
{| class="wikitable"
 |+ Action pair OS
 ! Action !! Window, Linux !! Mac OS X 
 |-
 | rotate around X,Y axes | left drag | mouse drag
 |-
 | rotate around Z axis | Shift + right drag | Shift + command + drag
 |-
 | translate along X,Y axes | right drag | command + drag
 |-
 | translate along Z axis (zoom in/out) | Shift + left drag | Shift + drag
 |}
For the detail,
* The reference manual [[jV3 Manual]] link:
* The install manual [[Installaion of jV3]]
Some examples
# Animation
# User jV with applet launcher


== Release note ==
Changes and improvements have been made as follows.

* version 3.1
** The following commands have been added; 'animrange', 'set adjustview', 'show godata', and 'show xps3'.
** The xPSSS expression has been added in order to select a group of atoms.
** Several public methods have been added to the applet so as to append molecule or polygon files after the applet started.
** The applet can send information about mouse-picked atoms to JavaScript.
* version 3.1.1
** Some problems in GUI menu [Options]-[Hetero Atoms] and [Hydrogens] have been fixed.
** Some problems in 'trace' command have been fixed.
* version 3.1.2
** eF-site ID has been changed to a new format.
* version 3.1.3
** Some problems in xps3 atom selection have been fixed.
* version 3.1.4
** Some problems in finalization process of openGL rendering have been fixed.
* version 3.1.5
** The output of 'show xps3' command has been modified.
** Some problems in 'save png/jpeg' command have been fixed.
* version 3.1.6
** Some problems in loading an empty polygon file have been fixed.
* version 3.1.7
** Some problems in initialization process of the applet have been fixed.
* version 3.2
** 'show site' command has been added.
* version 3.3 beta 1
** Availabe JOGL version is restricted to JSR-231 beta 5 only.
* version 3.3
** Both the previous JOGL (version 1.1.1) and JSR-231 are available.
** The following commands have been added; 'set viewpoint', 'show viewpoint', 'set imagesize', and 'show imagesize'.
* version 3.3.1
** Some problems in reading a pdbMLplus file have been fixed.
* version 3.4
** PDB format version 3 can be processed.</text>
    <sha1>dad801b0148ef20ccca1fef4e6b8c5771443fa39</sha1>
  </revision>
  <revision>
    <id>90</id>
    <parentid>89</parentid>
    <timestamp>2009-03-09T06:11:10Z</timestamp>
    <contributor>
      <username>127.0.0.1</username>
      <id>0</id>
    </contributor>
    <comment>/* How to use the minimum things */</comment>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="4149" xml:space="preserve">jV is an interactive 3D viewer program to visualize protein and nucleic acid molecules. The program reads in a PDBML file that is an XML format for PDB. Usual PDB format files are also accepted. More than one molecule files can be opened and displayed at the same time and their display models and transforms can be operated separately. In addition to molecule files, a polygon file written in XML can be read and displayed. More than one polygon files can be opened at the same time and superposed on molecule images. The [http://ef-site.hgc.jp/eF-site/schema/polygon12.xsd XML schema] of the polygon file is available. jV can perform an animation of molecules. The animation file is a PDB format file in which each frame is separated by a MODEL line.

jV runs on Java Runtime Environment ([http://java.sun.com/javase/index.jsp JRE]) and can be used both as a standalone program and an applet. The 3D rendering is performed with the use of [https://jogl.dev.java.net/ JOGL] API. The version requirements are as follows.

* JRE (includes Java Plug-in) 1.4.2 or later
* JOGL 1.1.1 or JSR-231

Here, [http://java.sun.com/products/plugin/ Java Plug-in] is required in order to use the program as an applet.

The program allows an interactive mouse control and command execution. The commnad syntax follows that of [http://www.rasmol.org/ Rasmol] with some modifications. In order to handle the transform of each molecule and polygon separately, every files are set to be either selected or not selected. The transform operation commands, such as rotate or translate, act only on selected files. On the other hand, every atoms in a molecule are also set to be either selected or not selected independently of whether the molecule itself is selected or not selected. Only selected atoms are the target of display model operations, such as wireframe or spacefill commands, and coloring operations.

== How to use the minimum things ==
The following table shows hot to do the minimum things with jV.&lt;br /&gt;
{| class="wikitable"
 |+ Action pair OS
 ! Action !! Window, Linux !! Mac OS X 
 |-
 ! rotate around X,Y axes
 | left drag | mouse drag
 |-
 ! rotate around Z axis
 | Shift + right drag | Shift + command + drag
 |-
 ! translate along X,Y axes
 | right drag | command + drag
 |-
 ! translate along Z axis (zoom in/out)
 | Shift + left drag | Shift + drag
 |}
For the detail,
* The reference manual [[jV3 Manual]] link:
* The install manual [[Installaion of jV3]]
Some examples
# Animation
# User jV with applet launcher

== Release note ==
Changes and improvements have been made as follows.

* version 3.1
** The following commands have been added; 'animrange', 'set adjustview', 'show godata', and 'show xps3'.
** The xPSSS expression has been added in order to select a group of atoms.
** Several public methods have been added to the applet so as to append molecule or polygon files after the applet started.
** The applet can send information about mouse-picked atoms to JavaScript.
* version 3.1.1
** Some problems in GUI menu [Options]-[Hetero Atoms] and [Hydrogens] have been fixed.
** Some problems in 'trace' command have been fixed.
* version 3.1.2
** eF-site ID has been changed to a new format.
* version 3.1.3
** Some problems in xps3 atom selection have been fixed.
* version 3.1.4
** Some problems in finalization process of openGL rendering have been fixed.
* version 3.1.5
** The output of 'show xps3' command has been modified.
** Some problems in 'save png/jpeg' command have been fixed.
* version 3.1.6
** Some problems in loading an empty polygon file have been fixed.
* version 3.1.7
** Some problems in initialization process of the applet have been fixed.
* version 3.2
** 'show site' command has been added.
* version 3.3 beta 1
** Availabe JOGL version is restricted to JSR-231 beta 5 only.
* version 3.3
** Both the previous JOGL (version 1.1.1) and JSR-231 are available.
** The following commands have been added; 'set viewpoint', 'show viewpoint', 'set imagesize', and 'show imagesize'.
* version 3.3.1
** Some problems in reading a pdbMLplus file have been fixed.
* version 3.4
** PDB format version 3 can be processed.</text>
    <sha1>7174ebb98d1ed66fa7111203d2d396983d7f887b</sha1>
  </revision>
  <revision>
    <id>91</id>
    <parentid>90</parentid>
    <timestamp>2009-03-09T06:11:38Z</timestamp>
    <contributor>
      <username>127.0.0.1</username>
      <id>0</id>
    </contributor>
    <comment>/* How to use the minimum things */</comment>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="4152" xml:space="preserve">jV is an interactive 3D viewer program to visualize protein and nucleic acid molecules. The program reads in a PDBML file that is an XML format for PDB. Usual PDB format files are also accepted. More than one molecule files can be opened and displayed at the same time and their display models and transforms can be operated separately. In addition to molecule files, a polygon file written in XML can be read and displayed. More than one polygon files can be opened at the same time and superposed on molecule images. The [http://ef-site.hgc.jp/eF-site/schema/polygon12.xsd XML schema] of the polygon file is available. jV can perform an animation of molecules. The animation file is a PDB format file in which each frame is separated by a MODEL line.

jV runs on Java Runtime Environment ([http://java.sun.com/javase/index.jsp JRE]) and can be used both as a standalone program and an applet. The 3D rendering is performed with the use of [https://jogl.dev.java.net/ JOGL] API. The version requirements are as follows.

* JRE (includes Java Plug-in) 1.4.2 or later
* JOGL 1.1.1 or JSR-231

Here, [http://java.sun.com/products/plugin/ Java Plug-in] is required in order to use the program as an applet.

The program allows an interactive mouse control and command execution. The commnad syntax follows that of [http://www.rasmol.org/ Rasmol] with some modifications. In order to handle the transform of each molecule and polygon separately, every files are set to be either selected or not selected. The transform operation commands, such as rotate or translate, act only on selected files. On the other hand, every atoms in a molecule are also set to be either selected or not selected independently of whether the molecule itself is selected or not selected. Only selected atoms are the target of display model operations, such as wireframe or spacefill commands, and coloring operations.

== How to use the minimum things ==
The following table shows hot to do the minimum things with jV.&lt;br /&gt;
{| class="wikitable"
 |+ Action pair OS
 ! Action !! Window, Linux !! Mac OS X 
 |-
 ! rotate around X,Y axes
 | left drag | mouse drag
 |-
 ! rotate around Z axis
 | Shift + right drag || Shift + command + drag
 |-
 ! translate along X,Y axes
 | right drag || command + drag
 |-
 ! translate along Z axis (zoom in/out)
 | Shift + left drag || Shift + drag
 |}
For the detail,
* The reference manual [[jV3 Manual]] link:
* The install manual [[Installaion of jV3]]
Some examples
# Animation
# User jV with applet launcher

== Release note ==
Changes and improvements have been made as follows.

* version 3.1
** The following commands have been added; 'animrange', 'set adjustview', 'show godata', and 'show xps3'.
** The xPSSS expression has been added in order to select a group of atoms.
** Several public methods have been added to the applet so as to append molecule or polygon files after the applet started.
** The applet can send information about mouse-picked atoms to JavaScript.
* version 3.1.1
** Some problems in GUI menu [Options]-[Hetero Atoms] and [Hydrogens] have been fixed.
** Some problems in 'trace' command have been fixed.
* version 3.1.2
** eF-site ID has been changed to a new format.
* version 3.1.3
** Some problems in xps3 atom selection have been fixed.
* version 3.1.4
** Some problems in finalization process of openGL rendering have been fixed.
* version 3.1.5
** The output of 'show xps3' command has been modified.
** Some problems in 'save png/jpeg' command have been fixed.
* version 3.1.6
** Some problems in loading an empty polygon file have been fixed.
* version 3.1.7
** Some problems in initialization process of the applet have been fixed.
* version 3.2
** 'show site' command has been added.
* version 3.3 beta 1
** Availabe JOGL version is restricted to JSR-231 beta 5 only.
* version 3.3
** Both the previous JOGL (version 1.1.1) and JSR-231 are available.
** The following commands have been added; 'set viewpoint', 'show viewpoint', 'set imagesize', and 'show imagesize'.
* version 3.3.1
** Some problems in reading a pdbMLplus file have been fixed.
* version 3.4
** PDB format version 3 can be processed.</text>
    <sha1>1f2d14d1b207147ede9649bea5a1f07124b57aca</sha1>
  </revision>
  <revision>
    <id>92</id>
    <parentid>91</parentid>
    <timestamp>2009-03-09T06:12:45Z</timestamp>
    <contributor>
      <username>127.0.0.1</username>
      <id>0</id>
    </contributor>
    <comment>/* How to use the minimum things */</comment>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="4164" xml:space="preserve">jV is an interactive 3D viewer program to visualize protein and nucleic acid molecules. The program reads in a PDBML file that is an XML format for PDB. Usual PDB format files are also accepted. More than one molecule files can be opened and displayed at the same time and their display models and transforms can be operated separately. In addition to molecule files, a polygon file written in XML can be read and displayed. More than one polygon files can be opened at the same time and superposed on molecule images. The [http://ef-site.hgc.jp/eF-site/schema/polygon12.xsd XML schema] of the polygon file is available. jV can perform an animation of molecules. The animation file is a PDB format file in which each frame is separated by a MODEL line.

jV runs on Java Runtime Environment ([http://java.sun.com/javase/index.jsp JRE]) and can be used both as a standalone program and an applet. The 3D rendering is performed with the use of [https://jogl.dev.java.net/ JOGL] API. The version requirements are as follows.

* JRE (includes Java Plug-in) 1.4.2 or later
* JOGL 1.1.1 or JSR-231

Here, [http://java.sun.com/products/plugin/ Java Plug-in] is required in order to use the program as an applet.

The program allows an interactive mouse control and command execution. The commnad syntax follows that of [http://www.rasmol.org/ Rasmol] with some modifications. In order to handle the transform of each molecule and polygon separately, every files are set to be either selected or not selected. The transform operation commands, such as rotate or translate, act only on selected files. On the other hand, every atoms in a molecule are also set to be either selected or not selected independently of whether the molecule itself is selected or not selected. Only selected atoms are the target of display model operations, such as wireframe or spacefill commands, and coloring operations.

== How to use the minimum things ==
The following table shows hot to do the minimum things with jV.&lt;br /&gt;
{| class="wikitable" border="1"
 |+ Action pair OS
 ! Action !! Window, Linux !! Mac OS X 
 |-
 ! rotate around X,Y axes
 | left drag || mouse drag
 |-
 ! rotate around Z axis
 | Shift + right drag || Shift + command + drag
 |-
 ! translate along X,Y axes
 | right drag || command + drag
 |-
 ! translate along Z axis (zoom in/out)
 | Shift + left drag || Shift + drag
 |}
For the detail,
* The reference manual [[jV3 Manual]] link:
* The install manual [[Installaion of jV3]]
Some examples
# Animation
# User jV with applet launcher

== Release note ==
Changes and improvements have been made as follows.

* version 3.1
** The following commands have been added; 'animrange', 'set adjustview', 'show godata', and 'show xps3'.
** The xPSSS expression has been added in order to select a group of atoms.
** Several public methods have been added to the applet so as to append molecule or polygon files after the applet started.
** The applet can send information about mouse-picked atoms to JavaScript.
* version 3.1.1
** Some problems in GUI menu [Options]-[Hetero Atoms] and [Hydrogens] have been fixed.
** Some problems in 'trace' command have been fixed.
* version 3.1.2
** eF-site ID has been changed to a new format.
* version 3.1.3
** Some problems in xps3 atom selection have been fixed.
* version 3.1.4
** Some problems in finalization process of openGL rendering have been fixed.
* version 3.1.5
** The output of 'show xps3' command has been modified.
** Some problems in 'save png/jpeg' command have been fixed.
* version 3.1.6
** Some problems in loading an empty polygon file have been fixed.
* version 3.1.7
** Some problems in initialization process of the applet have been fixed.
* version 3.2
** 'show site' command has been added.
* version 3.3 beta 1
** Availabe JOGL version is restricted to JSR-231 beta 5 only.
* version 3.3
** Both the previous JOGL (version 1.1.1) and JSR-231 are available.
** The following commands have been added; 'set viewpoint', 'show viewpoint', 'set imagesize', and 'show imagesize'.
* version 3.3.1
** Some problems in reading a pdbMLplus file have been fixed.
* version 3.4
** PDB format version 3 can be processed.</text>
    <sha1>4d07ebffcd1340df85e0fc466cc19d436693b33e</sha1>
  </revision>
  <revision>
    <id>93</id>
    <parentid>92</parentid>
    <timestamp>2009-03-09T06:13:00Z</timestamp>
    <contributor>
      <username>127.0.0.1</username>
      <id>0</id>
    </contributor>
    <comment>/* How to use the minimum things */</comment>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="4153" xml:space="preserve">jV is an interactive 3D viewer program to visualize protein and nucleic acid molecules. The program reads in a PDBML file that is an XML format for PDB. Usual PDB format files are also accepted. More than one molecule files can be opened and displayed at the same time and their display models and transforms can be operated separately. In addition to molecule files, a polygon file written in XML can be read and displayed. More than one polygon files can be opened at the same time and superposed on molecule images. The [http://ef-site.hgc.jp/eF-site/schema/polygon12.xsd XML schema] of the polygon file is available. jV can perform an animation of molecules. The animation file is a PDB format file in which each frame is separated by a MODEL line.

jV runs on Java Runtime Environment ([http://java.sun.com/javase/index.jsp JRE]) and can be used both as a standalone program and an applet. The 3D rendering is performed with the use of [https://jogl.dev.java.net/ JOGL] API. The version requirements are as follows.

* JRE (includes Java Plug-in) 1.4.2 or later
* JOGL 1.1.1 or JSR-231

Here, [http://java.sun.com/products/plugin/ Java Plug-in] is required in order to use the program as an applet.

The program allows an interactive mouse control and command execution. The commnad syntax follows that of [http://www.rasmol.org/ Rasmol] with some modifications. In order to handle the transform of each molecule and polygon separately, every files are set to be either selected or not selected. The transform operation commands, such as rotate or translate, act only on selected files. On the other hand, every atoms in a molecule are also set to be either selected or not selected independently of whether the molecule itself is selected or not selected. Only selected atoms are the target of display model operations, such as wireframe or spacefill commands, and coloring operations.

== How to use the minimum things ==
The following table shows hot to do the minimum things with jV.&lt;br /&gt;
{| class="wikitable"
 |+ Action pair OS
 ! Action !! Window, Linux !! Mac OS X 
 |-
 ! rotate around X,Y axes
 | left drag || mouse drag
 |-
 ! rotate around Z axis
 | Shift + right drag || Shift + command + drag
 |-
 ! translate along X,Y axes
 | right drag || command + drag
 |-
 ! translate along Z axis (zoom in/out)
 | Shift + left drag || Shift + drag
 |}
For the detail,
* The reference manual [[jV3 Manual]] link:
* The install manual [[Installaion of jV3]]
Some examples
# Animation
# User jV with applet launcher

== Release note ==
Changes and improvements have been made as follows.

* version 3.1
** The following commands have been added; 'animrange', 'set adjustview', 'show godata', and 'show xps3'.
** The xPSSS expression has been added in order to select a group of atoms.
** Several public methods have been added to the applet so as to append molecule or polygon files after the applet started.
** The applet can send information about mouse-picked atoms to JavaScript.
* version 3.1.1
** Some problems in GUI menu [Options]-[Hetero Atoms] and [Hydrogens] have been fixed.
** Some problems in 'trace' command have been fixed.
* version 3.1.2
** eF-site ID has been changed to a new format.
* version 3.1.3
** Some problems in xps3 atom selection have been fixed.
* version 3.1.4
** Some problems in finalization process of openGL rendering have been fixed.
* version 3.1.5
** The output of 'show xps3' command has been modified.
** Some problems in 'save png/jpeg' command have been fixed.
* version 3.1.6
** Some problems in loading an empty polygon file have been fixed.
* version 3.1.7
** Some problems in initialization process of the applet have been fixed.
* version 3.2
** 'show site' command has been added.
* version 3.3 beta 1
** Availabe JOGL version is restricted to JSR-231 beta 5 only.
* version 3.3
** Both the previous JOGL (version 1.1.1) and JSR-231 are available.
** The following commands have been added; 'set viewpoint', 'show viewpoint', 'set imagesize', and 'show imagesize'.
* version 3.3.1
** Some problems in reading a pdbMLplus file have been fixed.
* version 3.4
** PDB format version 3 can be processed.</text>
    <sha1>b80818bfd6042f71f34a36c5bbfab03ec7f41350</sha1>
  </revision>
  <revision>
    <id>94</id>
    <parentid>93</parentid>
    <timestamp>2009-03-09T06:14:22Z</timestamp>
    <contributor>
      <username>127.0.0.1</username>
      <id>0</id>
    </contributor>
    <comment>/* How to use the minimum things */</comment>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="4186" xml:space="preserve">jV is an interactive 3D viewer program to visualize protein and nucleic acid molecules. The program reads in a PDBML file that is an XML format for PDB. Usual PDB format files are also accepted. More than one molecule files can be opened and displayed at the same time and their display models and transforms can be operated separately. In addition to molecule files, a polygon file written in XML can be read and displayed. More than one polygon files can be opened at the same time and superposed on molecule images. The [http://ef-site.hgc.jp/eF-site/schema/polygon12.xsd XML schema] of the polygon file is available. jV can perform an animation of molecules. The animation file is a PDB format file in which each frame is separated by a MODEL line.

jV runs on Java Runtime Environment ([http://java.sun.com/javase/index.jsp JRE]) and can be used both as a standalone program and an applet. The 3D rendering is performed with the use of [https://jogl.dev.java.net/ JOGL] API. The version requirements are as follows.

* JRE (includes Java Plug-in) 1.4.2 or later
* JOGL 1.1.1 or JSR-231

Here, [http://java.sun.com/products/plugin/ Java Plug-in] is required in order to use the program as an applet.

The program allows an interactive mouse control and command execution. The commnad syntax follows that of [http://www.rasmol.org/ Rasmol] with some modifications. In order to handle the transform of each molecule and polygon separately, every files are set to be either selected or not selected. The transform operation commands, such as rotate or translate, act only on selected files. On the other hand, every atoms in a molecule are also set to be either selected or not selected independently of whether the molecule itself is selected or not selected. Only selected atoms are the target of display model operations, such as wireframe or spacefill commands, and coloring operations.

== How to use the minimum things ==
The following table shows hot to do the minimum things with jV.&lt;br /&gt;
{| class="wikitable" border="1" style="margin:0 auto"
 |+ Action pair OS
 ! Action !! Window, Linux !! Mac OS X 
 |-
 ! rotate around X,Y axes
 | left drag || mouse drag
 |-
 ! rotate around Z axis
 | Shift + right drag || Shift + command + drag
 |-
 ! translate along X,Y axes
 | right drag || command + drag
 |-
 ! translate along Z axis (zoom in/out)
 | Shift + left drag || Shift + drag
 |}
For the detail,
* The reference manual [[jV3 Manual]] link:
* The install manual [[Installaion of jV3]]
Some examples
# Animation
# User jV with applet launcher

== Release note ==
Changes and improvements have been made as follows.

* version 3.1
** The following commands have been added; 'animrange', 'set adjustview', 'show godata', and 'show xps3'.
** The xPSSS expression has been added in order to select a group of atoms.
** Several public methods have been added to the applet so as to append molecule or polygon files after the applet started.
** The applet can send information about mouse-picked atoms to JavaScript.
* version 3.1.1
** Some problems in GUI menu [Options]-[Hetero Atoms] and [Hydrogens] have been fixed.
** Some problems in 'trace' command have been fixed.
* version 3.1.2
** eF-site ID has been changed to a new format.
* version 3.1.3
** Some problems in xps3 atom selection have been fixed.
* version 3.1.4
** Some problems in finalization process of openGL rendering have been fixed.
* version 3.1.5
** The output of 'show xps3' command has been modified.
** Some problems in 'save png/jpeg' command have been fixed.
* version 3.1.6
** Some problems in loading an empty polygon file have been fixed.
* version 3.1.7
** Some problems in initialization process of the applet have been fixed.
* version 3.2
** 'show site' command has been added.
* version 3.3 beta 1
** Availabe JOGL version is restricted to JSR-231 beta 5 only.
* version 3.3
** Both the previous JOGL (version 1.1.1) and JSR-231 are available.
** The following commands have been added; 'set viewpoint', 'show viewpoint', 'set imagesize', and 'show imagesize'.
* version 3.3.1
** Some problems in reading a pdbMLplus file have been fixed.
* version 3.4
** PDB format version 3 can be processed.</text>
    <sha1>b37e1e1453e0c34f5880105bb958f5d6591c3988</sha1>
  </revision>
  <revision>
    <id>95</id>
    <parentid>94</parentid>
    <timestamp>2009-03-09T06:15:21Z</timestamp>
    <contributor>
      <username>127.0.0.1</username>
      <id>0</id>
    </contributor>
    <comment>/* How to use the minimum things */</comment>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="4220" xml:space="preserve">jV is an interactive 3D viewer program to visualize protein and nucleic acid molecules. The program reads in a PDBML file that is an XML format for PDB. Usual PDB format files are also accepted. More than one molecule files can be opened and displayed at the same time and their display models and transforms can be operated separately. In addition to molecule files, a polygon file written in XML can be read and displayed. More than one polygon files can be opened at the same time and superposed on molecule images. The [http://ef-site.hgc.jp/eF-site/schema/polygon12.xsd XML schema] of the polygon file is available. jV can perform an animation of molecules. The animation file is a PDB format file in which each frame is separated by a MODEL line.

jV runs on Java Runtime Environment ([http://java.sun.com/javase/index.jsp JRE]) and can be used both as a standalone program and an applet. The 3D rendering is performed with the use of [https://jogl.dev.java.net/ JOGL] API. The version requirements are as follows.

* JRE (includes Java Plug-in) 1.4.2 or later
* JOGL 1.1.1 or JSR-231

Here, [http://java.sun.com/products/plugin/ Java Plug-in] is required in order to use the program as an applet.

The program allows an interactive mouse control and command execution. The commnad syntax follows that of [http://www.rasmol.org/ Rasmol] with some modifications. In order to handle the transform of each molecule and polygon separately, every files are set to be either selected or not selected. The transform operation commands, such as rotate or translate, act only on selected files. On the other hand, every atoms in a molecule are also set to be either selected or not selected independently of whether the molecule itself is selected or not selected. Only selected atoms are the target of display model operations, such as wireframe or spacefill commands, and coloring operations.

== How to use the minimum things ==
The following table shows hot to do the minimum things with jV.&lt;br /&gt;
{| class="wikitable" border="1" style="margin:0 auto" style="text-align:left" | 左寄せのセル
 ! Action !! Window, Linux !! Mac OS X 
 |-
 ! rotate around X,Y axes
 | left drag || mouse drag
 |-
 ! rotate around Z axis
 | Shift + right drag || Shift + command + drag
 |-
 ! translate along X,Y axes
 | right drag || command + drag
 |-
 ! translate along Z axis (zoom in/out)
 | Shift + left drag || Shift + drag
 |}
For the detail,
* The reference manual [[jV3 Manual]] link:
* The install manual [[Installaion of jV3]]
Some examples
# [[Animation]]
# [[User jV with applet launcher]]

== Release note ==
Changes and improvements have been made as follows.

* version 3.1
** The following commands have been added; 'animrange', 'set adjustview', 'show godata', and 'show xps3'.
** The xPSSS expression has been added in order to select a group of atoms.
** Several public methods have been added to the applet so as to append molecule or polygon files after the applet started.
** The applet can send information about mouse-picked atoms to JavaScript.
* version 3.1.1
** Some problems in GUI menu [Options]-[Hetero Atoms] and [Hydrogens] have been fixed.
** Some problems in 'trace' command have been fixed.
* version 3.1.2
** eF-site ID has been changed to a new format.
* version 3.1.3
** Some problems in xps3 atom selection have been fixed.
* version 3.1.4
** Some problems in finalization process of openGL rendering have been fixed.
* version 3.1.5
** The output of 'show xps3' command has been modified.
** Some problems in 'save png/jpeg' command have been fixed.
* version 3.1.6
** Some problems in loading an empty polygon file have been fixed.
* version 3.1.7
** Some problems in initialization process of the applet have been fixed.
* version 3.2
** 'show site' command has been added.
* version 3.3 beta 1
** Availabe JOGL version is restricted to JSR-231 beta 5 only.
* version 3.3
** Both the previous JOGL (version 1.1.1) and JSR-231 are available.
** The following commands have been added; 'set viewpoint', 'show viewpoint', 'set imagesize', and 'show imagesize'.
* version 3.3.1
** Some problems in reading a pdbMLplus file have been fixed.
* version 3.4
** PDB format version 3 can be processed.</text>
    <sha1>dfc431ebb85002fdb1420e48735031f24e9fff67</sha1>
  </revision>
  <revision>
    <id>96</id>
    <parentid>95</parentid>
    <timestamp>2009-03-09T06:16:04Z</timestamp>
    <contributor>
      <username>127.0.0.1</username>
      <id>0</id>
    </contributor>
    <comment>/* How to use the minimum things */</comment>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="4200" xml:space="preserve">jV is an interactive 3D viewer program to visualize protein and nucleic acid molecules. The program reads in a PDBML file that is an XML format for PDB. Usual PDB format files are also accepted. More than one molecule files can be opened and displayed at the same time and their display models and transforms can be operated separately. In addition to molecule files, a polygon file written in XML can be read and displayed. More than one polygon files can be opened at the same time and superposed on molecule images. The [http://ef-site.hgc.jp/eF-site/schema/polygon12.xsd XML schema] of the polygon file is available. jV can perform an animation of molecules. The animation file is a PDB format file in which each frame is separated by a MODEL line.

jV runs on Java Runtime Environment ([http://java.sun.com/javase/index.jsp JRE]) and can be used both as a standalone program and an applet. The 3D rendering is performed with the use of [https://jogl.dev.java.net/ JOGL] API. The version requirements are as follows.

* JRE (includes Java Plug-in) 1.4.2 or later
* JOGL 1.1.1 or JSR-231

Here, [http://java.sun.com/products/plugin/ Java Plug-in] is required in order to use the program as an applet.

The program allows an interactive mouse control and command execution. The commnad syntax follows that of [http://www.rasmol.org/ Rasmol] with some modifications. In order to handle the transform of each molecule and polygon separately, every files are set to be either selected or not selected. The transform operation commands, such as rotate or translate, act only on selected files. On the other hand, every atoms in a molecule are also set to be either selected or not selected independently of whether the molecule itself is selected or not selected. Only selected atoms are the target of display model operations, such as wireframe or spacefill commands, and coloring operations.

== How to use the minimum things ==
The following table shows hot to do the minimum things with jV.&lt;br /&gt;
{| class="wikitable" border="1" style="margin:0 auto" 
 ! Action !! Window, Linux !! Mac OS X 
 |-
 ! style="text-align:left" rotate around X,Y axes
 | left drag || mouse drag
 |-
 ! rotate around Z axis
 | Shift + right drag || Shift + command + drag
 |-
 ! translate along X,Y axes
 | right drag || command + drag
 |-
 ! translate along Z axis (zoom in/out)
 | Shift + left drag || Shift + drag
 |}
For the detail,
* The reference manual [[jV3 Manual]] link:
* The install manual [[Installaion of jV3]]
Some examples
# [[Animation]]
# [[User jV with applet launcher]]

== Release note ==
Changes and improvements have been made as follows.

* version 3.1
** The following commands have been added; 'animrange', 'set adjustview', 'show godata', and 'show xps3'.
** The xPSSS expression has been added in order to select a group of atoms.
** Several public methods have been added to the applet so as to append molecule or polygon files after the applet started.
** The applet can send information about mouse-picked atoms to JavaScript.
* version 3.1.1
** Some problems in GUI menu [Options]-[Hetero Atoms] and [Hydrogens] have been fixed.
** Some problems in 'trace' command have been fixed.
* version 3.1.2
** eF-site ID has been changed to a new format.
* version 3.1.3
** Some problems in xps3 atom selection have been fixed.
* version 3.1.4
** Some problems in finalization process of openGL rendering have been fixed.
* version 3.1.5
** The output of 'show xps3' command has been modified.
** Some problems in 'save png/jpeg' command have been fixed.
* version 3.1.6
** Some problems in loading an empty polygon file have been fixed.
* version 3.1.7
** Some problems in initialization process of the applet have been fixed.
* version 3.2
** 'show site' command has been added.
* version 3.3 beta 1
** Availabe JOGL version is restricted to JSR-231 beta 5 only.
* version 3.3
** Both the previous JOGL (version 1.1.1) and JSR-231 are available.
** The following commands have been added; 'set viewpoint', 'show viewpoint', 'set imagesize', and 'show imagesize'.
* version 3.3.1
** Some problems in reading a pdbMLplus file have been fixed.
* version 3.4
** PDB format version 3 can be processed.</text>
    <sha1>d349a20913011a037621cae40dc7668b6675a25b</sha1>
  </revision>
  <revision>
    <id>97</id>
    <parentid>96</parentid>
    <timestamp>2009-03-09T06:16:21Z</timestamp>
    <contributor>
      <username>127.0.0.1</username>
      <id>0</id>
    </contributor>
    <comment>/* How to use the minimum things */</comment>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="4202" xml:space="preserve">jV is an interactive 3D viewer program to visualize protein and nucleic acid molecules. The program reads in a PDBML file that is an XML format for PDB. Usual PDB format files are also accepted. More than one molecule files can be opened and displayed at the same time and their display models and transforms can be operated separately. In addition to molecule files, a polygon file written in XML can be read and displayed. More than one polygon files can be opened at the same time and superposed on molecule images. The [http://ef-site.hgc.jp/eF-site/schema/polygon12.xsd XML schema] of the polygon file is available. jV can perform an animation of molecules. The animation file is a PDB format file in which each frame is separated by a MODEL line.

jV runs on Java Runtime Environment ([http://java.sun.com/javase/index.jsp JRE]) and can be used both as a standalone program and an applet. The 3D rendering is performed with the use of [https://jogl.dev.java.net/ JOGL] API. The version requirements are as follows.

* JRE (includes Java Plug-in) 1.4.2 or later
* JOGL 1.1.1 or JSR-231

Here, [http://java.sun.com/products/plugin/ Java Plug-in] is required in order to use the program as an applet.

The program allows an interactive mouse control and command execution. The commnad syntax follows that of [http://www.rasmol.org/ Rasmol] with some modifications. In order to handle the transform of each molecule and polygon separately, every files are set to be either selected or not selected. The transform operation commands, such as rotate or translate, act only on selected files. On the other hand, every atoms in a molecule are also set to be either selected or not selected independently of whether the molecule itself is selected or not selected. Only selected atoms are the target of display model operations, such as wireframe or spacefill commands, and coloring operations.

== How to use the minimum things ==
The following table shows hot to do the minimum things with jV.&lt;br /&gt;
{| class="wikitable" border="1" style="margin:0 auto" 
 ! Action !! Window, Linux !! Mac OS X 
 |-
 ! style="text-align:left" | rotate around X,Y axes
 | left drag || mouse drag
 |-
 ! rotate around Z axis
 | Shift + right drag || Shift + command + drag
 |-
 ! translate along X,Y axes
 | right drag || command + drag
 |-
 ! translate along Z axis (zoom in/out)
 | Shift + left drag || Shift + drag
 |}
For the detail,
* The reference manual [[jV3 Manual]] link:
* The install manual [[Installaion of jV3]]
Some examples
# [[Animation]]
# [[User jV with applet launcher]]

== Release note ==
Changes and improvements have been made as follows.

* version 3.1
** The following commands have been added; 'animrange', 'set adjustview', 'show godata', and 'show xps3'.
** The xPSSS expression has been added in order to select a group of atoms.
** Several public methods have been added to the applet so as to append molecule or polygon files after the applet started.
** The applet can send information about mouse-picked atoms to JavaScript.
* version 3.1.1
** Some problems in GUI menu [Options]-[Hetero Atoms] and [Hydrogens] have been fixed.
** Some problems in 'trace' command have been fixed.
* version 3.1.2
** eF-site ID has been changed to a new format.
* version 3.1.3
** Some problems in xps3 atom selection have been fixed.
* version 3.1.4
** Some problems in finalization process of openGL rendering have been fixed.
* version 3.1.5
** The output of 'show xps3' command has been modified.
** Some problems in 'save png/jpeg' command have been fixed.
* version 3.1.6
** Some problems in loading an empty polygon file have been fixed.
* version 3.1.7
** Some problems in initialization process of the applet have been fixed.
* version 3.2
** 'show site' command has been added.
* version 3.3 beta 1
** Availabe JOGL version is restricted to JSR-231 beta 5 only.
* version 3.3
** Both the previous JOGL (version 1.1.1) and JSR-231 are available.
** The following commands have been added; 'set viewpoint', 'show viewpoint', 'set imagesize', and 'show imagesize'.
* version 3.3.1
** Some problems in reading a pdbMLplus file have been fixed.
* version 3.4
** PDB format version 3 can be processed.</text>
    <sha1>357dafc0a361a6ad8a725bcda5df178d3a23a429</sha1>
  </revision>
  <revision>
    <id>98</id>
    <parentid>97</parentid>
    <timestamp>2009-03-09T06:16:37Z</timestamp>
    <contributor>
      <username>127.0.0.1</username>
      <id>0</id>
    </contributor>
    <comment>/* How to use the minimum things */</comment>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="4280" xml:space="preserve">jV is an interactive 3D viewer program to visualize protein and nucleic acid molecules. The program reads in a PDBML file that is an XML format for PDB. Usual PDB format files are also accepted. More than one molecule files can be opened and displayed at the same time and their display models and transforms can be operated separately. In addition to molecule files, a polygon file written in XML can be read and displayed. More than one polygon files can be opened at the same time and superposed on molecule images. The [http://ef-site.hgc.jp/eF-site/schema/polygon12.xsd XML schema] of the polygon file is available. jV can perform an animation of molecules. The animation file is a PDB format file in which each frame is separated by a MODEL line.

jV runs on Java Runtime Environment ([http://java.sun.com/javase/index.jsp JRE]) and can be used both as a standalone program and an applet. The 3D rendering is performed with the use of [https://jogl.dev.java.net/ JOGL] API. The version requirements are as follows.

* JRE (includes Java Plug-in) 1.4.2 or later
* JOGL 1.1.1 or JSR-231

Here, [http://java.sun.com/products/plugin/ Java Plug-in] is required in order to use the program as an applet.

The program allows an interactive mouse control and command execution. The commnad syntax follows that of [http://www.rasmol.org/ Rasmol] with some modifications. In order to handle the transform of each molecule and polygon separately, every files are set to be either selected or not selected. The transform operation commands, such as rotate or translate, act only on selected files. On the other hand, every atoms in a molecule are also set to be either selected or not selected independently of whether the molecule itself is selected or not selected. Only selected atoms are the target of display model operations, such as wireframe or spacefill commands, and coloring operations.

== How to use the minimum things ==
The following table shows hot to do the minimum things with jV.&lt;br /&gt;
{| class="wikitable" border="1" style="margin:0 auto" 
 ! Action !! Window, Linux !! Mac OS X 
 |-
 ! style="text-align:left" | rotate around X,Y axes
 | left drag || mouse drag
 |-
 ! style="text-align:left" | rotate around Z axis
 | Shift + right drag || Shift + command + drag
 |-
 ! style="text-align:left" | translate along X,Y axes
 | right drag || command + drag
 |-
 ! style="text-align:left" | translate along Z axis (zoom in/out)
 | Shift + left drag || Shift + drag
 |}
For the detail,
* The reference manual [[jV3 Manual]] link:
* The install manual [[Installaion of jV3]]
Some examples
# [[Animation]]
# [[User jV with applet launcher]]

== Release note ==
Changes and improvements have been made as follows.

* version 3.1
** The following commands have been added; 'animrange', 'set adjustview', 'show godata', and 'show xps3'.
** The xPSSS expression has been added in order to select a group of atoms.
** Several public methods have been added to the applet so as to append molecule or polygon files after the applet started.
** The applet can send information about mouse-picked atoms to JavaScript.
* version 3.1.1
** Some problems in GUI menu [Options]-[Hetero Atoms] and [Hydrogens] have been fixed.
** Some problems in 'trace' command have been fixed.
* version 3.1.2
** eF-site ID has been changed to a new format.
* version 3.1.3
** Some problems in xps3 atom selection have been fixed.
* version 3.1.4
** Some problems in finalization process of openGL rendering have been fixed.
* version 3.1.5
** The output of 'show xps3' command has been modified.
** Some problems in 'save png/jpeg' command have been fixed.
* version 3.1.6
** Some problems in loading an empty polygon file have been fixed.
* version 3.1.7
** Some problems in initialization process of the applet have been fixed.
* version 3.2
** 'show site' command has been added.
* version 3.3 beta 1
** Availabe JOGL version is restricted to JSR-231 beta 5 only.
* version 3.3
** Both the previous JOGL (version 1.1.1) and JSR-231 are available.
** The following commands have been added; 'set viewpoint', 'show viewpoint', 'set imagesize', and 'show imagesize'.
* version 3.3.1
** Some problems in reading a pdbMLplus file have been fixed.
* version 3.4
** PDB format version 3 can be processed.</text>
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  </revision>
  <revision>
    <id>99</id>
    <parentid>98</parentid>
    <timestamp>2009-03-09T06:22:08Z</timestamp>
    <contributor>
      <username>127.0.0.1</username>
      <id>0</id>
    </contributor>
    <comment>/* How to use the minimum things */</comment>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="4261" xml:space="preserve">jV is an interactive 3D viewer program to visualize protein and nucleic acid molecules. The program reads in a PDBML file that is an XML format for PDB. Usual PDB format files are also accepted. More than one molecule files can be opened and displayed at the same time and their display models and transforms can be operated separately. In addition to molecule files, a polygon file written in XML can be read and displayed. More than one polygon files can be opened at the same time and superposed on molecule images. The [http://ef-site.hgc.jp/eF-site/schema/polygon12.xsd XML schema] of the polygon file is available. jV can perform an animation of molecules. The animation file is a PDB format file in which each frame is separated by a MODEL line.

jV runs on Java Runtime Environment ([http://java.sun.com/javase/index.jsp JRE]) and can be used both as a standalone program and an applet. The 3D rendering is performed with the use of [https://jogl.dev.java.net/ JOGL] API. The version requirements are as follows.

* JRE (includes Java Plug-in) 1.4.2 or later
* JOGL 1.1.1 or JSR-231

Here, [http://java.sun.com/products/plugin/ Java Plug-in] is required in order to use the program as an applet.

The program allows an interactive mouse control and command execution. The commnad syntax follows that of [http://www.rasmol.org/ Rasmol] with some modifications. In order to handle the transform of each molecule and polygon separately, every files are set to be either selected or not selected. The transform operation commands, such as rotate or translate, act only on selected files. On the other hand, every atoms in a molecule are also set to be either selected or not selected independently of whether the molecule itself is selected or not selected. Only selected atoms are the target of display model operations, such as wireframe or spacefill commands, and coloring operations.

== How to use ==
The following table shows hot to do the minimum things with jV.&lt;br /&gt;
{| class="wikitable" border="1" style="margin:0 auto" 
 ! Action !! Window, Linux !! Mac OS X 
 |-
 ! style="text-align:left" | rotate around X,Y axes
 | left drag || mouse drag
 |-
 ! style="text-align:left" | rotate around Z axis
 | Shift + right drag || Shift + command + drag
 |-
 ! style="text-align:left" | translate along X,Y axes
 | right drag || command + drag
 |-
 ! style="text-align:left" | translate along Z axis (zoom in/out)
 | Shift + left drag || Shift + drag
 |}
For the detail,
* The reference manual [[jV3 Manual]] link:
* The install manual [[Installaion of jV3]]
Some examples
# [[Animation]]
# [[User jV with applet launcher]]

== Release note ==
Changes and improvements have been made as follows.

* version 3.1
** The following commands have been added; 'animrange', 'set adjustview', 'show godata', and 'show xps3'.
** The xPSSS expression has been added in order to select a group of atoms.
** Several public methods have been added to the applet so as to append molecule or polygon files after the applet started.
** The applet can send information about mouse-picked atoms to JavaScript.
* version 3.1.1
** Some problems in GUI menu [Options]-[Hetero Atoms] and [Hydrogens] have been fixed.
** Some problems in 'trace' command have been fixed.
* version 3.1.2
** eF-site ID has been changed to a new format.
* version 3.1.3
** Some problems in xps3 atom selection have been fixed.
* version 3.1.4
** Some problems in finalization process of openGL rendering have been fixed.
* version 3.1.5
** The output of 'show xps3' command has been modified.
** Some problems in 'save png/jpeg' command have been fixed.
* version 3.1.6
** Some problems in loading an empty polygon file have been fixed.
* version 3.1.7
** Some problems in initialization process of the applet have been fixed.
* version 3.2
** 'show site' command has been added.
* version 3.3 beta 1
** Availabe JOGL version is restricted to JSR-231 beta 5 only.
* version 3.3
** Both the previous JOGL (version 1.1.1) and JSR-231 are available.
** The following commands have been added; 'set viewpoint', 'show viewpoint', 'set imagesize', and 'show imagesize'.
* version 3.3.1
** Some problems in reading a pdbMLplus file have been fixed.
* version 3.4
** PDB format version 3 can be processed.</text>
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<page arvcontinue="20090303095249|51">
  <title>Animation</title>
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    <comment>Created page with 'A brief introduction to user animation in jV.  == Step-1: Minimum Example == To display the animation on the web using jV, you should prepare an animation file and a html file.  ...'</comment>
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    <format>text/x-wiki</format>
    <text bytes="1174" xml:space="preserve">A brief introduction to user animation in jV.

== Step-1: Minimum Example ==
To display the animation on the web using jV, you should prepare an animation file and a html file.

The format of the animation file is the same one as the PDB format of the NMR structure with multiple models. In other words, each frame is separated with MODEL recored. An example animation file can be obtained from [[here]].

The html file, shown below, should contain the applet tag to activate jV and it requires code parameter, codebase parameter and archive parameter. The parameter “code” is a kind of magic word to use jV. The codebase points the relative path to the jV jar file existing from the html file is stored, and archive parameter indicates the name of jar file. The jar file can be obtained from [[DOWNLOAD page]].

 &lt;html&gt;&lt;body&gt;
 &lt;applet code="org.pdbj.viewer.gui.ViewerApplet"
    codebase="."
    archive="jv3_3.jar"
    width=400 height=400
    &lt;param name="animURL"
        value="http://ef-site.hgc.jp/jV/example/1byi_1-anm.pdg"&gt;
    &lt;param name="commands"
        value="select all;wireframe on;anim forward"&gt;
 &lt;/applet&gt;
 &lt;/body&gt;&lt;/html&gt;

== Step-2:Make more fancy ==</text>
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</page>
<page arvcontinue="20090309064103|101">
  <title>Animation</title>
  <ns>0</ns>
  <id>12</id>
  <revision>
    <id>101</id>
    <parentid>100</parentid>
    <timestamp>2009-03-09T06:41:03Z</timestamp>
    <contributor>
      <username>127.0.0.1</username>
      <id>0</id>
    </contributor>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="2862" xml:space="preserve">A brief introduction to user animation in jV.

== Step-1: Minimum Example ==
To display the animation on the web using jV, you should prepare an animation file and a html file.

The format of the animation file is the same one as the PDB format of the NMR structure with multiple models. In other words, each frame is separated with MODEL recored. An example animation file can be obtained from [[here]].

The html file, shown below, should contain the applet tag to activate jV and it requires code parameter, codebase parameter and archive parameter. The parameter “code” is a kind of magic word to use jV. The codebase points the relative path to the jV jar file existing from the html file is stored, and archive parameter indicates the name of jar file. The jar file can be obtained from [[DOWNLOAD page]].

 &lt;html&gt;&lt;body&gt;
 &lt;applet code="org.pdbj.viewer.gui.ViewerApplet"
    codebase="."
    archive="jv3_3.jar"
    width=400 height=400
    &lt;param name="animURL"
        value="http://ef-site.hgc.jp/jV/example/1byi_1-anm.pdg"&gt;
    &lt;param name="commands"
        value="select all;wireframe on;anim forward"&gt;
 &lt;/applet&gt;
 &lt;/body&gt;&lt;/html&gt;

== Step-2:Make more fancy ==
To display cartoon and color from N-terminal to C-terminal in white background,change “wireframe on” to “cartoon on” &amp; add “color group;”
&lt;font size="1"&gt;NOTE: As in this example, any jV code (similar to Rasmol script) can be used in the commands parameter. And each jV command should be separated by “;”.&lt;/font&gt;
Complete Code until here.

 &lt;html&gt;&lt;body&gt;
 &lt;applet code="org.pdbj.viewer.gui.ViewerApplet"
    codebase="."
    archive="jv3_3.jar"
    width=400 height=400
    &lt;param name="animURL"
        value="http://ef-site.hgc.jp/jV/example/1byi_1-anm.pdb"&gt;
    &lt;param name="commands"
        value="background white;select all;background white;
               cartoon on; anim forward"&gt;
 &lt;/applet&gt;
 &lt;/body&gt;&lt;/html&gt;

== Step-3: Swing &amp; move quick! ==
To control the speed of animation and the animation mode (shown once, swing, or loop), add two commands, “animmode swing; animspeed 20;” (20 is just an example).

 &lt;html&gt;&lt;body&gt;
 &lt;applet code="org.pdbj.viewer.gui.ViewerApplet"
    codebase="."
    archive="jv3_3.jar"
    width=400 height=400
    &lt;param name="animURL"
        value="http://ef-site.hgc.jp/jV/example/1byi_1-anm.pdb"&gt;
    &lt;param name="commands"
        value="background white;select all;background white;
               cartoon on;
               animmode swing;animspeed 20;
               anim forward"&gt;
 &lt;/applet&gt;
 &lt;/body&gt;&lt;/html&gt;

== Step-4: Advance usage in ProMode ==
ProMode is a database of normal mode analysis of proteins. In the database Animations are provided with jV. You can see the [http://cube.socs.waseda.ac.jp/pages/jsp/indexn.jsp?cont=menu-jv&amp;mode=1&amp;sec=dif&amp;protein=1byi#bar case of 1BYI], which is used as an example of this page.</text>
    <sha1>78cd3fdbf83905ca26fa762fcce92449bab8fceb</sha1>
  </revision>
  <revision>
    <id>102</id>
    <parentid>101</parentid>
    <timestamp>2009-03-09T06:41:39Z</timestamp>
    <contributor>
      <username>127.0.0.1</username>
      <id>0</id>
    </contributor>
    <comment>/* Step-2:Make more fancy */</comment>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="2874" xml:space="preserve">A brief introduction to user animation in jV.

== Step-1: Minimum Example ==
To display the animation on the web using jV, you should prepare an animation file and a html file.

The format of the animation file is the same one as the PDB format of the NMR structure with multiple models. In other words, each frame is separated with MODEL recored. An example animation file can be obtained from [[here]].

The html file, shown below, should contain the applet tag to activate jV and it requires code parameter, codebase parameter and archive parameter. The parameter “code” is a kind of magic word to use jV. The codebase points the relative path to the jV jar file existing from the html file is stored, and archive parameter indicates the name of jar file. The jar file can be obtained from [[DOWNLOAD page]].

 &lt;html&gt;&lt;body&gt;
 &lt;applet code="org.pdbj.viewer.gui.ViewerApplet"
    codebase="."
    archive="jv3_3.jar"
    width=400 height=400
    &lt;param name="animURL"
        value="http://ef-site.hgc.jp/jV/example/1byi_1-anm.pdg"&gt;
    &lt;param name="commands"
        value="select all;wireframe on;anim forward"&gt;
 &lt;/applet&gt;
 &lt;/body&gt;&lt;/html&gt;

== Step-2:Make more fancy ==
To display cartoon and color from N-terminal to C-terminal in white background,change “wireframe on” to “cartoon on” &amp; add “color group;”&lt;br /&gt;
&lt;font size="1"&gt;NOTE: As in this example, any jV code (similar to Rasmol script) can be used in the commands parameter. And each jV command should be separated by “;”.&lt;/font&gt;&lt;br /&gt;
Complete Code until here.

 &lt;html&gt;&lt;body&gt;
 &lt;applet code="org.pdbj.viewer.gui.ViewerApplet"
    codebase="."
    archive="jv3_3.jar"
    width=400 height=400
    &lt;param name="animURL"
        value="http://ef-site.hgc.jp/jV/example/1byi_1-anm.pdb"&gt;
    &lt;param name="commands"
        value="background white;select all;background white;
               cartoon on; anim forward"&gt;
 &lt;/applet&gt;
 &lt;/body&gt;&lt;/html&gt;

== Step-3: Swing &amp; move quick! ==
To control the speed of animation and the animation mode (shown once, swing, or loop), add two commands, “animmode swing; animspeed 20;” (20 is just an example).

 &lt;html&gt;&lt;body&gt;
 &lt;applet code="org.pdbj.viewer.gui.ViewerApplet"
    codebase="."
    archive="jv3_3.jar"
    width=400 height=400
    &lt;param name="animURL"
        value="http://ef-site.hgc.jp/jV/example/1byi_1-anm.pdb"&gt;
    &lt;param name="commands"
        value="background white;select all;background white;
               cartoon on;
               animmode swing;animspeed 20;
               anim forward"&gt;
 &lt;/applet&gt;
 &lt;/body&gt;&lt;/html&gt;

== Step-4: Advance usage in ProMode ==
ProMode is a database of normal mode analysis of proteins. In the database Animations are provided with jV. You can see the [http://cube.socs.waseda.ac.jp/pages/jsp/indexn.jsp?cont=menu-jv&amp;mode=1&amp;sec=dif&amp;protein=1byi#bar case of 1BYI], which is used as an example of this page.</text>
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  </revision>
  <revision>
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    <parentid>102</parentid>
    <timestamp>2009-03-09T06:42:34Z</timestamp>
    <contributor>
      <username>127.0.0.1</username>
      <id>0</id>
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    <model>wikitext</model>
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    <text bytes="2910" xml:space="preserve">A brief introduction to user animation in jV.
{| style="float:right"
 |__TOC__
 |}
== Step-1: Minimum Example ==
To display the animation on the web using jV, you should prepare an animation file and a html file.

The format of the animation file is the same one as the PDB format of the NMR structure with multiple models. In other words, each frame is separated with MODEL recored. An example animation file can be obtained from [[here]].

The html file, shown below, should contain the applet tag to activate jV and it requires code parameter, codebase parameter and archive parameter. The parameter “code” is a kind of magic word to use jV. The codebase points the relative path to the jV jar file existing from the html file is stored, and archive parameter indicates the name of jar file. The jar file can be obtained from [[DOWNLOAD page]].

 &lt;html&gt;&lt;body&gt;
 &lt;applet code="org.pdbj.viewer.gui.ViewerApplet"
    codebase="."
    archive="jv3_3.jar"
    width=400 height=400
    &lt;param name="animURL"
        value="http://ef-site.hgc.jp/jV/example/1byi_1-anm.pdg"&gt;
    &lt;param name="commands"
        value="select all;wireframe on;anim forward"&gt;
 &lt;/applet&gt;
 &lt;/body&gt;&lt;/html&gt;

== Step-2:Make more fancy ==
To display cartoon and color from N-terminal to C-terminal in white background,change “wireframe on” to “cartoon on” &amp; add “color group;”&lt;br /&gt;
&lt;font size="1"&gt;NOTE: As in this example, any jV code (similar to Rasmol script) can be used in the commands parameter. And each jV command should be separated by “;”.&lt;/font&gt;&lt;br /&gt;
Complete Code until here.

 &lt;html&gt;&lt;body&gt;
 &lt;applet code="org.pdbj.viewer.gui.ViewerApplet"
    codebase="."
    archive="jv3_3.jar"
    width=400 height=400
    &lt;param name="animURL"
        value="http://ef-site.hgc.jp/jV/example/1byi_1-anm.pdb"&gt;
    &lt;param name="commands"
        value="background white;select all;background white;
               cartoon on; anim forward"&gt;
 &lt;/applet&gt;
 &lt;/body&gt;&lt;/html&gt;

== Step-3: Swing &amp; move quick! ==
To control the speed of animation and the animation mode (shown once, swing, or loop), add two commands, “animmode swing; animspeed 20;” (20 is just an example).

 &lt;html&gt;&lt;body&gt;
 &lt;applet code="org.pdbj.viewer.gui.ViewerApplet"
    codebase="."
    archive="jv3_3.jar"
    width=400 height=400
    &lt;param name="animURL"
        value="http://ef-site.hgc.jp/jV/example/1byi_1-anm.pdb"&gt;
    &lt;param name="commands"
        value="background white;select all;background white;
               cartoon on;
               animmode swing;animspeed 20;
               anim forward"&gt;
 &lt;/applet&gt;
 &lt;/body&gt;&lt;/html&gt;

== Step-4: Advance usage in ProMode ==
ProMode is a database of normal mode analysis of proteins. In the database Animations are provided with jV. You can see the [http://cube.socs.waseda.ac.jp/pages/jsp/indexn.jsp?cont=menu-jv&amp;mode=1&amp;sec=dif&amp;protein=1byi#bar case of 1BYI], which is used as an example of this page.</text>
    <sha1>e29276fff85497ebf71041f35dd7245d336bcaba</sha1>
  </revision>
  <revision>
    <id>105</id>
    <parentid>104</parentid>
    <timestamp>2009-03-09T06:42:51Z</timestamp>
    <contributor>
      <username>127.0.0.1</username>
      <id>0</id>
    </contributor>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="2911" xml:space="preserve">{| style="float:right"
 |__TOC__
 |}
A brief introduction to user animation in jV.

== Step-1: Minimum Example ==
To display the animation on the web using jV, you should prepare an animation file and a html file.

The format of the animation file is the same one as the PDB format of the NMR structure with multiple models. In other words, each frame is separated with MODEL recored. An example animation file can be obtained from [[here]].

The html file, shown below, should contain the applet tag to activate jV and it requires code parameter, codebase parameter and archive parameter. The parameter “code” is a kind of magic word to use jV. The codebase points the relative path to the jV jar file existing from the html file is stored, and archive parameter indicates the name of jar file. The jar file can be obtained from [[DOWNLOAD page]].

 &lt;html&gt;&lt;body&gt;
 &lt;applet code="org.pdbj.viewer.gui.ViewerApplet"
    codebase="."
    archive="jv3_3.jar"
    width=400 height=400
    &lt;param name="animURL"
        value="http://ef-site.hgc.jp/jV/example/1byi_1-anm.pdg"&gt;
    &lt;param name="commands"
        value="select all;wireframe on;anim forward"&gt;
 &lt;/applet&gt;
 &lt;/body&gt;&lt;/html&gt;

== Step-2:Make more fancy ==
To display cartoon and color from N-terminal to C-terminal in white background,change “wireframe on” to “cartoon on” &amp; add “color group;”&lt;br /&gt;
&lt;font size="1"&gt;NOTE: As in this example, any jV code (similar to Rasmol script) can be used in the commands parameter. And each jV command should be separated by “;”.&lt;/font&gt;&lt;br /&gt;
Complete Code until here.

 &lt;html&gt;&lt;body&gt;
 &lt;applet code="org.pdbj.viewer.gui.ViewerApplet"
    codebase="."
    archive="jv3_3.jar"
    width=400 height=400
    &lt;param name="animURL"
        value="http://ef-site.hgc.jp/jV/example/1byi_1-anm.pdb"&gt;
    &lt;param name="commands"
        value="background white;select all;background white;
               cartoon on; anim forward"&gt;
 &lt;/applet&gt;
 &lt;/body&gt;&lt;/html&gt;

== Step-3: Swing &amp; move quick! ==
To control the speed of animation and the animation mode (shown once, swing, or loop), add two commands, “animmode swing; animspeed 20;” (20 is just an example).

 &lt;html&gt;&lt;body&gt;
 &lt;applet code="org.pdbj.viewer.gui.ViewerApplet"
    codebase="."
    archive="jv3_3.jar"
    width=400 height=400
    &lt;param name="animURL"
        value="http://ef-site.hgc.jp/jV/example/1byi_1-anm.pdb"&gt;
    &lt;param name="commands"
        value="background white;select all;background white;
               cartoon on;
               animmode swing;animspeed 20;
               anim forward"&gt;
 &lt;/applet&gt;
 &lt;/body&gt;&lt;/html&gt;

== Step-4: Advance usage in ProMode ==
ProMode is a database of normal mode analysis of proteins. In the database Animations are provided with jV. You can see the [http://cube.socs.waseda.ac.jp/pages/jsp/indexn.jsp?cont=menu-jv&amp;mode=1&amp;sec=dif&amp;protein=1byi#bar case of 1BYI], which is used as an example of this page.</text>
    <sha1>31a3995b700c8ae05fd7067128d49fd4679ab492</sha1>
  </revision>
  <revision>
    <id>107</id>
    <parentid>105</parentid>
    <timestamp>2009-03-09T06:47:15Z</timestamp>
    <contributor>
      <username>127.0.0.1</username>
      <id>0</id>
    </contributor>
    <comment>/* Step-4: Advance usage in ProMode */</comment>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="3002" xml:space="preserve">{| style="float:right"
 |__TOC__
 |}
A brief introduction to user animation in jV.

== Step-1: Minimum Example ==
To display the animation on the web using jV, you should prepare an animation file and a html file.

The format of the animation file is the same one as the PDB format of the NMR structure with multiple models. In other words, each frame is separated with MODEL recored. An example animation file can be obtained from [[here]].

The html file, shown below, should contain the applet tag to activate jV and it requires code parameter, codebase parameter and archive parameter. The parameter “code” is a kind of magic word to use jV. The codebase points the relative path to the jV jar file existing from the html file is stored, and archive parameter indicates the name of jar file. The jar file can be obtained from [[DOWNLOAD page]].

 &lt;html&gt;&lt;body&gt;
 &lt;applet code="org.pdbj.viewer.gui.ViewerApplet"
    codebase="."
    archive="jv3_3.jar"
    width=400 height=400
    &lt;param name="animURL"
        value="http://ef-site.hgc.jp/jV/example/1byi_1-anm.pdg"&gt;
    &lt;param name="commands"
        value="select all;wireframe on;anim forward"&gt;
 &lt;/applet&gt;
 &lt;/body&gt;&lt;/html&gt;

== Step-2:Make more fancy ==
To display cartoon and color from N-terminal to C-terminal in white background,change “wireframe on” to “cartoon on” &amp; add “color group;”&lt;br /&gt;
&lt;font size="1"&gt;NOTE: As in this example, any jV code (similar to Rasmol script) can be used in the commands parameter. And each jV command should be separated by “;”.&lt;/font&gt;&lt;br /&gt;
Complete Code until here.

 &lt;html&gt;&lt;body&gt;
 &lt;applet code="org.pdbj.viewer.gui.ViewerApplet"
    codebase="."
    archive="jv3_3.jar"
    width=400 height=400
    &lt;param name="animURL"
        value="http://ef-site.hgc.jp/jV/example/1byi_1-anm.pdb"&gt;
    &lt;param name="commands"
        value="background white;select all;background white;
               cartoon on; anim forward"&gt;
 &lt;/applet&gt;
 &lt;/body&gt;&lt;/html&gt;

== Step-3: Swing &amp; move quick! ==
To control the speed of animation and the animation mode (shown once, swing, or loop), add two commands, “animmode swing; animspeed 20;” (20 is just an example).

 &lt;html&gt;&lt;body&gt;
 &lt;applet code="org.pdbj.viewer.gui.ViewerApplet"
    codebase="."
    archive="jv3_3.jar"
    width=400 height=400
    &lt;param name="animURL"
        value="http://ef-site.hgc.jp/jV/example/1byi_1-anm.pdb"&gt;
    &lt;param name="commands"
        value="background white;select all;background white;
               cartoon on;
               animmode swing;animspeed 20;
               anim forward"&gt;
 &lt;/applet&gt;
 &lt;/body&gt;&lt;/html&gt;

== Step-4: Advance usage in ProMode ==
[[File:Download.png|right|link=http://cube.socs.waseda.ac.jp/pages/jsp/index.jsp|ProMode]] ProMode is a database of normal mode analysis of proteins. In the database Animations are provided with jV. You can see the [http://cube.socs.waseda.ac.jp/pages/jsp/indexn.jsp?cont=menu-jv&amp;mode=1&amp;sec=dif&amp;protein=1byi#bar case of 1BYI], which is used as an example of this page.</text>
    <sha1>666fe29891558aec5cc2428aa44b345964155cd3</sha1>
  </revision>
  <revision>
    <id>109</id>
    <parentid>107</parentid>
    <timestamp>2009-03-09T06:49:03Z</timestamp>
    <contributor>
      <username>JVuser</username>
      <id>2</id>
    </contributor>
    <comment>/* Step-4: Advance usage in ProMode */</comment>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="3001" xml:space="preserve">{| style="float:right"
 |__TOC__
 |}
A brief introduction to user animation in jV.

== Step-1: Minimum Example ==
To display the animation on the web using jV, you should prepare an animation file and a html file.

The format of the animation file is the same one as the PDB format of the NMR structure with multiple models. In other words, each frame is separated with MODEL recored. An example animation file can be obtained from [[here]].

The html file, shown below, should contain the applet tag to activate jV and it requires code parameter, codebase parameter and archive parameter. The parameter “code” is a kind of magic word to use jV. The codebase points the relative path to the jV jar file existing from the html file is stored, and archive parameter indicates the name of jar file. The jar file can be obtained from [[DOWNLOAD page]].

 &lt;html&gt;&lt;body&gt;
 &lt;applet code="org.pdbj.viewer.gui.ViewerApplet"
    codebase="."
    archive="jv3_3.jar"
    width=400 height=400
    &lt;param name="animURL"
        value="http://ef-site.hgc.jp/jV/example/1byi_1-anm.pdg"&gt;
    &lt;param name="commands"
        value="select all;wireframe on;anim forward"&gt;
 &lt;/applet&gt;
 &lt;/body&gt;&lt;/html&gt;

== Step-2:Make more fancy ==
To display cartoon and color from N-terminal to C-terminal in white background,change “wireframe on” to “cartoon on” &amp; add “color group;”&lt;br /&gt;
&lt;font size="1"&gt;NOTE: As in this example, any jV code (similar to Rasmol script) can be used in the commands parameter. And each jV command should be separated by “;”.&lt;/font&gt;&lt;br /&gt;
Complete Code until here.

 &lt;html&gt;&lt;body&gt;
 &lt;applet code="org.pdbj.viewer.gui.ViewerApplet"
    codebase="."
    archive="jv3_3.jar"
    width=400 height=400
    &lt;param name="animURL"
        value="http://ef-site.hgc.jp/jV/example/1byi_1-anm.pdb"&gt;
    &lt;param name="commands"
        value="background white;select all;background white;
               cartoon on; anim forward"&gt;
 &lt;/applet&gt;
 &lt;/body&gt;&lt;/html&gt;

== Step-3: Swing &amp; move quick! ==
To control the speed of animation and the animation mode (shown once, swing, or loop), add two commands, “animmode swing; animspeed 20;” (20 is just an example).

 &lt;html&gt;&lt;body&gt;
 &lt;applet code="org.pdbj.viewer.gui.ViewerApplet"
    codebase="."
    archive="jv3_3.jar"
    width=400 height=400
    &lt;param name="animURL"
        value="http://ef-site.hgc.jp/jV/example/1byi_1-anm.pdb"&gt;
    &lt;param name="commands"
        value="background white;select all;background white;
               cartoon on;
               animmode swing;animspeed 20;
               anim forward"&gt;
 &lt;/applet&gt;
 &lt;/body&gt;&lt;/html&gt;

== Step-4: Advance usage in ProMode ==
[[File:Promode.jpg|right|link=http://cube.socs.waseda.ac.jp/pages/jsp/index.jsp|ProMode]] ProMode is a database of normal mode analysis of proteins. In the database Animations are provided with jV. You can see the [http://cube.socs.waseda.ac.jp/pages/jsp/indexn.jsp?cont=menu-jv&amp;mode=1&amp;sec=dif&amp;protein=1byi#bar case of 1BYI], which is used as an example of this page.</text>
    <sha1>a59a562b47c1713bd1b9b6b1f3d3cf81e42c5a88</sha1>
  </revision>
  <revision>
    <id>110</id>
    <parentid>109</parentid>
    <timestamp>2009-03-09T06:49:59Z</timestamp>
    <contributor>
      <username>JVuser</username>
      <id>2</id>
    </contributor>
    <comment>/* Step-4: Advance usage in ProMode */</comment>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="3001" xml:space="preserve">{| style="float:right"
 |__TOC__
 |}
A brief introduction to user animation in jV.

== Step-1: Minimum Example ==
To display the animation on the web using jV, you should prepare an animation file and a html file.

The format of the animation file is the same one as the PDB format of the NMR structure with multiple models. In other words, each frame is separated with MODEL recored. An example animation file can be obtained from [[here]].

The html file, shown below, should contain the applet tag to activate jV and it requires code parameter, codebase parameter and archive parameter. The parameter “code” is a kind of magic word to use jV. The codebase points the relative path to the jV jar file existing from the html file is stored, and archive parameter indicates the name of jar file. The jar file can be obtained from [[DOWNLOAD page]].

 &lt;html&gt;&lt;body&gt;
 &lt;applet code="org.pdbj.viewer.gui.ViewerApplet"
    codebase="."
    archive="jv3_3.jar"
    width=400 height=400
    &lt;param name="animURL"
        value="http://ef-site.hgc.jp/jV/example/1byi_1-anm.pdg"&gt;
    &lt;param name="commands"
        value="select all;wireframe on;anim forward"&gt;
 &lt;/applet&gt;
 &lt;/body&gt;&lt;/html&gt;

== Step-2:Make more fancy ==
To display cartoon and color from N-terminal to C-terminal in white background,change “wireframe on” to “cartoon on” &amp; add “color group;”&lt;br /&gt;
&lt;font size="1"&gt;NOTE: As in this example, any jV code (similar to Rasmol script) can be used in the commands parameter. And each jV command should be separated by “;”.&lt;/font&gt;&lt;br /&gt;
Complete Code until here.

 &lt;html&gt;&lt;body&gt;
 &lt;applet code="org.pdbj.viewer.gui.ViewerApplet"
    codebase="."
    archive="jv3_3.jar"
    width=400 height=400
    &lt;param name="animURL"
        value="http://ef-site.hgc.jp/jV/example/1byi_1-anm.pdb"&gt;
    &lt;param name="commands"
        value="background white;select all;background white;
               cartoon on; anim forward"&gt;
 &lt;/applet&gt;
 &lt;/body&gt;&lt;/html&gt;

== Step-3: Swing &amp; move quick! ==
To control the speed of animation and the animation mode (shown once, swing, or loop), add two commands, “animmode swing; animspeed 20;” (20 is just an example).

 &lt;html&gt;&lt;body&gt;
 &lt;applet code="org.pdbj.viewer.gui.ViewerApplet"
    codebase="."
    archive="jv3_3.jar"
    width=400 height=400
    &lt;param name="animURL"
        value="http://ef-site.hgc.jp/jV/example/1byi_1-anm.pdb"&gt;
    &lt;param name="commands"
        value="background white;select all;background white;
               cartoon on;
               animmode swing;animspeed 20;
               anim forward"&gt;
 &lt;/applet&gt;
 &lt;/body&gt;&lt;/html&gt;

== Step-4: Advance usage in ProMode ==
[[File:ProMode.jpg|right|link=http://cube.socs.waseda.ac.jp/pages/jsp/index.jsp|ProMode]] ProMode is a database of normal mode analysis of proteins. In the database Animations are provided with jV. You can see the [http://cube.socs.waseda.ac.jp/pages/jsp/indexn.jsp?cont=menu-jv&amp;mode=1&amp;sec=dif&amp;protein=1byi#bar case of 1BYI], which is used as an example of this page.</text>
    <sha1>75c1b1d90f4c5b29a849055689e26ffb0f8c1295</sha1>
  </revision>
  <revision>
    <id>111</id>
    <parentid>110</parentid>
    <timestamp>2009-03-09T06:51:28Z</timestamp>
    <contributor>
      <username>JVuser</username>
      <id>2</id>
    </contributor>
    <comment>/* Step-2:Make more fancy */</comment>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="3031" xml:space="preserve">{| style="float:right"
 |__TOC__
 |}
A brief introduction to user animation in jV.

== Step-1: Minimum Example ==
To display the animation on the web using jV, you should prepare an animation file and a html file.

The format of the animation file is the same one as the PDB format of the NMR structure with multiple models. In other words, each frame is separated with MODEL recored. An example animation file can be obtained from [[here]].

The html file, shown below, should contain the applet tag to activate jV and it requires code parameter, codebase parameter and archive parameter. The parameter “code” is a kind of magic word to use jV. The codebase points the relative path to the jV jar file existing from the html file is stored, and archive parameter indicates the name of jar file. The jar file can be obtained from [[DOWNLOAD page]].

 &lt;html&gt;&lt;body&gt;
 &lt;applet code="org.pdbj.viewer.gui.ViewerApplet"
    codebase="."
    archive="jv3_3.jar"
    width=400 height=400
    &lt;param name="animURL"
        value="http://ef-site.hgc.jp/jV/example/1byi_1-anm.pdg"&gt;
    &lt;param name="commands"
        value="select all;wireframe on;anim forward"&gt;
 &lt;/applet&gt;
 &lt;/body&gt;&lt;/html&gt;

== Step-2:Make more fancy ==
[File:step-2.jpg|right|step-2]To display cartoon and color from N-terminal to C-terminal in white background,change “wireframe on” to “cartoon on” &amp; add “color group;”&lt;br /&gt;
&lt;font size="1"&gt;NOTE: As in this example, any jV code (similar to Rasmol script) can be used in the commands parameter. And each jV command should be separated by “;”.&lt;/font&gt;&lt;br /&gt;
Complete Code until here.

 &lt;html&gt;&lt;body&gt;
 &lt;applet code="org.pdbj.viewer.gui.ViewerApplet"
    codebase="."
    archive="jv3_3.jar"
    width=400 height=400
    &lt;param name="animURL"
        value="http://ef-site.hgc.jp/jV/example/1byi_1-anm.pdb"&gt;
    &lt;param name="commands"
        value="background white;select all;background white;
               cartoon on; anim forward"&gt;
 &lt;/applet&gt;
 &lt;/body&gt;&lt;/html&gt;

== Step-3: Swing &amp; move quick! ==
To control the speed of animation and the animation mode (shown once, swing, or loop), add two commands, “animmode swing; animspeed 20;” (20 is just an example).

 &lt;html&gt;&lt;body&gt;
 &lt;applet code="org.pdbj.viewer.gui.ViewerApplet"
    codebase="."
    archive="jv3_3.jar"
    width=400 height=400
    &lt;param name="animURL"
        value="http://ef-site.hgc.jp/jV/example/1byi_1-anm.pdb"&gt;
    &lt;param name="commands"
        value="background white;select all;background white;
               cartoon on;
               animmode swing;animspeed 20;
               anim forward"&gt;
 &lt;/applet&gt;
 &lt;/body&gt;&lt;/html&gt;

== Step-4: Advance usage in ProMode ==
[[File:ProMode.jpg|right|link=http://cube.socs.waseda.ac.jp/pages/jsp/index.jsp|ProMode]] ProMode is a database of normal mode analysis of proteins. In the database Animations are provided with jV. You can see the [http://cube.socs.waseda.ac.jp/pages/jsp/indexn.jsp?cont=menu-jv&amp;mode=1&amp;sec=dif&amp;protein=1byi#bar case of 1BYI], which is used as an example of this page.</text>
    <sha1>4de9dc3fd7e7a84c06dc7ddb9de6b0e7f53f0d23</sha1>
  </revision>
  <revision>
    <id>112</id>
    <parentid>111</parentid>
    <timestamp>2009-03-09T06:51:51Z</timestamp>
    <contributor>
      <username>JVuser</username>
      <id>2</id>
    </contributor>
    <comment>/* Step-2:Make more fancy */</comment>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="3033" xml:space="preserve">{| style="float:right"
 |__TOC__
 |}
A brief introduction to user animation in jV.

== Step-1: Minimum Example ==
To display the animation on the web using jV, you should prepare an animation file and a html file.

The format of the animation file is the same one as the PDB format of the NMR structure with multiple models. In other words, each frame is separated with MODEL recored. An example animation file can be obtained from [[here]].

The html file, shown below, should contain the applet tag to activate jV and it requires code parameter, codebase parameter and archive parameter. The parameter “code” is a kind of magic word to use jV. The codebase points the relative path to the jV jar file existing from the html file is stored, and archive parameter indicates the name of jar file. The jar file can be obtained from [[DOWNLOAD page]].

 &lt;html&gt;&lt;body&gt;
 &lt;applet code="org.pdbj.viewer.gui.ViewerApplet"
    codebase="."
    archive="jv3_3.jar"
    width=400 height=400
    &lt;param name="animURL"
        value="http://ef-site.hgc.jp/jV/example/1byi_1-anm.pdg"&gt;
    &lt;param name="commands"
        value="select all;wireframe on;anim forward"&gt;
 &lt;/applet&gt;
 &lt;/body&gt;&lt;/html&gt;

== Step-2:Make more fancy ==
[[File:step-2.jpg|right|step-2]]To display cartoon and color from N-terminal to C-terminal in white background,change “wireframe on” to “cartoon on” &amp; add “color group;”&lt;br /&gt;
&lt;font size="1"&gt;NOTE: As in this example, any jV code (similar to Rasmol script) can be used in the commands parameter. And each jV command should be separated by “;”.&lt;/font&gt;&lt;br /&gt;
Complete Code until here.

 &lt;html&gt;&lt;body&gt;
 &lt;applet code="org.pdbj.viewer.gui.ViewerApplet"
    codebase="."
    archive="jv3_3.jar"
    width=400 height=400
    &lt;param name="animURL"
        value="http://ef-site.hgc.jp/jV/example/1byi_1-anm.pdb"&gt;
    &lt;param name="commands"
        value="background white;select all;background white;
               cartoon on; anim forward"&gt;
 &lt;/applet&gt;
 &lt;/body&gt;&lt;/html&gt;

== Step-3: Swing &amp; move quick! ==
To control the speed of animation and the animation mode (shown once, swing, or loop), add two commands, “animmode swing; animspeed 20;” (20 is just an example).

 &lt;html&gt;&lt;body&gt;
 &lt;applet code="org.pdbj.viewer.gui.ViewerApplet"
    codebase="."
    archive="jv3_3.jar"
    width=400 height=400
    &lt;param name="animURL"
        value="http://ef-site.hgc.jp/jV/example/1byi_1-anm.pdb"&gt;
    &lt;param name="commands"
        value="background white;select all;background white;
               cartoon on;
               animmode swing;animspeed 20;
               anim forward"&gt;
 &lt;/applet&gt;
 &lt;/body&gt;&lt;/html&gt;

== Step-4: Advance usage in ProMode ==
[[File:ProMode.jpg|right|link=http://cube.socs.waseda.ac.jp/pages/jsp/index.jsp|ProMode]] ProMode is a database of normal mode analysis of proteins. In the database Animations are provided with jV. You can see the [http://cube.socs.waseda.ac.jp/pages/jsp/indexn.jsp?cont=menu-jv&amp;mode=1&amp;sec=dif&amp;protein=1byi#bar case of 1BYI], which is used as an example of this page.</text>
    <sha1>95f1e64a713976b7b719d0eb24d3152b9e2475ca</sha1>
  </revision>
  <revision>
    <id>113</id>
    <parentid>112</parentid>
    <timestamp>2009-03-09T06:52:34Z</timestamp>
    <contributor>
      <username>JVuser</username>
      <id>2</id>
    </contributor>
    <comment>/* Step-1: Minimum Example */</comment>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="3065" xml:space="preserve">{| style="float:right"
 |__TOC__
 |}
A brief introduction to user animation in jV.

== Step-1: Minimum Example ==
To display the animation on the web using jV, you should prepare an animation file and a html file.

The format of the animation file is the same one as the PDB format of the NMR structure with multiple models. In other words, each frame is separated with MODEL recored. An example animation file can be obtained from [[here]].

[[File:step-1.jpg|right|step-1]]The html file, shown below, should contain the applet tag to activate jV and it requires code parameter, codebase parameter and archive parameter. The parameter “code” is a kind of magic word to use jV. The codebase points the relative path to the jV jar file existing from the html file is stored, and archive parameter indicates the name of jar file. The jar file can be obtained from [[DOWNLOAD page]].

 &lt;html&gt;&lt;body&gt;
 &lt;applet code="org.pdbj.viewer.gui.ViewerApplet"
    codebase="."
    archive="jv3_3.jar"
    width=400 height=400
    &lt;param name="animURL"
        value="http://ef-site.hgc.jp/jV/example/1byi_1-anm.pdg"&gt;
    &lt;param name="commands"
        value="select all;wireframe on;anim forward"&gt;
 &lt;/applet&gt;
 &lt;/body&gt;&lt;/html&gt;

== Step-2:Make more fancy ==
[[File:step-2.jpg|right|step-2]]To display cartoon and color from N-terminal to C-terminal in white background,change “wireframe on” to “cartoon on” &amp; add “color group;”&lt;br /&gt;
&lt;font size="1"&gt;NOTE: As in this example, any jV code (similar to Rasmol script) can be used in the commands parameter. And each jV command should be separated by “;”.&lt;/font&gt;&lt;br /&gt;
Complete Code until here.

 &lt;html&gt;&lt;body&gt;
 &lt;applet code="org.pdbj.viewer.gui.ViewerApplet"
    codebase="."
    archive="jv3_3.jar"
    width=400 height=400
    &lt;param name="animURL"
        value="http://ef-site.hgc.jp/jV/example/1byi_1-anm.pdb"&gt;
    &lt;param name="commands"
        value="background white;select all;background white;
               cartoon on; anim forward"&gt;
 &lt;/applet&gt;
 &lt;/body&gt;&lt;/html&gt;

== Step-3: Swing &amp; move quick! ==
To control the speed of animation and the animation mode (shown once, swing, or loop), add two commands, “animmode swing; animspeed 20;” (20 is just an example).

 &lt;html&gt;&lt;body&gt;
 &lt;applet code="org.pdbj.viewer.gui.ViewerApplet"
    codebase="."
    archive="jv3_3.jar"
    width=400 height=400
    &lt;param name="animURL"
        value="http://ef-site.hgc.jp/jV/example/1byi_1-anm.pdb"&gt;
    &lt;param name="commands"
        value="background white;select all;background white;
               cartoon on;
               animmode swing;animspeed 20;
               anim forward"&gt;
 &lt;/applet&gt;
 &lt;/body&gt;&lt;/html&gt;

== Step-4: Advance usage in ProMode ==
[[File:ProMode.jpg|right|link=http://cube.socs.waseda.ac.jp/pages/jsp/index.jsp|ProMode]] ProMode is a database of normal mode analysis of proteins. In the database Animations are provided with jV. You can see the [http://cube.socs.waseda.ac.jp/pages/jsp/indexn.jsp?cont=menu-jv&amp;mode=1&amp;sec=dif&amp;protein=1byi#bar case of 1BYI], which is used as an example of this page.</text>
    <sha1>4d2e8924336045f6f2f8a5c285c89a1d92d5675c</sha1>
  </revision>
  <revision>
    <id>116</id>
    <parentid>113</parentid>
    <timestamp>2009-03-09T06:54:07Z</timestamp>
    <contributor>
      <username>JVuser</username>
      <id>2</id>
    </contributor>
    <comment>/* Step-1: Minimum Example */</comment>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="3065" xml:space="preserve">{| style="float:right"
 |__TOC__
 |}
A brief introduction to user animation in jV.

== Step-1: Minimum Example ==
To display the animation on the web using jV, you should prepare an animation file and a html file.

[[File:step-1.jpg|right|step-1]]The format of the animation file is the same one as the PDB format of the NMR structure with multiple models. In other words, each frame is separated with MODEL recored. An example animation file can be obtained from [[here]].

The html file, shown below, should contain the applet tag to activate jV and it requires code parameter, codebase parameter and archive parameter. The parameter “code” is a kind of magic word to use jV. The codebase points the relative path to the jV jar file existing from the html file is stored, and archive parameter indicates the name of jar file. The jar file can be obtained from [[DOWNLOAD page]].

 &lt;html&gt;&lt;body&gt;
 &lt;applet code="org.pdbj.viewer.gui.ViewerApplet"
    codebase="."
    archive="jv3_3.jar"
    width=400 height=400
    &lt;param name="animURL"
        value="http://ef-site.hgc.jp/jV/example/1byi_1-anm.pdg"&gt;
    &lt;param name="commands"
        value="select all;wireframe on;anim forward"&gt;
 &lt;/applet&gt;
 &lt;/body&gt;&lt;/html&gt;

== Step-2:Make more fancy ==
[[File:step-2.jpg|right|step-2]]To display cartoon and color from N-terminal to C-terminal in white background,change “wireframe on” to “cartoon on” &amp; add “color group;”&lt;br /&gt;
&lt;font size="1"&gt;NOTE: As in this example, any jV code (similar to Rasmol script) can be used in the commands parameter. And each jV command should be separated by “;”.&lt;/font&gt;&lt;br /&gt;
Complete Code until here.

 &lt;html&gt;&lt;body&gt;
 &lt;applet code="org.pdbj.viewer.gui.ViewerApplet"
    codebase="."
    archive="jv3_3.jar"
    width=400 height=400
    &lt;param name="animURL"
        value="http://ef-site.hgc.jp/jV/example/1byi_1-anm.pdb"&gt;
    &lt;param name="commands"
        value="background white;select all;background white;
               cartoon on; anim forward"&gt;
 &lt;/applet&gt;
 &lt;/body&gt;&lt;/html&gt;

== Step-3: Swing &amp; move quick! ==
To control the speed of animation and the animation mode (shown once, swing, or loop), add two commands, “animmode swing; animspeed 20;” (20 is just an example).

 &lt;html&gt;&lt;body&gt;
 &lt;applet code="org.pdbj.viewer.gui.ViewerApplet"
    codebase="."
    archive="jv3_3.jar"
    width=400 height=400
    &lt;param name="animURL"
        value="http://ef-site.hgc.jp/jV/example/1byi_1-anm.pdb"&gt;
    &lt;param name="commands"
        value="background white;select all;background white;
               cartoon on;
               animmode swing;animspeed 20;
               anim forward"&gt;
 &lt;/applet&gt;
 &lt;/body&gt;&lt;/html&gt;

== Step-4: Advance usage in ProMode ==
[[File:ProMode.jpg|right|link=http://cube.socs.waseda.ac.jp/pages/jsp/index.jsp|ProMode]] ProMode is a database of normal mode analysis of proteins. In the database Animations are provided with jV. You can see the [http://cube.socs.waseda.ac.jp/pages/jsp/indexn.jsp?cont=menu-jv&amp;mode=1&amp;sec=dif&amp;protein=1byi#bar case of 1BYI], which is used as an example of this page.</text>
    <sha1>6bfa888a1d74b6c4281e51a2a164727bd7b20b2e</sha1>
  </revision>
  <revision>
    <id>117</id>
    <parentid>116</parentid>
    <timestamp>2009-03-09T06:54:41Z</timestamp>
    <contributor>
      <username>JVuser</username>
      <id>2</id>
    </contributor>
    <comment>/* Step-1: Minimum Example */</comment>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="3064" xml:space="preserve">{| style="float:right"
 |__TOC__
 |}
A brief introduction to user animation in jV.

== Step-1: Minimum Example ==
To display the animation on the web using jV, you should prepare an animation file and a html file.

[[File:step-1.jpg|left|step-1]]The format of the animation file is the same one as the PDB format of the NMR structure with multiple models. In other words, each frame is separated with MODEL recored. An example animation file can be obtained from [[here]].

The html file, shown below, should contain the applet tag to activate jV and it requires code parameter, codebase parameter and archive parameter. The parameter “code” is a kind of magic word to use jV. The codebase points the relative path to the jV jar file existing from the html file is stored, and archive parameter indicates the name of jar file. The jar file can be obtained from [[DOWNLOAD page]].

 &lt;html&gt;&lt;body&gt;
 &lt;applet code="org.pdbj.viewer.gui.ViewerApplet"
    codebase="."
    archive="jv3_3.jar"
    width=400 height=400
    &lt;param name="animURL"
        value="http://ef-site.hgc.jp/jV/example/1byi_1-anm.pdg"&gt;
    &lt;param name="commands"
        value="select all;wireframe on;anim forward"&gt;
 &lt;/applet&gt;
 &lt;/body&gt;&lt;/html&gt;

== Step-2:Make more fancy ==
[[File:step-2.jpg|right|step-2]]To display cartoon and color from N-terminal to C-terminal in white background,change “wireframe on” to “cartoon on” &amp; add “color group;”&lt;br /&gt;
&lt;font size="1"&gt;NOTE: As in this example, any jV code (similar to Rasmol script) can be used in the commands parameter. And each jV command should be separated by “;”.&lt;/font&gt;&lt;br /&gt;
Complete Code until here.

 &lt;html&gt;&lt;body&gt;
 &lt;applet code="org.pdbj.viewer.gui.ViewerApplet"
    codebase="."
    archive="jv3_3.jar"
    width=400 height=400
    &lt;param name="animURL"
        value="http://ef-site.hgc.jp/jV/example/1byi_1-anm.pdb"&gt;
    &lt;param name="commands"
        value="background white;select all;background white;
               cartoon on; anim forward"&gt;
 &lt;/applet&gt;
 &lt;/body&gt;&lt;/html&gt;

== Step-3: Swing &amp; move quick! ==
To control the speed of animation and the animation mode (shown once, swing, or loop), add two commands, “animmode swing; animspeed 20;” (20 is just an example).

 &lt;html&gt;&lt;body&gt;
 &lt;applet code="org.pdbj.viewer.gui.ViewerApplet"
    codebase="."
    archive="jv3_3.jar"
    width=400 height=400
    &lt;param name="animURL"
        value="http://ef-site.hgc.jp/jV/example/1byi_1-anm.pdb"&gt;
    &lt;param name="commands"
        value="background white;select all;background white;
               cartoon on;
               animmode swing;animspeed 20;
               anim forward"&gt;
 &lt;/applet&gt;
 &lt;/body&gt;&lt;/html&gt;

== Step-4: Advance usage in ProMode ==
[[File:ProMode.jpg|right|link=http://cube.socs.waseda.ac.jp/pages/jsp/index.jsp|ProMode]] ProMode is a database of normal mode analysis of proteins. In the database Animations are provided with jV. You can see the [http://cube.socs.waseda.ac.jp/pages/jsp/indexn.jsp?cont=menu-jv&amp;mode=1&amp;sec=dif&amp;protein=1byi#bar case of 1BYI], which is used as an example of this page.</text>
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  </revision>
</page>
<page arvcontinue="20090309064103|101">
  <title>Main Page</title>
  <ns>0</ns>
  <id>1</id>
  <revision>
    <id>103</id>
    <parentid>86</parentid>
    <timestamp>2009-03-09T06:42:14Z</timestamp>
    <contributor>
      <username>127.0.0.1</username>
      <id>0</id>
    </contributor>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="3739" xml:space="preserve">&lt;big&gt;'''Welcome to jV wiki.'''&lt;/big&gt;
jV version3 (formerly known as PDBjViewer) is a program to display molecular graphics of protein and nucleic acids. 
jV can use as a stand-alone program and can operate on a web browser as an Java applet. jV is used by PDBj services([http://ef-site.hgc.jp/eF-site/index.jsp eF-site], [http://ef-site.hgc.jp/eF-seek/index.jsp eF-seek], the molecular structure surface database of the protein functional part).

jV supports the following features:
* jV can read and display PDBML files, the canonical XML format for the Protein Data Bank.
* Of course, jV can read and display the traditional PDB format files, too.
* RasMol-like usability.
* jV can process more than one molecules.
* jV can display polygons specified by XML. ([http://ef-site.hgc.jp/eF-site/schema/polygon12.xsd XML Schema for polygons] is available.)
* Multiple polygons can be processed simultaneously, and be superimposed onto molecular images.
* Animation can be realized.
* The graphics of jV is based on OpenGL [https://jogl.dev.java.net/ JOGL]), thereby producing fairly beautiful pictures.
* jV runs on the Java Runtime Environment ([http://java.sun.com/javase/index.jsp JRE]) so that it can work as a stand-alone application as well as an applet.

The program 'jV' has been developed by [http://www.hgc.jp/~kinosita/TOP.html Kengo Kinoshita] ([http://www.hgc.jp/english/ Human Genome Center], [http://www.ims.u-tokyo.ac.jp/imsut/en/ Insutitute for Medical Science],[http://www.u-tokyo.ac.jp/index_e.html University of Tokyo]) and [http://www.protein.osaka-u.ac.jp/rcsfp/pi/ Haruki Nakamura] ([http://www.protein.osaka-u.ac.jp/index_e.php Institute for Protein Research], [http://www.osaka-u.ac.jp/eng/index.html Osaka Univeristy]), with the support from [http://www-bird.jst.go.jp/index_e.html JST-BIRD].

-[[jV version 3]] has indicated more detailed explanation.&lt;br /&gt;
-[[Installation of jV3]] is a procedure installed in a local machine.&lt;br /&gt;
-[[jV3 Manual]]　is　how to use jV3.&lt;br /&gt;

&lt;font size="1"&gt;The [[old version]](jV version1 &amp; jV version2) has not carried out use recommendation.&lt;/font&gt;

&lt;gallery&gt;
File:Spacefill.jpg
File:Cartoon.jpg
File:Surface.jpg
File:edmap.jpg
&lt;/gallery&gt;

== jV3 Outline ==
[[File:Download.png|right|link=http://ef-site.hgc.jp/eF-site/servlet/DownloadViewerBinary|Download]] jV version 3 is now used to display molecules and their surfaces as a Java applet program.&lt;br /&gt;&lt;font size="1"&gt;Version 3.6 was released on 11, Aug, 2008.&lt;br /&gt;This version is fully compativle with [https://applet-launcher.dev.java.net/ applet-launcher].&lt;/font&gt;&lt;br /&gt;Go to [[jV version 3]].
&lt;br /&gt;
It requires the following softwares.
* [http://java.sun.com/products/plugin/index-1.4.html JRE] 1.4.2 or later  (recommend 1.4.2_12)
* [https://jogl.dev.java.net/ JOGL] 1.0, 1.1.1 or JSR-231 1.0.0  (recommend JSR-231)&lt;br /&gt;
** version 1.0 [[http://ef-site.hgc.jp/eF-site/jV/JOGL1.0_win32.zip Windows],[http://ef-site.hgc.jp/eF-site/jV/JOGL1.0_macosx.tar.gz Mac OS X],[http://ef-site.hgc.jp/eF-site/jV/JOGL1.0_linux.tar.gz Linux]]
** version 1.1.1 [[http://ef-site.hgc.jp/eF-site/jV/JOGL1.1.1_win32.zip Windows],[http://ef-site.hgc.jp/eF-site/jV/JOGL1.1.1_macosx.tar.gz Mac OS X], [http://ef-site.hgc.jp/eF-site/jV/JOGL1.1.1_linux.tar.gz Linux]]
** JSR-231 1.0.0 [[http://ef-site.hgc.jp/eF-site/jV/JOGL_JSR231_win32.zip Windows], [http://ef-site.hgc.jp/eF-site/jV/JOGL_JSR231_macosx_ppc.tar.gz Mac OS X ppc], [http://ef-site.hgc.jp/eF-site/jV/JOGL_JSR231_macosx_universal.tar.gz Mac OS X universal], [http://ef-site.hgc.jp/eF-site/jV/JOGL_JSR231_linux_i586.tar.gz Linux]]

&lt;font size="1"&gt;Note: &amp;nbsp; JOGL 1.0 and 1.1.1 are not available for Intel Mac.The latest version of JOGL, JSR-231 1.0.0, runs on Intel Mac.&lt;/font&gt;</text>
    <sha1>408bc4f000a068160c69d9174f8d6a91fb5ced65</sha1>
  </revision>
  <revision>
    <id>119</id>
    <parentid>103</parentid>
    <timestamp>2009-03-09T07:15:26Z</timestamp>
    <contributor>
      <username>JVuser</username>
      <id>2</id>
    </contributor>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="3709" xml:space="preserve">&lt;big&gt;'''Welcome to jV wiki.'''&lt;/big&gt;
jV version3 (formerly known as PDBjViewer) is a program to display molecular graphics of protein and nucleic acids. 
jV can use as a stand-alone program and can operate on a web browser as an Java applet. jV is used by PDBj services([http://ef-site.hgc.jp/eF-site/index.jsp eF-site], [http://ef-site.hgc.jp/eF-seek/index.jsp eF-seek], the molecular structure surface database of the protein functional part).

jV supports the following features:
* jV can read and display PDBML files, the canonical XML format for the Protein Data Bank.
* Of course, jV can read and display the traditional PDB format files, too.
* RasMol-like usability.
* jV can process more than one molecules.
* jV can display polygons specified by XML. ([http://ef-site.hgc.jp/eF-site/schema/polygon12.xsd XML Schema for polygons] is available.)
* Multiple polygons can be processed simultaneously, and be superimposed onto molecular images.
* Animation can be realized.
* The graphics of jV is based on OpenGL [https://jogl.dev.java.net/ JOGL]), thereby producing fairly beautiful pictures.
* jV runs on the Java Runtime Environment ([http://java.sun.com/javase/index.jsp JRE]) so that it can work as a stand-alone application as well as an applet.

The program 'jV' has been developed by [http://www.hgc.jp/~kinosita/TOP.html Kengo Kinoshita] ([http://www.hgc.jp/english/ Human Genome Center], [http://www.ims.u-tokyo.ac.jp/imsut/en/ Insutitute for Medical Science],[http://www.u-tokyo.ac.jp/index_e.html University of Tokyo]) and [http://www.protein.osaka-u.ac.jp/rcsfp/pi/ Haruki Nakamura] ([http://www.protein.osaka-u.ac.jp/index_e.php Institute for Protein Research], [http://www.osaka-u.ac.jp/eng/index.html Osaka Univeristy]), with the support from [http://www-bird.jst.go.jp/index_e.html JST-BIRD].

-[[jV version 3]] has indicated more detailed explanation and how to use.&lt;br /&gt;
-[[Installation of jV3]] is a procedure installed in a local machine.&lt;br /&gt;

&lt;font size="1"&gt;The [[old version]](jV version1 &amp; jV version2) has not carried out use recommendation.&lt;/font&gt;

&lt;gallery&gt;
File:Spacefill.jpg
File:Cartoon.jpg
File:Surface.jpg
File:edmap.jpg
&lt;/gallery&gt;

== jV3 Outline ==
[[File:Download.png|right|link=http://ef-site.hgc.jp/eF-site/servlet/DownloadViewerBinary|Download]] jV version 3 is now used to display molecules and their surfaces as a Java applet program.&lt;br /&gt;&lt;font size="1"&gt;Version 3.6 was released on 11, Aug, 2008.&lt;br /&gt;This version is fully compativle with [https://applet-launcher.dev.java.net/ applet-launcher].&lt;/font&gt;&lt;br /&gt;Go to [[jV version 3]].
&lt;br /&gt;
It requires the following softwares.
* [http://java.sun.com/products/plugin/index-1.4.html JRE] 1.4.2 or later  (recommend 1.4.2_12)
* [https://jogl.dev.java.net/ JOGL] 1.0, 1.1.1 or JSR-231 1.0.0  (recommend JSR-231)&lt;br /&gt;
** version 1.0 [[http://ef-site.hgc.jp/eF-site/jV/JOGL1.0_win32.zip Windows],[http://ef-site.hgc.jp/eF-site/jV/JOGL1.0_macosx.tar.gz Mac OS X],[http://ef-site.hgc.jp/eF-site/jV/JOGL1.0_linux.tar.gz Linux]]
** version 1.1.1 [[http://ef-site.hgc.jp/eF-site/jV/JOGL1.1.1_win32.zip Windows],[http://ef-site.hgc.jp/eF-site/jV/JOGL1.1.1_macosx.tar.gz Mac OS X], [http://ef-site.hgc.jp/eF-site/jV/JOGL1.1.1_linux.tar.gz Linux]]
** JSR-231 1.0.0 [[http://ef-site.hgc.jp/eF-site/jV/JOGL_JSR231_win32.zip Windows], [http://ef-site.hgc.jp/eF-site/jV/JOGL_JSR231_macosx_ppc.tar.gz Mac OS X ppc], [http://ef-site.hgc.jp/eF-site/jV/JOGL_JSR231_macosx_universal.tar.gz Mac OS X universal], [http://ef-site.hgc.jp/eF-site/jV/JOGL_JSR231_linux_i586.tar.gz Linux]]

&lt;font size="1"&gt;Note: &amp;nbsp; JOGL 1.0 and 1.1.1 are not available for Intel Mac.The latest version of JOGL, JSR-231 1.0.0, runs on Intel Mac.&lt;/font&gt;</text>
    <sha1>e1356d8b577a8d0c41041aebab6297082ae85f00</sha1>
  </revision>
  <revision>
    <id>120</id>
    <parentid>119</parentid>
    <timestamp>2009-03-09T07:15:43Z</timestamp>
    <contributor>
      <username>JVuser</username>
      <id>2</id>
    </contributor>
    <comment>/* jV3 Outline */</comment>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="3718" xml:space="preserve">&lt;big&gt;'''Welcome to jV wiki.'''&lt;/big&gt;
jV version3 (formerly known as PDBjViewer) is a program to display molecular graphics of protein and nucleic acids. 
jV can use as a stand-alone program and can operate on a web browser as an Java applet. jV is used by PDBj services([http://ef-site.hgc.jp/eF-site/index.jsp eF-site], [http://ef-site.hgc.jp/eF-seek/index.jsp eF-seek], the molecular structure surface database of the protein functional part).

jV supports the following features:
* jV can read and display PDBML files, the canonical XML format for the Protein Data Bank.
* Of course, jV can read and display the traditional PDB format files, too.
* RasMol-like usability.
* jV can process more than one molecules.
* jV can display polygons specified by XML. ([http://ef-site.hgc.jp/eF-site/schema/polygon12.xsd XML Schema for polygons] is available.)
* Multiple polygons can be processed simultaneously, and be superimposed onto molecular images.
* Animation can be realized.
* The graphics of jV is based on OpenGL [https://jogl.dev.java.net/ JOGL]), thereby producing fairly beautiful pictures.
* jV runs on the Java Runtime Environment ([http://java.sun.com/javase/index.jsp JRE]) so that it can work as a stand-alone application as well as an applet.

The program 'jV' has been developed by [http://www.hgc.jp/~kinosita/TOP.html Kengo Kinoshita] ([http://www.hgc.jp/english/ Human Genome Center], [http://www.ims.u-tokyo.ac.jp/imsut/en/ Insutitute for Medical Science],[http://www.u-tokyo.ac.jp/index_e.html University of Tokyo]) and [http://www.protein.osaka-u.ac.jp/rcsfp/pi/ Haruki Nakamura] ([http://www.protein.osaka-u.ac.jp/index_e.php Institute for Protein Research], [http://www.osaka-u.ac.jp/eng/index.html Osaka Univeristy]), with the support from [http://www-bird.jst.go.jp/index_e.html JST-BIRD].

-[[jV version 3]] has indicated more detailed explanation and how to use.&lt;br /&gt;
-[[Installation of jV3]] is a procedure installed in a local machine.&lt;br /&gt;

&lt;font size="1"&gt;The [[old version]](jV version1 &amp; jV version2) has not carried out use recommendation.&lt;/font&gt;

&lt;gallery&gt;
File:Spacefill.jpg
File:Cartoon.jpg
File:Surface.jpg
File:edmap.jpg
&lt;/gallery&gt;

== jV version 3 Outline ==
[[File:Download.png|right|link=http://ef-site.hgc.jp/eF-site/servlet/DownloadViewerBinary|Download]] jV version 3 is now used to display molecules and their surfaces as a Java applet program.&lt;br /&gt;&lt;font size="1"&gt;Version 3.6 was released on 11, Aug, 2008.&lt;br /&gt;This version is fully compativle with [https://applet-launcher.dev.java.net/ applet-launcher].&lt;/font&gt;&lt;br /&gt;Go to [[jV version 3]].
&lt;br /&gt;
It requires the following softwares.
* [http://java.sun.com/products/plugin/index-1.4.html JRE] 1.4.2 or later  (recommend 1.4.2_12)
* [https://jogl.dev.java.net/ JOGL] 1.0, 1.1.1 or JSR-231 1.0.0  (recommend JSR-231)&lt;br /&gt;
** version 1.0 [[http://ef-site.hgc.jp/eF-site/jV/JOGL1.0_win32.zip Windows],[http://ef-site.hgc.jp/eF-site/jV/JOGL1.0_macosx.tar.gz Mac OS X],[http://ef-site.hgc.jp/eF-site/jV/JOGL1.0_linux.tar.gz Linux]]
** version 1.1.1 [[http://ef-site.hgc.jp/eF-site/jV/JOGL1.1.1_win32.zip Windows],[http://ef-site.hgc.jp/eF-site/jV/JOGL1.1.1_macosx.tar.gz Mac OS X], [http://ef-site.hgc.jp/eF-site/jV/JOGL1.1.1_linux.tar.gz Linux]]
** JSR-231 1.0.0 [[http://ef-site.hgc.jp/eF-site/jV/JOGL_JSR231_win32.zip Windows], [http://ef-site.hgc.jp/eF-site/jV/JOGL_JSR231_macosx_ppc.tar.gz Mac OS X ppc], [http://ef-site.hgc.jp/eF-site/jV/JOGL_JSR231_macosx_universal.tar.gz Mac OS X universal], [http://ef-site.hgc.jp/eF-site/jV/JOGL_JSR231_linux_i586.tar.gz Linux]]

&lt;font size="1"&gt;Note: &amp;nbsp; JOGL 1.0 and 1.1.1 are not available for Intel Mac.The latest version of JOGL, JSR-231 1.0.0, runs on Intel Mac.&lt;/font&gt;</text>
    <sha1>28c8bd7ea5e24ea2f822f64d7408f39e603c7cf8</sha1>
  </revision>
</page>
<page arvcontinue="20090309064103|101">
  <title>How to use</title>
  <ns>0</ns>
  <id>11</id>
  <revision>
    <id>106</id>
    <parentid>99</parentid>
    <timestamp>2009-03-09T06:45:44Z</timestamp>
    <contributor>
      <username>127.0.0.1</username>
      <id>0</id>
    </contributor>
    <comment>/* How to use */</comment>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="4262" xml:space="preserve">jV is an interactive 3D viewer program to visualize protein and nucleic acid molecules. The program reads in a PDBML file that is an XML format for PDB. Usual PDB format files are also accepted. More than one molecule files can be opened and displayed at the same time and their display models and transforms can be operated separately. In addition to molecule files, a polygon file written in XML can be read and displayed. More than one polygon files can be opened at the same time and superposed on molecule images. The [http://ef-site.hgc.jp/eF-site/schema/polygon12.xsd XML schema] of the polygon file is available. jV can perform an animation of molecules. The animation file is a PDB format file in which each frame is separated by a MODEL line.

jV runs on Java Runtime Environment ([http://java.sun.com/javase/index.jsp JRE]) and can be used both as a standalone program and an applet. The 3D rendering is performed with the use of [https://jogl.dev.java.net/ JOGL] API. The version requirements are as follows.

* JRE (includes Java Plug-in) 1.4.2 or later
* JOGL 1.1.1 or JSR-231

Here, [http://java.sun.com/products/plugin/ Java Plug-in] is required in order to use the program as an applet.

The program allows an interactive mouse control and command execution. The commnad syntax follows that of [http://www.rasmol.org/ Rasmol] with some modifications. In order to handle the transform of each molecule and polygon separately, every files are set to be either selected or not selected. The transform operation commands, such as rotate or translate, act only on selected files. On the other hand, every atoms in a molecule are also set to be either selected or not selected independently of whether the molecule itself is selected or not selected. Only selected atoms are the target of display model operations, such as wireframe or spacefill commands, and coloring operations.

== How to use ==
The following table shows hot to do the minimum things with jV.&lt;br /&gt;
{| class="wikitable" border="1" style="margin:0 auto" 
 ! Action !! Window, Linux !! Mac OS X 
 |-
 ! style="text-align:left" | rotate around X,Y axes
 | left drag || mouse drag
 |-
 ! style="text-align:left" | rotate around Z axis
 | Shift + right drag || Shift + command + drag
 |-
 ! style="text-align:left" | translate along X,Y axes
 | right drag || command + drag
 |-
 ! style="text-align:left" | translate along Z axis (zoom in/out)
 | Shift + left drag || Shift + drag
 |}
For the detail,
* The install manual [[Installaion of jV3]]
* The reference manual [[jV3 Manual]] link:

Some examples
# [[Animation]]
# [[User jV with applet launcher]]

== Release note ==
Changes and improvements have been made as follows.

* version 3.1
** The following commands have been added; 'animrange', 'set adjustview', 'show godata', and 'show xps3'.
** The xPSSS expression has been added in order to select a group of atoms.
** Several public methods have been added to the applet so as to append molecule or polygon files after the applet started.
** The applet can send information about mouse-picked atoms to JavaScript.
* version 3.1.1
** Some problems in GUI menu [Options]-[Hetero Atoms] and [Hydrogens] have been fixed.
** Some problems in 'trace' command have been fixed.
* version 3.1.2
** eF-site ID has been changed to a new format.
* version 3.1.3
** Some problems in xps3 atom selection have been fixed.
* version 3.1.4
** Some problems in finalization process of openGL rendering have been fixed.
* version 3.1.5
** The output of 'show xps3' command has been modified.
** Some problems in 'save png/jpeg' command have been fixed.
* version 3.1.6
** Some problems in loading an empty polygon file have been fixed.
* version 3.1.7
** Some problems in initialization process of the applet have been fixed.
* version 3.2
** 'show site' command has been added.
* version 3.3 beta 1
** Availabe JOGL version is restricted to JSR-231 beta 5 only.
* version 3.3
** Both the previous JOGL (version 1.1.1) and JSR-231 are available.
** The following commands have been added; 'set viewpoint', 'show viewpoint', 'set imagesize', and 'show imagesize'.
* version 3.3.1
** Some problems in reading a pdbMLplus file have been fixed.
* version 3.4
** PDB format version 3 can be processed.</text>
    <sha1>65c2fe3f229c2b78523a90a7a933441ad65d8417</sha1>
  </revision>
  <revision>
    <id>121</id>
    <parentid>106</parentid>
    <timestamp>2009-03-09T07:22:12Z</timestamp>
    <contributor>
      <username>JVuser</username>
      <id>2</id>
    </contributor>
    <comment>/* How to use */</comment>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="4455" xml:space="preserve">jV is an interactive 3D viewer program to visualize protein and nucleic acid molecules. The program reads in a PDBML file that is an XML format for PDB. Usual PDB format files are also accepted. More than one molecule files can be opened and displayed at the same time and their display models and transforms can be operated separately. In addition to molecule files, a polygon file written in XML can be read and displayed. More than one polygon files can be opened at the same time and superposed on molecule images. The [http://ef-site.hgc.jp/eF-site/schema/polygon12.xsd XML schema] of the polygon file is available. jV can perform an animation of molecules. The animation file is a PDB format file in which each frame is separated by a MODEL line.

jV runs on Java Runtime Environment ([http://java.sun.com/javase/index.jsp JRE]) and can be used both as a standalone program and an applet. The 3D rendering is performed with the use of [https://jogl.dev.java.net/ JOGL] API. The version requirements are as follows.

* JRE (includes Java Plug-in) 1.4.2 or later
* JOGL 1.1.1 or JSR-231

Here, [http://java.sun.com/products/plugin/ Java Plug-in] is required in order to use the program as an applet.

The program allows an interactive mouse control and command execution. The commnad syntax follows that of [http://www.rasmol.org/ Rasmol] with some modifications. In order to handle the transform of each molecule and polygon separately, every files are set to be either selected or not selected. The transform operation commands, such as rotate or translate, act only on selected files. On the other hand, every atoms in a molecule are also set to be either selected or not selected independently of whether the molecule itself is selected or not selected. Only selected atoms are the target of display model operations, such as wireframe or spacefill commands, and coloring operations.

== How to use ==
The following table shows hot to do the minimum things with jV.&lt;br /&gt;
{| class="wikitable" border="1" style="margin:0 auto" 
 ! Action !! Window, Linux !! Mac OS X 
 |-
 ! style="text-align:left" | rotate around X,Y axes
 | left drag || mouse drag
 |-
 ! style="text-align:left" | rotate around Z axis
 | Shift + right drag || Shift + command + drag
 |-
 ! style="text-align:left" | translate along X,Y axes
 | right drag || command + drag
 |-
 ! style="text-align:left" | translate along Z axis (zoom in/out)
 | Shift + left drag || Shift + drag
 |}
For the detail,
* The install manual [[Installaion of jV3]]
* The reference manual
  # [[Command List]]
  # [[Atom Expression]]
  # [[Vertex Expression]]
  # [[Use as Applet]]
  # [[Tutorials]]
  # [[GUI]]
  # [[Document type of the polygon file]]
  # [[Functional site information for molecules]]
Some examples
# [[Animation]]
# [[User jV with applet launcher]]

== Release note ==
Changes and improvements have been made as follows.

* version 3.1
** The following commands have been added; 'animrange', 'set adjustview', 'show godata', and 'show xps3'.
** The xPSSS expression has been added in order to select a group of atoms.
** Several public methods have been added to the applet so as to append molecule or polygon files after the applet started.
** The applet can send information about mouse-picked atoms to JavaScript.
* version 3.1.1
** Some problems in GUI menu [Options]-[Hetero Atoms] and [Hydrogens] have been fixed.
** Some problems in 'trace' command have been fixed.
* version 3.1.2
** eF-site ID has been changed to a new format.
* version 3.1.3
** Some problems in xps3 atom selection have been fixed.
* version 3.1.4
** Some problems in finalization process of openGL rendering have been fixed.
* version 3.1.5
** The output of 'show xps3' command has been modified.
** Some problems in 'save png/jpeg' command have been fixed.
* version 3.1.6
** Some problems in loading an empty polygon file have been fixed.
* version 3.1.7
** Some problems in initialization process of the applet have been fixed.
* version 3.2
** 'show site' command has been added.
* version 3.3 beta 1
** Availabe JOGL version is restricted to JSR-231 beta 5 only.
* version 3.3
** Both the previous JOGL (version 1.1.1) and JSR-231 are available.
** The following commands have been added; 'set viewpoint', 'show viewpoint', 'set imagesize', and 'show imagesize'.
* version 3.3.1
** Some problems in reading a pdbMLplus file have been fixed.
* version 3.4
** PDB format version 3 can be processed.</text>
    <sha1>3736d449584ffb240d921c6b3a7df06ca1fecd16</sha1>
  </revision>
  <revision>
    <id>122</id>
    <parentid>121</parentid>
    <timestamp>2009-03-09T07:22:30Z</timestamp>
    <contributor>
      <username>JVuser</username>
      <id>2</id>
    </contributor>
    <comment>/* How to use */</comment>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="4439" xml:space="preserve">jV is an interactive 3D viewer program to visualize protein and nucleic acid molecules. The program reads in a PDBML file that is an XML format for PDB. Usual PDB format files are also accepted. More than one molecule files can be opened and displayed at the same time and their display models and transforms can be operated separately. In addition to molecule files, a polygon file written in XML can be read and displayed. More than one polygon files can be opened at the same time and superposed on molecule images. The [http://ef-site.hgc.jp/eF-site/schema/polygon12.xsd XML schema] of the polygon file is available. jV can perform an animation of molecules. The animation file is a PDB format file in which each frame is separated by a MODEL line.

jV runs on Java Runtime Environment ([http://java.sun.com/javase/index.jsp JRE]) and can be used both as a standalone program and an applet. The 3D rendering is performed with the use of [https://jogl.dev.java.net/ JOGL] API. The version requirements are as follows.

* JRE (includes Java Plug-in) 1.4.2 or later
* JOGL 1.1.1 or JSR-231

Here, [http://java.sun.com/products/plugin/ Java Plug-in] is required in order to use the program as an applet.

The program allows an interactive mouse control and command execution. The commnad syntax follows that of [http://www.rasmol.org/ Rasmol] with some modifications. In order to handle the transform of each molecule and polygon separately, every files are set to be either selected or not selected. The transform operation commands, such as rotate or translate, act only on selected files. On the other hand, every atoms in a molecule are also set to be either selected or not selected independently of whether the molecule itself is selected or not selected. Only selected atoms are the target of display model operations, such as wireframe or spacefill commands, and coloring operations.

== How to use ==
The following table shows hot to do the minimum things with jV.&lt;br /&gt;
{| class="wikitable" border="1" style="margin:0 auto" 
 ! Action !! Window, Linux !! Mac OS X 
 |-
 ! style="text-align:left" | rotate around X,Y axes
 | left drag || mouse drag
 |-
 ! style="text-align:left" | rotate around Z axis
 | Shift + right drag || Shift + command + drag
 |-
 ! style="text-align:left" | translate along X,Y axes
 | right drag || command + drag
 |-
 ! style="text-align:left" | translate along Z axis (zoom in/out)
 | Shift + left drag || Shift + drag
 |}
For the detail,
* The install manual [[Installaion of jV3]]
* The reference manual
# [[Command List]]
# [[Atom Expression]]
# [[Vertex Expression]]
# [[Use as Applet]]
# [[Tutorials]]
# [[GUI]]
# [[Document type of the polygon file]]
# [[Functional site information for molecules]]
Some examples
# [[Animation]]
# [[User jV with applet launcher]]

== Release note ==
Changes and improvements have been made as follows.

* version 3.1
** The following commands have been added; 'animrange', 'set adjustview', 'show godata', and 'show xps3'.
** The xPSSS expression has been added in order to select a group of atoms.
** Several public methods have been added to the applet so as to append molecule or polygon files after the applet started.
** The applet can send information about mouse-picked atoms to JavaScript.
* version 3.1.1
** Some problems in GUI menu [Options]-[Hetero Atoms] and [Hydrogens] have been fixed.
** Some problems in 'trace' command have been fixed.
* version 3.1.2
** eF-site ID has been changed to a new format.
* version 3.1.3
** Some problems in xps3 atom selection have been fixed.
* version 3.1.4
** Some problems in finalization process of openGL rendering have been fixed.
* version 3.1.5
** The output of 'show xps3' command has been modified.
** Some problems in 'save png/jpeg' command have been fixed.
* version 3.1.6
** Some problems in loading an empty polygon file have been fixed.
* version 3.1.7
** Some problems in initialization process of the applet have been fixed.
* version 3.2
** 'show site' command has been added.
* version 3.3 beta 1
** Availabe JOGL version is restricted to JSR-231 beta 5 only.
* version 3.3
** Both the previous JOGL (version 1.1.1) and JSR-231 are available.
** The following commands have been added; 'set viewpoint', 'show viewpoint', 'set imagesize', and 'show imagesize'.
* version 3.3.1
** Some problems in reading a pdbMLplus file have been fixed.
* version 3.4
** PDB format version 3 can be processed.</text>
    <sha1>25198536f860ae7997b3eac83acbdd5812e80ff2</sha1>
  </revision>
  <revision>
    <id>123</id>
    <parentid>122</parentid>
    <timestamp>2009-03-09T07:23:35Z</timestamp>
    <contributor>
      <username>JVuser</username>
      <id>2</id>
    </contributor>
    <comment>/* How to use */</comment>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="4485" xml:space="preserve">jV is an interactive 3D viewer program to visualize protein and nucleic acid molecules. The program reads in a PDBML file that is an XML format for PDB. Usual PDB format files are also accepted. More than one molecule files can be opened and displayed at the same time and their display models and transforms can be operated separately. In addition to molecule files, a polygon file written in XML can be read and displayed. More than one polygon files can be opened at the same time and superposed on molecule images. The [http://ef-site.hgc.jp/eF-site/schema/polygon12.xsd XML schema] of the polygon file is available. jV can perform an animation of molecules. The animation file is a PDB format file in which each frame is separated by a MODEL line.

jV runs on Java Runtime Environment ([http://java.sun.com/javase/index.jsp JRE]) and can be used both as a standalone program and an applet. The 3D rendering is performed with the use of [https://jogl.dev.java.net/ JOGL] API. The version requirements are as follows.

* JRE (includes Java Plug-in) 1.4.2 or later
* JOGL 1.1.1 or JSR-231

Here, [http://java.sun.com/products/plugin/ Java Plug-in] is required in order to use the program as an applet.

The program allows an interactive mouse control and command execution. The commnad syntax follows that of [http://www.rasmol.org/ Rasmol] with some modifications. In order to handle the transform of each molecule and polygon separately, every files are set to be either selected or not selected. The transform operation commands, such as rotate or translate, act only on selected files. On the other hand, every atoms in a molecule are also set to be either selected or not selected independently of whether the molecule itself is selected or not selected. Only selected atoms are the target of display model operations, such as wireframe or spacefill commands, and coloring operations.

== How to use ==
The following table shows hot to do the minimum things with jV.&lt;br /&gt;
{| class="wikitable" border="1" style="margin:0 auto" 
 ! Action !! Window, Linux !! Mac OS X 
 |-
 ! style="text-align:left" | rotate around X,Y axes
 | left drag || mouse drag
 |-
 ! style="text-align:left" | rotate around Z axis
 | Shift + right drag || Shift + command + drag
 |-
 ! style="text-align:left" | translate along X,Y axes
 | right drag || command + drag
 |-
 ! style="text-align:left" | translate along Z axis (zoom in/out)
 | Shift + left drag || Shift + drag
 |}
For the detail,
* The install manual [[Installaion of jV3]]
* The reference manual
# [[Command List]]
# [[Atom Expression]]
# [[Vertex Expression]]
# [[Use as Applet]]
# [[Tutorials]]
# [[GUI]]
# [[Document type of the polygon file]]
# [[Functional site information for molecules]]
Some examples
# [[Animation]]
# [[User jV with applet launcher]]
PDF Document..
[[jV Manual]]
[[User's Guide]]

== Release note ==
Changes and improvements have been made as follows.

* version 3.1
** The following commands have been added; 'animrange', 'set adjustview', 'show godata', and 'show xps3'.
** The xPSSS expression has been added in order to select a group of atoms.
** Several public methods have been added to the applet so as to append molecule or polygon files after the applet started.
** The applet can send information about mouse-picked atoms to JavaScript.
* version 3.1.1
** Some problems in GUI menu [Options]-[Hetero Atoms] and [Hydrogens] have been fixed.
** Some problems in 'trace' command have been fixed.
* version 3.1.2
** eF-site ID has been changed to a new format.
* version 3.1.3
** Some problems in xps3 atom selection have been fixed.
* version 3.1.4
** Some problems in finalization process of openGL rendering have been fixed.
* version 3.1.5
** The output of 'show xps3' command has been modified.
** Some problems in 'save png/jpeg' command have been fixed.
* version 3.1.6
** Some problems in loading an empty polygon file have been fixed.
* version 3.1.7
** Some problems in initialization process of the applet have been fixed.
* version 3.2
** 'show site' command has been added.
* version 3.3 beta 1
** Availabe JOGL version is restricted to JSR-231 beta 5 only.
* version 3.3
** Both the previous JOGL (version 1.1.1) and JSR-231 are available.
** The following commands have been added; 'set viewpoint', 'show viewpoint', 'set imagesize', and 'show imagesize'.
* version 3.3.1
** Some problems in reading a pdbMLplus file have been fixed.
* version 3.4
** PDB format version 3 can be processed.</text>
    <sha1>5ae5c9b70f283c5a476a9a99717c426fc2ecc257</sha1>
  </revision>
  <revision>
    <id>124</id>
    <parentid>123</parentid>
    <timestamp>2009-03-09T07:24:11Z</timestamp>
    <contributor>
      <username>JVuser</username>
      <id>2</id>
    </contributor>
    <comment>/* How to use */</comment>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="4486" xml:space="preserve">jV is an interactive 3D viewer program to visualize protein and nucleic acid molecules. The program reads in a PDBML file that is an XML format for PDB. Usual PDB format files are also accepted. More than one molecule files can be opened and displayed at the same time and their display models and transforms can be operated separately. In addition to molecule files, a polygon file written in XML can be read and displayed. More than one polygon files can be opened at the same time and superposed on molecule images. The [http://ef-site.hgc.jp/eF-site/schema/polygon12.xsd XML schema] of the polygon file is available. jV can perform an animation of molecules. The animation file is a PDB format file in which each frame is separated by a MODEL line.

jV runs on Java Runtime Environment ([http://java.sun.com/javase/index.jsp JRE]) and can be used both as a standalone program and an applet. The 3D rendering is performed with the use of [https://jogl.dev.java.net/ JOGL] API. The version requirements are as follows.

* JRE (includes Java Plug-in) 1.4.2 or later
* JOGL 1.1.1 or JSR-231

Here, [http://java.sun.com/products/plugin/ Java Plug-in] is required in order to use the program as an applet.

The program allows an interactive mouse control and command execution. The commnad syntax follows that of [http://www.rasmol.org/ Rasmol] with some modifications. In order to handle the transform of each molecule and polygon separately, every files are set to be either selected or not selected. The transform operation commands, such as rotate or translate, act only on selected files. On the other hand, every atoms in a molecule are also set to be either selected or not selected independently of whether the molecule itself is selected or not selected. Only selected atoms are the target of display model operations, such as wireframe or spacefill commands, and coloring operations.

== How to use ==
The following table shows hot to do the minimum things with jV.&lt;br /&gt;
{| class="wikitable" border="1" style="margin:0 auto" 
 ! Action !! Window, Linux !! Mac OS X 
 |-
 ! style="text-align:left" | rotate around X,Y axes
 | left drag || mouse drag
 |-
 ! style="text-align:left" | rotate around Z axis
 | Shift + right drag || Shift + command + drag
 |-
 ! style="text-align:left" | translate along X,Y axes
 | right drag || command + drag
 |-
 ! style="text-align:left" | translate along Z axis (zoom in/out)
 | Shift + left drag || Shift + drag
 |}
For the detail,
PDF Document: [[jV Manual]] | [[User's Guide]]
* The install manual [[Installaion of jV3]]
* The reference manual
# [[Command List]]
# [[Atom Expression]]
# [[Vertex Expression]]
# [[Use as Applet]]
# [[Tutorials]]
# [[GUI]]
# [[Document type of the polygon file]]
# [[Functional site information for molecules]]
Some examples
# [[Animation]]
# [[User jV with applet launcher]]

== Release note ==
Changes and improvements have been made as follows.

* version 3.1
** The following commands have been added; 'animrange', 'set adjustview', 'show godata', and 'show xps3'.
** The xPSSS expression has been added in order to select a group of atoms.
** Several public methods have been added to the applet so as to append molecule or polygon files after the applet started.
** The applet can send information about mouse-picked atoms to JavaScript.
* version 3.1.1
** Some problems in GUI menu [Options]-[Hetero Atoms] and [Hydrogens] have been fixed.
** Some problems in 'trace' command have been fixed.
* version 3.1.2
** eF-site ID has been changed to a new format.
* version 3.1.3
** Some problems in xps3 atom selection have been fixed.
* version 3.1.4
** Some problems in finalization process of openGL rendering have been fixed.
* version 3.1.5
** The output of 'show xps3' command has been modified.
** Some problems in 'save png/jpeg' command have been fixed.
* version 3.1.6
** Some problems in loading an empty polygon file have been fixed.
* version 3.1.7
** Some problems in initialization process of the applet have been fixed.
* version 3.2
** 'show site' command has been added.
* version 3.3 beta 1
** Availabe JOGL version is restricted to JSR-231 beta 5 only.
* version 3.3
** Both the previous JOGL (version 1.1.1) and JSR-231 are available.
** The following commands have been added; 'set viewpoint', 'show viewpoint', 'set imagesize', and 'show imagesize'.
* version 3.3.1
** Some problems in reading a pdbMLplus file have been fixed.
* version 3.4
** PDB format version 3 can be processed.</text>
    <sha1>2cc36036d5e5bbff888405dfa0e61030476eb1ae</sha1>
  </revision>
  <revision>
    <id>125</id>
    <parentid>124</parentid>
    <timestamp>2009-03-09T07:24:42Z</timestamp>
    <contributor>
      <username>JVuser</username>
      <id>2</id>
    </contributor>
    <comment>/* How to use */</comment>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="4492" xml:space="preserve">jV is an interactive 3D viewer program to visualize protein and nucleic acid molecules. The program reads in a PDBML file that is an XML format for PDB. Usual PDB format files are also accepted. More than one molecule files can be opened and displayed at the same time and their display models and transforms can be operated separately. In addition to molecule files, a polygon file written in XML can be read and displayed. More than one polygon files can be opened at the same time and superposed on molecule images. The [http://ef-site.hgc.jp/eF-site/schema/polygon12.xsd XML schema] of the polygon file is available. jV can perform an animation of molecules. The animation file is a PDB format file in which each frame is separated by a MODEL line.

jV runs on Java Runtime Environment ([http://java.sun.com/javase/index.jsp JRE]) and can be used both as a standalone program and an applet. The 3D rendering is performed with the use of [https://jogl.dev.java.net/ JOGL] API. The version requirements are as follows.

* JRE (includes Java Plug-in) 1.4.2 or later
* JOGL 1.1.1 or JSR-231

Here, [http://java.sun.com/products/plugin/ Java Plug-in] is required in order to use the program as an applet.

The program allows an interactive mouse control and command execution. The commnad syntax follows that of [http://www.rasmol.org/ Rasmol] with some modifications. In order to handle the transform of each molecule and polygon separately, every files are set to be either selected or not selected. The transform operation commands, such as rotate or translate, act only on selected files. On the other hand, every atoms in a molecule are also set to be either selected or not selected independently of whether the molecule itself is selected or not selected. Only selected atoms are the target of display model operations, such as wireframe or spacefill commands, and coloring operations.

== How to use ==
The following table shows hot to do the minimum things with jV.&lt;br /&gt;
{| class="wikitable" border="1" style="margin:0 auto" 
 ! Action !! Window, Linux !! Mac OS X 
 |-
 ! style="text-align:left" | rotate around X,Y axes
 | left drag || mouse drag
 |-
 ! style="text-align:left" | rotate around Z axis
 | Shift + right drag || Shift + command + drag
 |-
 ! style="text-align:left" | translate along X,Y axes
 | right drag || command + drag
 |-
 ! style="text-align:left" | translate along Z axis (zoom in/out)
 | Shift + left drag || Shift + drag
 |}
For the detail,&lt;br /&gt;
PDF Document: [[jV Manual]] | [[User's Guide]]
* The install manual [[Installaion of jV3]]
* The reference manual
# [[Command List]]
# [[Atom Expression]]
# [[Vertex Expression]]
# [[Use as Applet]]
# [[Tutorials]]
# [[GUI]]
# [[Document type of the polygon file]]
# [[Functional site information for molecules]]
Some examples
# [[Animation]]
# [[User jV with applet launcher]]

== Release note ==
Changes and improvements have been made as follows.

* version 3.1
** The following commands have been added; 'animrange', 'set adjustview', 'show godata', and 'show xps3'.
** The xPSSS expression has been added in order to select a group of atoms.
** Several public methods have been added to the applet so as to append molecule or polygon files after the applet started.
** The applet can send information about mouse-picked atoms to JavaScript.
* version 3.1.1
** Some problems in GUI menu [Options]-[Hetero Atoms] and [Hydrogens] have been fixed.
** Some problems in 'trace' command have been fixed.
* version 3.1.2
** eF-site ID has been changed to a new format.
* version 3.1.3
** Some problems in xps3 atom selection have been fixed.
* version 3.1.4
** Some problems in finalization process of openGL rendering have been fixed.
* version 3.1.5
** The output of 'show xps3' command has been modified.
** Some problems in 'save png/jpeg' command have been fixed.
* version 3.1.6
** Some problems in loading an empty polygon file have been fixed.
* version 3.1.7
** Some problems in initialization process of the applet have been fixed.
* version 3.2
** 'show site' command has been added.
* version 3.3 beta 1
** Availabe JOGL version is restricted to JSR-231 beta 5 only.
* version 3.3
** Both the previous JOGL (version 1.1.1) and JSR-231 are available.
** The following commands have been added; 'set viewpoint', 'show viewpoint', 'set imagesize', and 'show imagesize'.
* version 3.3.1
** Some problems in reading a pdbMLplus file have been fixed.
* version 3.4
** PDB format version 3 can be processed.</text>
    <sha1>502c4ff3191bad9810dfcc477d4d779ecc133e61</sha1>
  </revision>
  <revision>
    <id>126</id>
    <parentid>125</parentid>
    <timestamp>2009-03-09T07:27:24Z</timestamp>
    <contributor>
      <username>JVuser</username>
      <id>2</id>
    </contributor>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="4509" xml:space="preserve">jV is an interactive 3D viewer program to visualize protein and nucleic acid molecules. The program reads in a PDBML file that is an XML format for PDB. Usual PDB format files are also accepted. More than one molecule files can be opened and displayed at the same time and their display models and transforms can be operated separately. In addition to molecule files, a polygon file written in XML can be read and displayed. More than one polygon files can be opened at the same time and superposed on molecule images. The [http://ef-site.hgc.jp/eF-site/schema/polygon12.xsd XML schema] of the polygon file is available. jV can perform an animation of molecules. The animation file is a PDB format file in which each frame is separated by a MODEL line.

jV runs on Java Runtime Environment ([http://java.sun.com/javase/index.jsp JRE]) and can be used both as a standalone program and an applet. The 3D rendering is performed with the use of [https://jogl.dev.java.net/ JOGL] API. The version requirements are as follows.

* JRE (includes Java Plug-in) 1.4.2 or later
* JOGL 1.1.1 or JSR-231

Here, [http://java.sun.com/products/plugin/ Java Plug-in] is required in order to use the program as an applet.

The program allows an interactive mouse control and command execution. The commnad syntax follows that of [http://www.rasmol.org/ Rasmol] with some modifications. In order to handle the transform of each molecule and polygon separately, every files are set to be either selected or not selected. The transform operation commands, such as rotate or translate, act only on selected files. On the other hand, every atoms in a molecule are also set to be either selected or not selected independently of whether the molecule itself is selected or not selected. Only selected atoms are the target of display model operations, such as wireframe or spacefill commands, and coloring operations.

[[Release note]]
== How to use ==
The following table shows hot to do the minimum things with jV.&lt;br /&gt;
{| class="wikitable" border="1" style="margin:0 auto" 
 ! Action !! Window, Linux !! Mac OS X 
 |-
 ! style="text-align:left" | rotate around X,Y axes
 | left drag || mouse drag
 |-
 ! style="text-align:left" | rotate around Z axis
 | Shift + right drag || Shift + command + drag
 |-
 ! style="text-align:left" | translate along X,Y axes
 | right drag || command + drag
 |-
 ! style="text-align:left" | translate along Z axis (zoom in/out)
 | Shift + left drag || Shift + drag
 |}
For the detail,&lt;br /&gt;
PDF Document: [[jV Manual]] | [[User's Guide]]
* The install manual [[Installaion of jV3]]
* The reference manual
# [[Command List]]
# [[Atom Expression]]
# [[Vertex Expression]]
# [[Use as Applet]]
# [[Tutorials]]
# [[GUI]]
# [[Document type of the polygon file]]
# [[Functional site information for molecules]]
Some examples
# [[Animation]]
# [[User jV with applet launcher]]

== Release note ==
Changes and improvements have been made as follows.

* version 3.1
** The following commands have been added; 'animrange', 'set adjustview', 'show godata', and 'show xps3'.
** The xPSSS expression has been added in order to select a group of atoms.
** Several public methods have been added to the applet so as to append molecule or polygon files after the applet started.
** The applet can send information about mouse-picked atoms to JavaScript.
* version 3.1.1
** Some problems in GUI menu [Options]-[Hetero Atoms] and [Hydrogens] have been fixed.
** Some problems in 'trace' command have been fixed.
* version 3.1.2
** eF-site ID has been changed to a new format.
* version 3.1.3
** Some problems in xps3 atom selection have been fixed.
* version 3.1.4
** Some problems in finalization process of openGL rendering have been fixed.
* version 3.1.5
** The output of 'show xps3' command has been modified.
** Some problems in 'save png/jpeg' command have been fixed.
* version 3.1.6
** Some problems in loading an empty polygon file have been fixed.
* version 3.1.7
** Some problems in initialization process of the applet have been fixed.
* version 3.2
** 'show site' command has been added.
* version 3.3 beta 1
** Availabe JOGL version is restricted to JSR-231 beta 5 only.
* version 3.3
** Both the previous JOGL (version 1.1.1) and JSR-231 are available.
** The following commands have been added; 'set viewpoint', 'show viewpoint', 'set imagesize', and 'show imagesize'.
* version 3.3.1
** Some problems in reading a pdbMLplus file have been fixed.
* version 3.4
** PDB format version 3 can be processed.</text>
    <sha1>e402b4ce69ba00bc2424e41ab52c9ed400b2f751</sha1>
  </revision>
  <revision>
    <id>127</id>
    <parentid>126</parentid>
    <timestamp>2009-03-09T07:27:58Z</timestamp>
    <contributor>
      <username>JVuser</username>
      <id>2</id>
    </contributor>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="2877" xml:space="preserve">jV is an interactive 3D viewer program to visualize protein and nucleic acid molecules. The program reads in a PDBML file that is an XML format for PDB. Usual PDB format files are also accepted. More than one molecule files can be opened and displayed at the same time and their display models and transforms can be operated separately. In addition to molecule files, a polygon file written in XML can be read and displayed. More than one polygon files can be opened at the same time and superposed on molecule images. The [http://ef-site.hgc.jp/eF-site/schema/polygon12.xsd XML schema] of the polygon file is available. jV can perform an animation of molecules. The animation file is a PDB format file in which each frame is separated by a MODEL line.

jV runs on Java Runtime Environment ([http://java.sun.com/javase/index.jsp JRE]) and can be used both as a standalone program and an applet. The 3D rendering is performed with the use of [https://jogl.dev.java.net/ JOGL] API. The version requirements are as follows.

* JRE (includes Java Plug-in) 1.4.2 or later
* JOGL 1.1.1 or JSR-231

Here, [http://java.sun.com/products/plugin/ Java Plug-in] is required in order to use the program as an applet.

The program allows an interactive mouse control and command execution. The commnad syntax follows that of [http://www.rasmol.org/ Rasmol] with some modifications. In order to handle the transform of each molecule and polygon separately, every files are set to be either selected or not selected. The transform operation commands, such as rotate or translate, act only on selected files. On the other hand, every atoms in a molecule are also set to be either selected or not selected independently of whether the molecule itself is selected or not selected. Only selected atoms are the target of display model operations, such as wireframe or spacefill commands, and coloring operations.

[[Release note]]
== How to use ==
The following table shows hot to do the minimum things with jV.&lt;br /&gt;
{| class="wikitable" border="1" style="margin:0 auto" 
 ! Action !! Window, Linux !! Mac OS X 
 |-
 ! style="text-align:left" | rotate around X,Y axes
 | left drag || mouse drag
 |-
 ! style="text-align:left" | rotate around Z axis
 | Shift + right drag || Shift + command + drag
 |-
 ! style="text-align:left" | translate along X,Y axes
 | right drag || command + drag
 |-
 ! style="text-align:left" | translate along Z axis (zoom in/out)
 | Shift + left drag || Shift + drag
 |}
For the detail,&lt;br /&gt;
PDF Document: [[jV Manual]] | [[User's Guide]]
* The install manual [[Installaion of jV3]]
* The reference manual
# [[Command List]]
# [[Atom Expression]]
# [[Vertex Expression]]
# [[Use as Applet]]
# [[Tutorials]]
# [[GUI]]
# [[Document type of the polygon file]]
# [[Functional site information for molecules]]
Some examples
# [[Animation]]
# [[User jV with applet launcher]]</text>
    <sha1>67d63a31bbbe7c339676ca4dab10cc15f968390c</sha1>
  </revision>
  <revision>
    <id>131</id>
    <parentid>127</parentid>
    <timestamp>2009-03-09T07:33:13Z</timestamp>
    <contributor>
      <username>JVuser</username>
      <id>2</id>
    </contributor>
    <comment>/* How to use */</comment>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="2896" xml:space="preserve">jV is an interactive 3D viewer program to visualize protein and nucleic acid molecules. The program reads in a PDBML file that is an XML format for PDB. Usual PDB format files are also accepted. More than one molecule files can be opened and displayed at the same time and their display models and transforms can be operated separately. In addition to molecule files, a polygon file written in XML can be read and displayed. More than one polygon files can be opened at the same time and superposed on molecule images. The [http://ef-site.hgc.jp/eF-site/schema/polygon12.xsd XML schema] of the polygon file is available. jV can perform an animation of molecules. The animation file is a PDB format file in which each frame is separated by a MODEL line.

jV runs on Java Runtime Environment ([http://java.sun.com/javase/index.jsp JRE]) and can be used both as a standalone program and an applet. The 3D rendering is performed with the use of [https://jogl.dev.java.net/ JOGL] API. The version requirements are as follows.

* JRE (includes Java Plug-in) 1.4.2 or later
* JOGL 1.1.1 or JSR-231

Here, [http://java.sun.com/products/plugin/ Java Plug-in] is required in order to use the program as an applet.

The program allows an interactive mouse control and command execution. The commnad syntax follows that of [http://www.rasmol.org/ Rasmol] with some modifications. In order to handle the transform of each molecule and polygon separately, every files are set to be either selected or not selected. The transform operation commands, such as rotate or translate, act only on selected files. On the other hand, every atoms in a molecule are also set to be either selected or not selected independently of whether the molecule itself is selected or not selected. Only selected atoms are the target of display model operations, such as wireframe or spacefill commands, and coloring operations.

[[Release note]]
== How to use ==
The following table shows hot to do the minimum things with jV.&lt;br /&gt;
{| class="wikitable" border="1" style="margin:0 auto" 
 ! Action !! Window, Linux !! Mac OS X 
 |-
 ! style="text-align:left" | rotate around X,Y axes
 | left drag || mouse drag
 |-
 ! style="text-align:left" | rotate around Z axis
 | Shift + right drag || Shift + command + drag
 |-
 ! style="text-align:left" | translate along X,Y axes
 | right drag || command + drag
 |-
 ! style="text-align:left" | translate along Z axis (zoom in/out)
 | Shift + left drag || Shift + drag
 |}
For the detail,&lt;br /&gt;
PDF Document: [[File:JV_Manual.pdf|jV Manual]] | [[User's Guide]]
* The install manual [[Installaion of jV3]]
* The reference manual
# [[Command List]]
# [[Atom Expression]]
# [[Vertex Expression]]
# [[Use as Applet]]
# [[Tutorials]]
# [[GUI]]
# [[Document type of the polygon file]]
# [[Functional site information for molecules]]
Some examples
# [[Animation]]
# [[User jV with applet launcher]]</text>
    <sha1>844d852abb081b37f8eef67a85f27806fdd4ef73</sha1>
  </revision>
  <revision>
    <id>132</id>
    <parentid>131</parentid>
    <timestamp>2009-03-09T07:34:11Z</timestamp>
    <contributor>
      <username>JVuser</username>
      <id>2</id>
    </contributor>
    <comment>/* How to use */</comment>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="2921" xml:space="preserve">jV is an interactive 3D viewer program to visualize protein and nucleic acid molecules. The program reads in a PDBML file that is an XML format for PDB. Usual PDB format files are also accepted. More than one molecule files can be opened and displayed at the same time and their display models and transforms can be operated separately. In addition to molecule files, a polygon file written in XML can be read and displayed. More than one polygon files can be opened at the same time and superposed on molecule images. The [http://ef-site.hgc.jp/eF-site/schema/polygon12.xsd XML schema] of the polygon file is available. jV can perform an animation of molecules. The animation file is a PDB format file in which each frame is separated by a MODEL line.

jV runs on Java Runtime Environment ([http://java.sun.com/javase/index.jsp JRE]) and can be used both as a standalone program and an applet. The 3D rendering is performed with the use of [https://jogl.dev.java.net/ JOGL] API. The version requirements are as follows.

* JRE (includes Java Plug-in) 1.4.2 or later
* JOGL 1.1.1 or JSR-231

Here, [http://java.sun.com/products/plugin/ Java Plug-in] is required in order to use the program as an applet.

The program allows an interactive mouse control and command execution. The commnad syntax follows that of [http://www.rasmol.org/ Rasmol] with some modifications. In order to handle the transform of each molecule and polygon separately, every files are set to be either selected or not selected. The transform operation commands, such as rotate or translate, act only on selected files. On the other hand, every atoms in a molecule are also set to be either selected or not selected independently of whether the molecule itself is selected or not selected. Only selected atoms are the target of display model operations, such as wireframe or spacefill commands, and coloring operations.

[[Release note]]
== How to use ==
The following table shows hot to do the minimum things with jV.&lt;br /&gt;
{| class="wikitable" border="1" style="margin:0 auto" 
 ! Action !! Window, Linux !! Mac OS X 
 |-
 ! style="text-align:left" | rotate around X,Y axes
 | left drag || mouse drag
 |-
 ! style="text-align:left" | rotate around Z axis
 | Shift + right drag || Shift + command + drag
 |-
 ! style="text-align:left" | translate along X,Y axes
 | right drag || command + drag
 |-
 ! style="text-align:left" | translate along Z axis (zoom in/out)
 | Shift + left drag || Shift + drag
 |}
For the detail,&lt;br /&gt;
PDF Document: [[File:JV_manual.pdf|jV Manual]] | [[File:JV3_User'sGuide.pdf|User's Guide]]
* The install manual [[Installaion of jV3]]
* The reference manual
# [[Command List]]
# [[Atom Expression]]
# [[Vertex Expression]]
# [[Use as Applet]]
# [[Tutorials]]
# [[GUI]]
# [[Document type of the polygon file]]
# [[Functional site information for molecules]]
Some examples
# [[Animation]]
# [[User jV with applet launcher]]</text>
    <sha1>f316c44ba3895b10a6d6155791e449d20123e531</sha1>
  </revision>
  <revision>
    <id>133</id>
    <parentid>132</parentid>
    <timestamp>2009-03-09T07:38:34Z</timestamp>
    <contributor>
      <username>JVuser</username>
      <id>2</id>
    </contributor>
    <comment>/* How to use */</comment>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="2923" xml:space="preserve">jV is an interactive 3D viewer program to visualize protein and nucleic acid molecules. The program reads in a PDBML file that is an XML format for PDB. Usual PDB format files are also accepted. More than one molecule files can be opened and displayed at the same time and their display models and transforms can be operated separately. In addition to molecule files, a polygon file written in XML can be read and displayed. More than one polygon files can be opened at the same time and superposed on molecule images. The [http://ef-site.hgc.jp/eF-site/schema/polygon12.xsd XML schema] of the polygon file is available. jV can perform an animation of molecules. The animation file is a PDB format file in which each frame is separated by a MODEL line.

jV runs on Java Runtime Environment ([http://java.sun.com/javase/index.jsp JRE]) and can be used both as a standalone program and an applet. The 3D rendering is performed with the use of [https://jogl.dev.java.net/ JOGL] API. The version requirements are as follows.

* JRE (includes Java Plug-in) 1.4.2 or later
* JOGL 1.1.1 or JSR-231

Here, [http://java.sun.com/products/plugin/ Java Plug-in] is required in order to use the program as an applet.

The program allows an interactive mouse control and command execution. The commnad syntax follows that of [http://www.rasmol.org/ Rasmol] with some modifications. In order to handle the transform of each molecule and polygon separately, every files are set to be either selected or not selected. The transform operation commands, such as rotate or translate, act only on selected files. On the other hand, every atoms in a molecule are also set to be either selected or not selected independently of whether the molecule itself is selected or not selected. Only selected atoms are the target of display model operations, such as wireframe or spacefill commands, and coloring operations.

[[Release note]]
== How to use ==
The following table shows hot to do the minimum things with jV.&lt;br /&gt;
{| class="wikitable" border="1" style="margin:0 auto" 
 ! Action !! Window, Linux !! Mac OS X 
 |-
 ! style="text-align:left" | rotate around X,Y axes
 | left drag || mouse drag
 |-
 ! style="text-align:left" | rotate around Z axis
 | Shift + right drag || Shift + command + drag
 |-
 ! style="text-align:left" | translate along X,Y axes
 | right drag || command + drag
 |-
 ! style="text-align:left" | translate along Z axis (zoom in/out)
 | Shift + left drag || Shift + drag
 |}
For the detail,&lt;br /&gt;
PDF Document: [[Media:JV_manual.pdf|jV Manual]] | [[Media:JV3_User'sGuide.pdf|User's Guide]]
* The install manual [[Installaion of jV3]]
* The reference manual
# [[Command List]]
# [[Atom Expression]]
# [[Vertex Expression]]
# [[Use as Applet]]
# [[Tutorials]]
# [[GUI]]
# [[Document type of the polygon file]]
# [[Functional site information for molecules]]
Some examples
# [[Animation]]
# [[User jV with applet launcher]]</text>
    <sha1>64a587a277ba7ee5b59c14821d755598e08105e1</sha1>
  </revision>
  <revision>
    <id>134</id>
    <parentid>133</parentid>
    <timestamp>2009-03-09T07:39:38Z</timestamp>
    <contributor>
      <username>JVuser</username>
      <id>2</id>
    </contributor>
    <comment>/* How to use */</comment>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="2947" xml:space="preserve">jV is an interactive 3D viewer program to visualize protein and nucleic acid molecules. The program reads in a PDBML file that is an XML format for PDB. Usual PDB format files are also accepted. More than one molecule files can be opened and displayed at the same time and their display models and transforms can be operated separately. In addition to molecule files, a polygon file written in XML can be read and displayed. More than one polygon files can be opened at the same time and superposed on molecule images. The [http://ef-site.hgc.jp/eF-site/schema/polygon12.xsd XML schema] of the polygon file is available. jV can perform an animation of molecules. The animation file is a PDB format file in which each frame is separated by a MODEL line.

jV runs on Java Runtime Environment ([http://java.sun.com/javase/index.jsp JRE]) and can be used both as a standalone program and an applet. The 3D rendering is performed with the use of [https://jogl.dev.java.net/ JOGL] API. The version requirements are as follows.

* JRE (includes Java Plug-in) 1.4.2 or later
* JOGL 1.1.1 or JSR-231

Here, [http://java.sun.com/products/plugin/ Java Plug-in] is required in order to use the program as an applet.

The program allows an interactive mouse control and command execution. The commnad syntax follows that of [http://www.rasmol.org/ Rasmol] with some modifications. In order to handle the transform of each molecule and polygon separately, every files are set to be either selected or not selected. The transform operation commands, such as rotate or translate, act only on selected files. On the other hand, every atoms in a molecule are also set to be either selected or not selected independently of whether the molecule itself is selected or not selected. Only selected atoms are the target of display model operations, such as wireframe or spacefill commands, and coloring operations.

[[Release note]]
== How to use ==
The following table shows hot to do the minimum things with jV.&lt;br /&gt;
{| class="wikitable" border="1" style="margin:0 auto" 
 ! Action !! Window, Linux !! Mac OS X 
 |-
 ! style="text-align:left" | rotate around X,Y axes
 | left drag || mouse drag
 |-
 ! style="text-align:left" | rotate around Z axis
 | Shift + right drag || Shift + command + drag
 |-
 ! style="text-align:left" | translate along X,Y axes
 | right drag || command + drag
 |-
 ! style="text-align:left" | translate along Z axis (zoom in/out)
 | Shift + left drag || Shift + drag
 |}
For the detail,&lt;br /&gt;
PDF Document: [[Media:JV_manual.pdf|jV Manual]] &amp;nbsp;&amp;nbsp;|&amp;nbsp;&amp;nbsp; [[Media:JV3_User'sGuide.pdf|User's Guide]]
* The install manual [[Installaion of jV3]]
* The reference manual
# [[Command List]]
# [[Atom Expression]]
# [[Vertex Expression]]
# [[Use as Applet]]
# [[Tutorials]]
# [[GUI]]
# [[Document type of the polygon file]]
# [[Functional site information for molecules]]
Some examples
# [[Animation]]
# [[User jV with applet launcher]]</text>
    <sha1>c09636ff609947f99bc0158573a5926e1d51cf49</sha1>
  </revision>
  <revision>
    <id>135</id>
    <parentid>134</parentid>
    <timestamp>2009-03-09T07:39:54Z</timestamp>
    <contributor>
      <username>JVuser</username>
      <id>2</id>
    </contributor>
    <comment>/* How to use */</comment>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="2959" xml:space="preserve">jV is an interactive 3D viewer program to visualize protein and nucleic acid molecules. The program reads in a PDBML file that is an XML format for PDB. Usual PDB format files are also accepted. More than one molecule files can be opened and displayed at the same time and their display models and transforms can be operated separately. In addition to molecule files, a polygon file written in XML can be read and displayed. More than one polygon files can be opened at the same time and superposed on molecule images. The [http://ef-site.hgc.jp/eF-site/schema/polygon12.xsd XML schema] of the polygon file is available. jV can perform an animation of molecules. The animation file is a PDB format file in which each frame is separated by a MODEL line.

jV runs on Java Runtime Environment ([http://java.sun.com/javase/index.jsp JRE]) and can be used both as a standalone program and an applet. The 3D rendering is performed with the use of [https://jogl.dev.java.net/ JOGL] API. The version requirements are as follows.

* JRE (includes Java Plug-in) 1.4.2 or later
* JOGL 1.1.1 or JSR-231

Here, [http://java.sun.com/products/plugin/ Java Plug-in] is required in order to use the program as an applet.

The program allows an interactive mouse control and command execution. The commnad syntax follows that of [http://www.rasmol.org/ Rasmol] with some modifications. In order to handle the transform of each molecule and polygon separately, every files are set to be either selected or not selected. The transform operation commands, such as rotate or translate, act only on selected files. On the other hand, every atoms in a molecule are also set to be either selected or not selected independently of whether the molecule itself is selected or not selected. Only selected atoms are the target of display model operations, such as wireframe or spacefill commands, and coloring operations.

[[Release note]]
== How to use ==
The following table shows hot to do the minimum things with jV.&lt;br /&gt;
{| class="wikitable" border="1" style="margin:0 auto" 
 ! Action !! Window, Linux !! Mac OS X 
 |-
 ! style="text-align:left" | rotate around X,Y axes
 | left drag || mouse drag
 |-
 ! style="text-align:left" | rotate around Z axis
 | Shift + right drag || Shift + command + drag
 |-
 ! style="text-align:left" | translate along X,Y axes
 | right drag || command + drag
 |-
 ! style="text-align:left" | translate along Z axis (zoom in/out)
 | Shift + left drag || Shift + drag
 |}
For the detail,&lt;br /&gt;
PDF Document: &amp;nbsp;&amp;nbsp;[[Media:JV_manual.pdf|jV Manual]] &amp;nbsp;&amp;nbsp;|&amp;nbsp;&amp;nbsp; [[Media:JV3_User'sGuide.pdf|User's Guide]]
* The install manual [[Installaion of jV3]]
* The reference manual
# [[Command List]]
# [[Atom Expression]]
# [[Vertex Expression]]
# [[Use as Applet]]
# [[Tutorials]]
# [[GUI]]
# [[Document type of the polygon file]]
# [[Functional site information for molecules]]
Some examples
# [[Animation]]
# [[User jV with applet launcher]]</text>
    <sha1>99e95240e8227ef13b3704ad9248bc09069fe5b6</sha1>
  </revision>
  <revision>
    <id>136</id>
    <parentid>135</parentid>
    <timestamp>2009-03-09T07:40:55Z</timestamp>
    <contributor>
      <username>JVuser</username>
      <id>2</id>
    </contributor>
    <comment>/* How to use */</comment>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="2993" xml:space="preserve">jV is an interactive 3D viewer program to visualize protein and nucleic acid molecules. The program reads in a PDBML file that is an XML format for PDB. Usual PDB format files are also accepted. More than one molecule files can be opened and displayed at the same time and their display models and transforms can be operated separately. In addition to molecule files, a polygon file written in XML can be read and displayed. More than one polygon files can be opened at the same time and superposed on molecule images. The [http://ef-site.hgc.jp/eF-site/schema/polygon12.xsd XML schema] of the polygon file is available. jV can perform an animation of molecules. The animation file is a PDB format file in which each frame is separated by a MODEL line.

jV runs on Java Runtime Environment ([http://java.sun.com/javase/index.jsp JRE]) and can be used both as a standalone program and an applet. The 3D rendering is performed with the use of [https://jogl.dev.java.net/ JOGL] API. The version requirements are as follows.

* JRE (includes Java Plug-in) 1.4.2 or later
* JOGL 1.1.1 or JSR-231

Here, [http://java.sun.com/products/plugin/ Java Plug-in] is required in order to use the program as an applet.

The program allows an interactive mouse control and command execution. The commnad syntax follows that of [http://www.rasmol.org/ Rasmol] with some modifications. In order to handle the transform of each molecule and polygon separately, every files are set to be either selected or not selected. The transform operation commands, such as rotate or translate, act only on selected files. On the other hand, every atoms in a molecule are also set to be either selected or not selected independently of whether the molecule itself is selected or not selected. Only selected atoms are the target of display model operations, such as wireframe or spacefill commands, and coloring operations.

[[Release note]]
== How to use ==
The following table shows hot to do the minimum things with jV.&lt;br /&gt;
{| class="wikitable" border="1" style="margin:0 auto" 
 ! Action !! Window, Linux !! Mac OS X 
 |-
 ! style="text-align:left" | rotate around X,Y axes
 | left drag || mouse drag
 |-
 ! style="text-align:left" | rotate around Z axis
 | Shift + right drag || Shift + command + drag
 |-
 ! style="text-align:left" | translate along X,Y axes
 | right drag || command + drag
 |-
 ! style="text-align:left" | translate along Z axis (zoom in/out)
 | Shift + left drag || Shift + drag
 |}
For the detail,&lt;br /&gt;
PDF Document: &amp;nbsp;&amp;nbsp;[[Media:JV_manual.pdf|jV Manual]](30 October 2006) &amp;nbsp;&amp;nbsp;|&amp;nbsp;&amp;nbsp; [[Media:JV3_User'sGuide.pdf|User's Guide]](30 Octover 2006)
* The install manual [[Installaion of jV3]]
* The reference manual
# [[Command List]]
# [[Atom Expression]]
# [[Vertex Expression]]
# [[Use as Applet]]
# [[Tutorials]]
# [[GUI]]
# [[Document type of the polygon file]]
# [[Functional site information for molecules]]
Some examples
# [[Animation]]
# [[User jV with applet launcher]]</text>
    <sha1>f760145e951d0e4d1c48547bc41e2f22861a4640</sha1>
  </revision>
  <revision>
    <id>139</id>
    <parentid>136</parentid>
    <timestamp>2009-03-09T07:48:54Z</timestamp>
    <contributor>
      <username>JVuser</username>
      <id>2</id>
    </contributor>
    <comment>/* How to use */</comment>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="2993" xml:space="preserve">jV is an interactive 3D viewer program to visualize protein and nucleic acid molecules. The program reads in a PDBML file that is an XML format for PDB. Usual PDB format files are also accepted. More than one molecule files can be opened and displayed at the same time and their display models and transforms can be operated separately. In addition to molecule files, a polygon file written in XML can be read and displayed. More than one polygon files can be opened at the same time and superposed on molecule images. The [http://ef-site.hgc.jp/eF-site/schema/polygon12.xsd XML schema] of the polygon file is available. jV can perform an animation of molecules. The animation file is a PDB format file in which each frame is separated by a MODEL line.

jV runs on Java Runtime Environment ([http://java.sun.com/javase/index.jsp JRE]) and can be used both as a standalone program and an applet. The 3D rendering is performed with the use of [https://jogl.dev.java.net/ JOGL] API. The version requirements are as follows.

* JRE (includes Java Plug-in) 1.4.2 or later
* JOGL 1.1.1 or JSR-231

Here, [http://java.sun.com/products/plugin/ Java Plug-in] is required in order to use the program as an applet.

The program allows an interactive mouse control and command execution. The commnad syntax follows that of [http://www.rasmol.org/ Rasmol] with some modifications. In order to handle the transform of each molecule and polygon separately, every files are set to be either selected or not selected. The transform operation commands, such as rotate or translate, act only on selected files. On the other hand, every atoms in a molecule are also set to be either selected or not selected independently of whether the molecule itself is selected or not selected. Only selected atoms are the target of display model operations, such as wireframe or spacefill commands, and coloring operations.

[[Release note]]
== How to use ==
The following table shows hot to do the minimum things with jV.&lt;br /&gt;
{| class="wikitable" border="1" style="margin:0 auto" 
 ! Action !! Window, Linux !! Mac OS X 
 |-
 ! style="text-align:left" | rotate around X,Y axes
 | left drag || mouse drag
 |-
 ! style="text-align:left" | rotate around Z axis
 | Shift + right drag || Shift + command + drag
 |-
 ! style="text-align:left" | translate along X,Y axes
 | right drag || command + drag
 |-
 ! style="text-align:left" | translate along Z axis (zoom in/out)
 | Shift + left drag || Shift + drag
 |}
For the detail,&lt;br /&gt;
PDF Document: &amp;nbsp;&amp;nbsp;[[Media:JV3_User'sGuide.pdf|User's Guide]](30 October 2006) &amp;nbsp;&amp;nbsp;|&amp;nbsp;&amp;nbsp; [[Media:JV_manual.pdf|jV Manual]](30 Octover 2006)
* The install manual [[Installaion of jV3]]
* The reference manual
# [[Tutorials]]
# [[GUI]]
# [[Document type of the polygon file]]
# [[Functional site information for molecules]]
# [[Command List]]
# [[Atom Expression]]
# [[Vertex Expression]]
# [[Use as Applet]]
Some examples
# [[Animation]]
# [[User jV with applet launcher]]</text>
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<page arvcontinue="20090309064103|101">
  <title>File:ProMode.jpg</title>
  <ns>6</ns>
  <id>13</id>
  <revision>
    <id>108</id>
    <timestamp>2009-03-09T06:48:33Z</timestamp>
    <contributor>
      <username>JVuser</username>
      <id>2</id>
    </contributor>
    <comment>{{Information|
 |Description=ProMode
 |Source=ProMode
 |Date=20090309
 |Author=WASEDA Univ,Japan.
}}</comment>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="100" xml:space="preserve">{{Information|
 |Description=ProMode
 |Source=ProMode
 |Date=20090309
 |Author=WASEDA Univ,Japan.
}}</text>
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  <title>File:Step-1.jpg</title>
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  <revision>
    <id>114</id>
    <timestamp>2009-03-09T06:53:21Z</timestamp>
    <contributor>
      <username>JVuser</username>
      <id>2</id>
    </contributor>
    <comment>{{Information|
 |Description=step-1
 |Source=eF-site jV
 |Date=20090309
 |Author=jV
}}</comment>
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 |Description=step-1
 |Source=eF-site jV
 |Date=20090309
 |Author=jV
}}</text>
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  <title>File:Step-2.jpg</title>
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  <revision>
    <id>115</id>
    <timestamp>2009-03-09T06:53:39Z</timestamp>
    <contributor>
      <username>JVuser</username>
      <id>2</id>
    </contributor>
    <comment>{{Information|
 |Description=step-2
 |Source=eF-site jV
 |Date=20090309
 |Author=jV
}}</comment>
    <model>wikitext</model>
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    <text bytes="86" xml:space="preserve">{{Information|
 |Description=step-2
 |Source=eF-site jV
 |Date=20090309
 |Author=jV
}}</text>
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</page>
<page arvcontinue="20090309064103|101">
  <title>Use jV applet with applet launcher</title>
  <ns>0</ns>
  <id>16</id>
  <revision>
    <id>118</id>
    <timestamp>2009-03-09T07:14:28Z</timestamp>
    <contributor>
      <username>JVuser</username>
      <id>2</id>
    </contributor>
    <comment>Created page with 'A brief introduction to use jV in applet.  == Minimum Example == To use jV applet, the best way is to with applet-launcher. jV after v3.6 is fully compatible with applet-launcher...'</comment>
    <model>wikitext</model>
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    <text bytes="1809" xml:space="preserve">A brief introduction to use jV in applet.

== Minimum Example ==
To use jV applet, the best way is to with applet-launcher. jV after v3.6 is fully compatible with applet-launcher.

 &lt;applet
   hspace="0" vspace="0" align="middle"
   name="jVwindow" height="600" width="600"
   archive="applet-launcher.jar,
   http://download.java.net/media/jogl/builds/archive/jsr-231-webstart-current/jogl.jar,
   http://download.java.net/media/gluegen/webstart/gluegen-rt.jar,jv3_6.jar"
   code="org.jdesktop.applet.util.JNLPAppletLauncher"&gt;
 &lt;!-- param for applet-launcher --&gt;
   &lt;param name="subapplet.classname" value="org.pdbj.viewer.gui.ViewerApplet"&gt;
   &lt;param name="subapplet.displayname" value="jV applet"&gt;
   &lt;param name="noddraw.check" value="true"/&gt;
   &lt;param name="noddraw.check.silent" value="true"/&gt;
   &lt;param name="progressbar" value="true"/&gt;
   &lt;param name="jnlpNumExtensions" value="1"/&gt;
   &lt;param name="jnlpExtension1"
    value="http://download.java.net/media/jogl/builds/archive/jsr-231-webstart-current/jogl.jnlp"/&gt;
 &lt;!-- param for jV --&gt;
   &lt;param value="" name="pdbURL"&gt;
    &lt;!-- replace the following with an appropriate URL --&gt;
   &lt;param name="pdbmlURL" value="http://eprots.protein.osaka-u.ac.jp/Rep_PDBML/1ashA1.xml.gz"&gt;
   &lt;param value="" name="polygonURL"&gt;
   &lt;param value="set picking ident;background black;wireframe off;cartoon;color group" name="commands"&gt;
 &lt;/applet&gt;

Upper part is almost same as the usual usage of applet launcher. See the [https://applet-launcher.dev.java.net/ applet-launcher page] for details. The latter part is for jV parameters.

Only the &lt;B&gt;bold face&lt;/B&gt; part is specific for jV.

To use this template, you need to get applet-launcher.jar from http://download.java.net/media/applet-launcher/applet-launcher.jar, and put it in the same server that jv.jar is placed.</text>
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</page>
<page arvcontinue="20090309064103|101">
  <title>Release note</title>
  <ns>0</ns>
  <id>17</id>
  <revision>
    <id>128</id>
    <timestamp>2009-03-09T07:28:15Z</timestamp>
    <contributor>
      <username>JVuser</username>
      <id>2</id>
    </contributor>
    <comment>Created page with 'Changes and improvements have been made as follows.  * version 3.1 ** The following commands have been added; 'animrange', 'set adjustview', 'show godata', and 'show xps3'. ** Th...'</comment>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="1611" xml:space="preserve">Changes and improvements have been made as follows.

* version 3.1
** The following commands have been added; 'animrange', 'set adjustview', 'show godata', and 'show xps3'.
** The xPSSS expression has been added in order to select a group of atoms.
** Several public methods have been added to the applet so as to append molecule or polygon files after the applet started.
** The applet can send information about mouse-picked atoms to JavaScript.
* version 3.1.1
** Some problems in GUI menu [Options]-[Hetero Atoms] and [Hydrogens] have been fixed.
** Some problems in 'trace' command have been fixed.
* version 3.1.2
** eF-site ID has been changed to a new format.
* version 3.1.3
** Some problems in xps3 atom selection have been fixed.
* version 3.1.4
** Some problems in finalization process of openGL rendering have been fixed.
* version 3.1.5
** The output of 'show xps3' command has been modified.
** Some problems in 'save png/jpeg' command have been fixed.
* version 3.1.6
** Some problems in loading an empty polygon file have been fixed.
* version 3.1.7
** Some problems in initialization process of the applet have been fixed.
* version 3.2
** 'show site' command has been added.
* version 3.3 beta 1
** Availabe JOGL version is restricted to JSR-231 beta 5 only.
* version 3.3
** Both the previous JOGL (version 1.1.1) and JSR-231 are available.
** The following commands have been added; 'set viewpoint', 'show viewpoint', 'set imagesize', and 'show imagesize'.
* version 3.3.1
** Some problems in reading a pdbMLplus file have been fixed.
* version 3.4
** PDB format version 3 can be processed.</text>
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  </revision>
</page>
<page arvcontinue="20090309064103|101">
  <title>File:JV3 User'sGuide.pdf</title>
  <ns>6</ns>
  <id>18</id>
  <revision>
    <id>129</id>
    <timestamp>2009-03-09T07:32:02Z</timestamp>
    <contributor>
      <username>JVuser</username>
      <id>2</id>
    </contributor>
    <comment>{{Information|
 |Description=jV3_User's Guide
 |Source=eF-site jV
 |Date=20090309
 |Author=jV
}}</comment>
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 |Description=jV3_User's Guide
 |Source=eF-site jV
 |Date=20090309
 |Author=jV
}}</text>
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  </revision>
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<page arvcontinue="20090309064103|101">
  <title>File:JV manual.pdf</title>
  <ns>6</ns>
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  <revision>
    <id>130</id>
    <timestamp>2009-03-09T07:32:36Z</timestamp>
    <contributor>
      <username>JVuser</username>
      <id>2</id>
    </contributor>
    <comment>{{Information|
 |Description=jV manual
 |Source=eF-site jV
 |Date=20090309
 |Author=jV
}}</comment>
    <model>wikitext</model>
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    <text bytes="89" xml:space="preserve">{{Information|
 |Description=jV manual
 |Source=eF-site jV
 |Date=20090309
 |Author=jV
}}</text>
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  </revision>
</page>
<page arvcontinue="20090309064103|101">
  <title>Command List</title>
  <ns>0</ns>
  <id>20</id>
  <revision>
    <id>137</id>
    <timestamp>2009-03-09T07:47:30Z</timestamp>
    <contributor>
      <username>JVuser</username>
      <id>2</id>
    </contributor>
    <comment>Created page with 'Command usage of jV follows that of Rasmol with some modifications. In the following part, command arguments that can take an arbitrary value are denoted as &lt;value&gt; for example, ...'</comment>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="1480" xml:space="preserve">Command usage of jV follows that of Rasmol with some modifications. In the following part, command arguments that can take an arbitrary value are denoted as &lt;value&gt; for example, arguments restricted to several possible values are listed with / as a delimiter, and arguments that can be omitted are put in brackets {}.
== anim ==
== animframe ==
== animmode ==
== animrange ==
== animselect ==
== animspeed ==
== animstep ==
== backbone ==
== background ==
== cartoon ==
== center ==
== color ==
== colorvertex ==
== cpk ==
== define ==
== display ==
== displayvertex ==
== echo ==
== exit ==
== fit ==
== fselect ==
== hbonds ==
== load ==
== pause ==
== quit ==
== refresh ==
== reset ==
=== default ===
=== cartoon ===
=== line_width ===
=== pickradius ===
=== point_size ===
=== polyline_width ===
=== transparency ===
== ribbons ==
== rotate ==
== save ==
== script ==
== select ==
== selectvertex ==
== set ==
=== adjustview ===
=== background ===
=== bondmode ===
=== cartoon ===
=== center ===
=== drawlevel ===
=== hbonds ===
=== hetero ===
=== hydrogen ===
=== imagesize ===
=== line_width ===
=== loadcenter ===
=== picking ===
=== pickradius ===
=== point_size ===
=== polyline_width ===
=== projection ===
=== specular ===
=== specpower ===
=== ssbonds ===
=== stereo ===
=== transparency ===
=== viewpoint ===
== show ==
== slab ==
== spacefill ==
== ssbonds ==
== stereo ==
== structure ==
== trace ==
== translate ==
== wireframe ==
== write ==
== zap ==
== zoom ==</text>
    <sha1>38937597c2954d0702657310ec169c3d58db76a1</sha1>
  </revision>
  <revision>
    <id>138</id>
    <parentid>137</parentid>
    <timestamp>2009-03-09T07:47:58Z</timestamp>
    <contributor>
      <username>JVuser</username>
      <id>2</id>
    </contributor>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="1520" xml:space="preserve"> {| style="float:right"
  |__TOC__
  |}
Command usage of jV follows that of Rasmol with some modifications. In the following part, command arguments that can take an arbitrary value are denoted as &lt;value&gt; for example, arguments restricted to several possible values are listed with / as a delimiter, and arguments that can be omitted are put in brackets {}.
== anim ==
== animframe ==
== animmode ==
== animrange ==
== animselect ==
== animspeed ==
== animstep ==
== backbone ==
== background ==
== cartoon ==
== center ==
== color ==
== colorvertex ==
== cpk ==
== define ==
== display ==
== displayvertex ==
== echo ==
== exit ==
== fit ==
== fselect ==
== hbonds ==
== load ==
== pause ==
== quit ==
== refresh ==
== reset ==
=== default ===
=== cartoon ===
=== line_width ===
=== pickradius ===
=== point_size ===
=== polyline_width ===
=== transparency ===
== ribbons ==
== rotate ==
== save ==
== script ==
== select ==
== selectvertex ==
== set ==
=== adjustview ===
=== background ===
=== bondmode ===
=== cartoon ===
=== center ===
=== drawlevel ===
=== hbonds ===
=== hetero ===
=== hydrogen ===
=== imagesize ===
=== line_width ===
=== loadcenter ===
=== picking ===
=== pickradius ===
=== point_size ===
=== polyline_width ===
=== projection ===
=== specular ===
=== specpower ===
=== ssbonds ===
=== stereo ===
=== transparency ===
=== viewpoint ===
== show ==
== slab ==
== spacefill ==
== ssbonds ==
== stereo ==
== structure ==
== trace ==
== translate ==
== wireframe ==
== write ==
== zap ==
== zoom ==</text>
    <sha1>92b0078de908e0c0098c5165af0b2939787b5fb7</sha1>
  </revision>
  <revision>
    <id>140</id>
    <parentid>138</parentid>
    <timestamp>2009-03-09T07:49:32Z</timestamp>
    <contributor>
      <username>JVuser</username>
      <id>2</id>
    </contributor>
    <comment>/* anim */</comment>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="1804" xml:space="preserve"> {| style="float:right"
  |__TOC__
  |}
Command usage of jV follows that of Rasmol with some modifications. In the following part, command arguments that can take an arbitrary value are denoted as &lt;value&gt; for example, arguments restricted to several possible values are listed with / as a delimiter, and arguments that can be omitted are put in brackets {}.
== anim ==
 anim forward {&lt;value&gt;}
Starts animation forward. If the &lt;value&gt; is given, just move frames forward by the specified amount.

 anim backward {&lt;value&gt;}
Starts animation backward. If the &lt;value&gt; is given, just move frames backward by the specified amount.

 anim stop
Stops animation.

== animframe ==
== animmode ==
== animrange ==
== animselect ==
== animspeed ==
== animstep ==
== backbone ==
== background ==
== cartoon ==
== center ==
== color ==
== colorvertex ==
== cpk ==
== define ==
== display ==
== displayvertex ==
== echo ==
== exit ==
== fit ==
== fselect ==
== hbonds ==
== load ==
== pause ==
== quit ==
== refresh ==
== reset ==
=== default ===
=== cartoon ===
=== line_width ===
=== pickradius ===
=== point_size ===
=== polyline_width ===
=== transparency ===
== ribbons ==
== rotate ==
== save ==
== script ==
== select ==
== selectvertex ==
== set ==
=== adjustview ===
=== background ===
=== bondmode ===
=== cartoon ===
=== center ===
=== drawlevel ===
=== hbonds ===
=== hetero ===
=== hydrogen ===
=== imagesize ===
=== line_width ===
=== loadcenter ===
=== picking ===
=== pickradius ===
=== point_size ===
=== polyline_width ===
=== projection ===
=== specular ===
=== specpower ===
=== ssbonds ===
=== stereo ===
=== transparency ===
=== viewpoint ===
== show ==
== slab ==
== spacefill ==
== ssbonds ==
== stereo ==
== structure ==
== trace ==
== translate ==
== wireframe ==
== write ==
== zap ==
== zoom ==</text>
    <sha1>6c3a9e377172766c104e9272e9fbe36a6316ab9d</sha1>
  </revision>
  <revision>
    <id>141</id>
    <parentid>140</parentid>
    <timestamp>2009-03-09T07:50:03Z</timestamp>
    <contributor>
      <username>JVuser</username>
      <id>2</id>
    </contributor>
    <comment>/* animframe */</comment>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="1962" xml:space="preserve"> {| style="float:right"
  |__TOC__
  |}
Command usage of jV follows that of Rasmol with some modifications. In the following part, command arguments that can take an arbitrary value are denoted as &lt;value&gt; for example, arguments restricted to several possible values are listed with / as a delimiter, and arguments that can be omitted are put in brackets {}.
== anim ==
 anim forward {&lt;value&gt;}
Starts animation forward. If the &lt;value&gt; is given, just move frames forward by the specified amount.

 anim backward {&lt;value&gt;}
Starts animation backward. If the &lt;value&gt; is given, just move frames backward by the specified amount.

 anim stop
Stops animation.

== animframe ==
 animframe &lt;frame&gt; {&lt;file_ID&gt;}
Sets the frame of all animation files for the specified value. When &lt;file_ID&gt; is given, only the specified file is processed.

== animmode ==
== animrange ==
== animselect ==
== animspeed ==
== animstep ==
== backbone ==
== background ==
== cartoon ==
== center ==
== color ==
== colorvertex ==
== cpk ==
== define ==
== display ==
== displayvertex ==
== echo ==
== exit ==
== fit ==
== fselect ==
== hbonds ==
== load ==
== pause ==
== quit ==
== refresh ==
== reset ==
=== default ===
=== cartoon ===
=== line_width ===
=== pickradius ===
=== point_size ===
=== polyline_width ===
=== transparency ===
== ribbons ==
== rotate ==
== save ==
== script ==
== select ==
== selectvertex ==
== set ==
=== adjustview ===
=== background ===
=== bondmode ===
=== cartoon ===
=== center ===
=== drawlevel ===
=== hbonds ===
=== hetero ===
=== hydrogen ===
=== imagesize ===
=== line_width ===
=== loadcenter ===
=== picking ===
=== pickradius ===
=== point_size ===
=== polyline_width ===
=== projection ===
=== specular ===
=== specpower ===
=== ssbonds ===
=== stereo ===
=== transparency ===
=== viewpoint ===
== show ==
== slab ==
== spacefill ==
== ssbonds ==
== stereo ==
== structure ==
== trace ==
== translate ==
== wireframe ==
== write ==
== zap ==
== zoom ==</text>
    <sha1>0e3cec0bc1812834fd7dc3cf9568fe679b6b9e0c</sha1>
  </revision>
  <revision>
    <id>142</id>
    <parentid>141</parentid>
    <timestamp>2009-03-09T07:50:20Z</timestamp>
    <contributor>
      <username>JVuser</username>
      <id>2</id>
    </contributor>
    <comment>/* animmode */</comment>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="2375" xml:space="preserve"> {| style="float:right"
  |__TOC__
  |}
Command usage of jV follows that of Rasmol with some modifications. In the following part, command arguments that can take an arbitrary value are denoted as &lt;value&gt; for example, arguments restricted to several possible values are listed with / as a delimiter, and arguments that can be omitted are put in brackets {}.
== anim ==
 anim forward {&lt;value&gt;}
Starts animation forward. If the &lt;value&gt; is given, just move frames forward by the specified amount.

 anim backward {&lt;value&gt;}
Starts animation backward. If the &lt;value&gt; is given, just move frames backward by the specified amount.

 anim stop
Stops animation.

== animframe ==
 animframe &lt;frame&gt; {&lt;file_ID&gt;}
Sets the frame of all animation files for the specified value. When &lt;file_ID&gt; is given, only the specified file is processed.

== animmode ==
 animmode once
Sets the behavior of animation for 'once'. When the frame reaches the last one, animation is stopped.

 animmode loop
Sets the behavior of animation for 'loop'. When the frame reaches the last one, animation is reset to the first frame and continues playing.

 animmode swing
Sets the behavior of animation for 'swing'. When the frame reaches the last one, the direction of animation is reversed.

== animrange ==
== animselect ==
== animspeed ==
== animstep ==
== backbone ==
== background ==
== cartoon ==
== center ==
== color ==
== colorvertex ==
== cpk ==
== define ==
== display ==
== displayvertex ==
== echo ==
== exit ==
== fit ==
== fselect ==
== hbonds ==
== load ==
== pause ==
== quit ==
== refresh ==
== reset ==
=== default ===
=== cartoon ===
=== line_width ===
=== pickradius ===
=== point_size ===
=== polyline_width ===
=== transparency ===
== ribbons ==
== rotate ==
== save ==
== script ==
== select ==
== selectvertex ==
== set ==
=== adjustview ===
=== background ===
=== bondmode ===
=== cartoon ===
=== center ===
=== drawlevel ===
=== hbonds ===
=== hetero ===
=== hydrogen ===
=== imagesize ===
=== line_width ===
=== loadcenter ===
=== picking ===
=== pickradius ===
=== point_size ===
=== polyline_width ===
=== projection ===
=== specular ===
=== specpower ===
=== ssbonds ===
=== stereo ===
=== transparency ===
=== viewpoint ===
== show ==
== slab ==
== spacefill ==
== ssbonds ==
== stereo ==
== structure ==
== trace ==
== translate ==
== wireframe ==
== write ==
== zap ==
== zoom ==</text>
    <sha1>50bf4e68e1322613db1e11b8bda5d0e2d81312bc</sha1>
  </revision>
  <revision>
    <id>143</id>
    <parentid>142</parentid>
    <timestamp>2009-03-09T07:50:34Z</timestamp>
    <contributor>
      <username>JVuser</username>
      <id>2</id>
    </contributor>
    <comment>/* animrange */</comment>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="2518" xml:space="preserve"> {| style="float:right"
  |__TOC__
  |}
Command usage of jV follows that of Rasmol with some modifications. In the following part, command arguments that can take an arbitrary value are denoted as &lt;value&gt; for example, arguments restricted to several possible values are listed with / as a delimiter, and arguments that can be omitted are put in brackets {}.
== anim ==
 anim forward {&lt;value&gt;}
Starts animation forward. If the &lt;value&gt; is given, just move frames forward by the specified amount.

 anim backward {&lt;value&gt;}
Starts animation backward. If the &lt;value&gt; is given, just move frames backward by the specified amount.

 anim stop
Stops animation.

== animframe ==
 animframe &lt;frame&gt; {&lt;file_ID&gt;}
Sets the frame of all animation files for the specified value. When &lt;file_ID&gt; is given, only the specified file is processed.

== animmode ==
 animmode once
Sets the behavior of animation for 'once'. When the frame reaches the last one, animation is stopped.

 animmode loop
Sets the behavior of animation for 'loop'. When the frame reaches the last one, animation is reset to the first frame and continues playing.

 animmode swing
Sets the behavior of animation for 'swing'. When the frame reaches the last one, the direction of animation is reversed.

== animrange ==
 animrange &lt;init_frame&gt;-&lt;term_frame&gt; {&lt;file_IDs&gt;}
Sets the range of all animation files. When is given, only the specified file is processed.

== animselect ==
== animspeed ==
== animstep ==
== backbone ==
== background ==
== cartoon ==
== center ==
== color ==
== colorvertex ==
== cpk ==
== define ==
== display ==
== displayvertex ==
== echo ==
== exit ==
== fit ==
== fselect ==
== hbonds ==
== load ==
== pause ==
== quit ==
== refresh ==
== reset ==
=== default ===
=== cartoon ===
=== line_width ===
=== pickradius ===
=== point_size ===
=== polyline_width ===
=== transparency ===
== ribbons ==
== rotate ==
== save ==
== script ==
== select ==
== selectvertex ==
== set ==
=== adjustview ===
=== background ===
=== bondmode ===
=== cartoon ===
=== center ===
=== drawlevel ===
=== hbonds ===
=== hetero ===
=== hydrogen ===
=== imagesize ===
=== line_width ===
=== loadcenter ===
=== picking ===
=== pickradius ===
=== point_size ===
=== polyline_width ===
=== projection ===
=== specular ===
=== specpower ===
=== ssbonds ===
=== stereo ===
=== transparency ===
=== viewpoint ===
== show ==
== slab ==
== spacefill ==
== ssbonds ==
== stereo ==
== structure ==
== trace ==
== translate ==
== wireframe ==
== write ==
== zap ==
== zoom ==</text>
    <sha1>286a8b0abeab3b53954a05027cfe99b685a56f8e</sha1>
  </revision>
  <revision>
    <id>144</id>
    <parentid>143</parentid>
    <timestamp>2009-03-09T07:50:50Z</timestamp>
    <contributor>
      <username>JVuser</username>
      <id>2</id>
    </contributor>
    <comment>/* animselect */</comment>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="2864" xml:space="preserve"> {| style="float:right"
  |__TOC__
  |}
Command usage of jV follows that of Rasmol with some modifications. In the following part, command arguments that can take an arbitrary value are denoted as &lt;value&gt; for example, arguments restricted to several possible values are listed with / as a delimiter, and arguments that can be omitted are put in brackets {}.
== anim ==
 anim forward {&lt;value&gt;}
Starts animation forward. If the &lt;value&gt; is given, just move frames forward by the specified amount.

 anim backward {&lt;value&gt;}
Starts animation backward. If the &lt;value&gt; is given, just move frames backward by the specified amount.

 anim stop
Stops animation.

== animframe ==
 animframe &lt;frame&gt; {&lt;file_ID&gt;}
Sets the frame of all animation files for the specified value. When &lt;file_ID&gt; is given, only the specified file is processed.

== animmode ==
 animmode once
Sets the behavior of animation for 'once'. When the frame reaches the last one, animation is stopped.

 animmode loop
Sets the behavior of animation for 'loop'. When the frame reaches the last one, animation is reset to the first frame and continues playing.

 animmode swing
Sets the behavior of animation for 'swing'. When the frame reaches the last one, the direction of animation is reversed.

== animrange ==
 animrange &lt;init_frame&gt;-&lt;term_frame&gt; {&lt;file_IDs&gt;}
Sets the range of all animation files. When is given, only the specified file is processed.

== animselect ==
 animselect {-a/-r} &lt;file_IDs&gt;
Selects the specified files and makes the others not selected. More than one file IDs can be specified by putting commas as the delimiter. When the option -a or -r is specified, only the selection status of the specified files are modified, selected or not selected, respectively, and the others remain unchanged.

== animspeed ==
== animstep ==
== backbone ==
== background ==
== cartoon ==
== center ==
== color ==
== colorvertex ==
== cpk ==
== define ==
== display ==
== displayvertex ==
== echo ==
== exit ==
== fit ==
== fselect ==
== hbonds ==
== load ==
== pause ==
== quit ==
== refresh ==
== reset ==
=== default ===
=== cartoon ===
=== line_width ===
=== pickradius ===
=== point_size ===
=== polyline_width ===
=== transparency ===
== ribbons ==
== rotate ==
== save ==
== script ==
== select ==
== selectvertex ==
== set ==
=== adjustview ===
=== background ===
=== bondmode ===
=== cartoon ===
=== center ===
=== drawlevel ===
=== hbonds ===
=== hetero ===
=== hydrogen ===
=== imagesize ===
=== line_width ===
=== loadcenter ===
=== picking ===
=== pickradius ===
=== point_size ===
=== polyline_width ===
=== projection ===
=== specular ===
=== specpower ===
=== ssbonds ===
=== stereo ===
=== transparency ===
=== viewpoint ===
== show ==
== slab ==
== spacefill ==
== ssbonds ==
== stereo ==
== structure ==
== trace ==
== translate ==
== wireframe ==
== write ==
== zap ==
== zoom ==</text>
    <sha1>8a0fe8421d8f06742720f244d94db1acaa4736a7</sha1>
  </revision>
  <revision>
    <id>145</id>
    <parentid>144</parentid>
    <timestamp>2009-03-09T07:51:03Z</timestamp>
    <contributor>
      <username>JVuser</username>
      <id>2</id>
    </contributor>
    <comment>/* animspeed */</comment>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="2964" xml:space="preserve"> {| style="float:right"
  |__TOC__
  |}
Command usage of jV follows that of Rasmol with some modifications. In the following part, command arguments that can take an arbitrary value are denoted as &lt;value&gt; for example, arguments restricted to several possible values are listed with / as a delimiter, and arguments that can be omitted are put in brackets {}.
== anim ==
 anim forward {&lt;value&gt;}
Starts animation forward. If the &lt;value&gt; is given, just move frames forward by the specified amount.

 anim backward {&lt;value&gt;}
Starts animation backward. If the &lt;value&gt; is given, just move frames backward by the specified amount.

 anim stop
Stops animation.

== animframe ==
 animframe &lt;frame&gt; {&lt;file_ID&gt;}
Sets the frame of all animation files for the specified value. When &lt;file_ID&gt; is given, only the specified file is processed.

== animmode ==
 animmode once
Sets the behavior of animation for 'once'. When the frame reaches the last one, animation is stopped.

 animmode loop
Sets the behavior of animation for 'loop'. When the frame reaches the last one, animation is reset to the first frame and continues playing.

 animmode swing
Sets the behavior of animation for 'swing'. When the frame reaches the last one, the direction of animation is reversed.

== animrange ==
 animrange &lt;init_frame&gt;-&lt;term_frame&gt; {&lt;file_IDs&gt;}
Sets the range of all animation files. When is given, only the specified file is processed.

== animselect ==
 animselect {-a/-r} &lt;file_IDs&gt;
Selects the specified files and makes the others not selected. More than one file IDs can be specified by putting commas as the delimiter. When the option -a or -r is specified, only the selection status of the specified files are modified, selected or not selected, respectively, and the others remain unchanged.

== animspeed ==
 animspeed &lt;speed&gt;
Sets the animation speed. The argument should be an integer value from 1 to 20.

== animstep ==
== backbone ==
== background ==
== cartoon ==
== center ==
== color ==
== colorvertex ==
== cpk ==
== define ==
== display ==
== displayvertex ==
== echo ==
== exit ==
== fit ==
== fselect ==
== hbonds ==
== load ==
== pause ==
== quit ==
== refresh ==
== reset ==
=== default ===
=== cartoon ===
=== line_width ===
=== pickradius ===
=== point_size ===
=== polyline_width ===
=== transparency ===
== ribbons ==
== rotate ==
== save ==
== script ==
== select ==
== selectvertex ==
== set ==
=== adjustview ===
=== background ===
=== bondmode ===
=== cartoon ===
=== center ===
=== drawlevel ===
=== hbonds ===
=== hetero ===
=== hydrogen ===
=== imagesize ===
=== line_width ===
=== loadcenter ===
=== picking ===
=== pickradius ===
=== point_size ===
=== polyline_width ===
=== projection ===
=== specular ===
=== specpower ===
=== ssbonds ===
=== stereo ===
=== transparency ===
=== viewpoint ===
== show ==
== slab ==
== spacefill ==
== ssbonds ==
== stereo ==
== structure ==
== trace ==
== translate ==
== wireframe ==
== write ==
== zap ==
== zoom ==</text>
    <sha1>cf8d2190b1dd76c6183ff82877d8957a9f3ebfe5</sha1>
  </revision>
  <revision>
    <id>146</id>
    <parentid>145</parentid>
    <timestamp>2009-03-09T07:51:16Z</timestamp>
    <contributor>
      <username>JVuser</username>
      <id>2</id>
    </contributor>
    <comment>/* animstep */</comment>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="3119" xml:space="preserve"> {| style="float:right"
  |__TOC__
  |}
Command usage of jV follows that of Rasmol with some modifications. In the following part, command arguments that can take an arbitrary value are denoted as &lt;value&gt; for example, arguments restricted to several possible values are listed with / as a delimiter, and arguments that can be omitted are put in brackets {}.
== anim ==
 anim forward {&lt;value&gt;}
Starts animation forward. If the &lt;value&gt; is given, just move frames forward by the specified amount.

 anim backward {&lt;value&gt;}
Starts animation backward. If the &lt;value&gt; is given, just move frames backward by the specified amount.

 anim stop
Stops animation.

== animframe ==
 animframe &lt;frame&gt; {&lt;file_ID&gt;}
Sets the frame of all animation files for the specified value. When &lt;file_ID&gt; is given, only the specified file is processed.

== animmode ==
 animmode once
Sets the behavior of animation for 'once'. When the frame reaches the last one, animation is stopped.

 animmode loop
Sets the behavior of animation for 'loop'. When the frame reaches the last one, animation is reset to the first frame and continues playing.

 animmode swing
Sets the behavior of animation for 'swing'. When the frame reaches the last one, the direction of animation is reversed.

== animrange ==
 animrange &lt;init_frame&gt;-&lt;term_frame&gt; {&lt;file_IDs&gt;}
Sets the range of all animation files. When is given, only the specified file is processed.

== animselect ==
 animselect {-a/-r} &lt;file_IDs&gt;
Selects the specified files and makes the others not selected. More than one file IDs can be specified by putting commas as the delimiter. When the option -a or -r is specified, only the selection status of the specified files are modified, selected or not selected, respectively, and the others remain unchanged.

== animspeed ==
 animspeed &lt;speed&gt;
Sets the animation speed. The argument should be an integer value from 1 to 20.

== animstep ==
 animstep &lt;step&gt; {&lt;file_ID&gt;}
Sets the step of all animation files for the specified value. When &lt;file_ID&gt; is given, only the specified file is processed.

== backbone ==
== background ==
== cartoon ==
== center ==
== color ==
== colorvertex ==
== cpk ==
== define ==
== display ==
== displayvertex ==
== echo ==
== exit ==
== fit ==
== fselect ==
== hbonds ==
== load ==
== pause ==
== quit ==
== refresh ==
== reset ==
=== default ===
=== cartoon ===
=== line_width ===
=== pickradius ===
=== point_size ===
=== polyline_width ===
=== transparency ===
== ribbons ==
== rotate ==
== save ==
== script ==
== select ==
== selectvertex ==
== set ==
=== adjustview ===
=== background ===
=== bondmode ===
=== cartoon ===
=== center ===
=== drawlevel ===
=== hbonds ===
=== hetero ===
=== hydrogen ===
=== imagesize ===
=== line_width ===
=== loadcenter ===
=== picking ===
=== pickradius ===
=== point_size ===
=== polyline_width ===
=== projection ===
=== specular ===
=== specpower ===
=== ssbonds ===
=== stereo ===
=== transparency ===
=== viewpoint ===
== show ==
== slab ==
== spacefill ==
== ssbonds ==
== stereo ==
== structure ==
== trace ==
== translate ==
== wireframe ==
== write ==
== zap ==
== zoom ==</text>
    <sha1>6dddf26cb58d1318b5c1ad95fcba16e2d09792e7</sha1>
  </revision>
  <revision>
    <id>147</id>
    <parentid>146</parentid>
    <timestamp>2009-03-09T07:51:27Z</timestamp>
    <contributor>
      <username>JVuser</username>
      <id>2</id>
    </contributor>
    <comment>/* backbone */</comment>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="3384" xml:space="preserve"> {| style="float:right"
  |__TOC__
  |}
Command usage of jV follows that of Rasmol with some modifications. In the following part, command arguments that can take an arbitrary value are denoted as &lt;value&gt; for example, arguments restricted to several possible values are listed with / as a delimiter, and arguments that can be omitted are put in brackets {}.
== anim ==
 anim forward {&lt;value&gt;}
Starts animation forward. If the &lt;value&gt; is given, just move frames forward by the specified amount.

 anim backward {&lt;value&gt;}
Starts animation backward. If the &lt;value&gt; is given, just move frames backward by the specified amount.

 anim stop
Stops animation.

== animframe ==
 animframe &lt;frame&gt; {&lt;file_ID&gt;}
Sets the frame of all animation files for the specified value. When &lt;file_ID&gt; is given, only the specified file is processed.

== animmode ==
 animmode once
Sets the behavior of animation for 'once'. When the frame reaches the last one, animation is stopped.

 animmode loop
Sets the behavior of animation for 'loop'. When the frame reaches the last one, animation is reset to the first frame and continues playing.

 animmode swing
Sets the behavior of animation for 'swing'. When the frame reaches the last one, the direction of animation is reversed.

== animrange ==
 animrange &lt;init_frame&gt;-&lt;term_frame&gt; {&lt;file_IDs&gt;}
Sets the range of all animation files. When is given, only the specified file is processed.

== animselect ==
 animselect {-a/-r} &lt;file_IDs&gt;
Selects the specified files and makes the others not selected. More than one file IDs can be specified by putting commas as the delimiter. When the option -a or -r is specified, only the selection status of the specified files are modified, selected or not selected, respectively, and the others remain unchanged.

== animspeed ==
 animspeed &lt;speed&gt;
Sets the animation speed. The argument should be an integer value from 1 to 20.

== animstep ==
 animstep &lt;step&gt; {&lt;file_ID&gt;}
Sets the step of all animation files for the specified value. When &lt;file_ID&gt; is given, only the specified file is processed.

== backbone ==
 backbone {on/true}
Turns on the selected backbone bonds.

 backbone off/false
Turns off the selected backbone bonds.

 backbone &lt;radius&gt;
Turns on the selected backbone bonds with the specified raidus (angstrom or Rasmol unit). The maximum parameter value is 2.0.

== background ==
== cartoon ==
== center ==
== color ==
== colorvertex ==
== cpk ==
== define ==
== display ==
== displayvertex ==
== echo ==
== exit ==
== fit ==
== fselect ==
== hbonds ==
== load ==
== pause ==
== quit ==
== refresh ==
== reset ==
=== default ===
=== cartoon ===
=== line_width ===
=== pickradius ===
=== point_size ===
=== polyline_width ===
=== transparency ===
== ribbons ==
== rotate ==
== save ==
== script ==
== select ==
== selectvertex ==
== set ==
=== adjustview ===
=== background ===
=== bondmode ===
=== cartoon ===
=== center ===
=== drawlevel ===
=== hbonds ===
=== hetero ===
=== hydrogen ===
=== imagesize ===
=== line_width ===
=== loadcenter ===
=== picking ===
=== pickradius ===
=== point_size ===
=== polyline_width ===
=== projection ===
=== specular ===
=== specpower ===
=== ssbonds ===
=== stereo ===
=== transparency ===
=== viewpoint ===
== show ==
== slab ==
== spacefill ==
== ssbonds ==
== stereo ==
== structure ==
== trace ==
== translate ==
== wireframe ==
== write ==
== zap ==
== zoom ==</text>
    <sha1>191ec0ed4934535b303f0852bd704ebb69f9abcc</sha1>
  </revision>
  <revision>
    <id>148</id>
    <parentid>147</parentid>
    <timestamp>2009-03-09T07:51:36Z</timestamp>
    <contributor>
      <username>JVuser</username>
      <id>2</id>
    </contributor>
    <comment>/* background */</comment>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="3508" xml:space="preserve"> {| style="float:right"
  |__TOC__
  |}
Command usage of jV follows that of Rasmol with some modifications. In the following part, command arguments that can take an arbitrary value are denoted as &lt;value&gt; for example, arguments restricted to several possible values are listed with / as a delimiter, and arguments that can be omitted are put in brackets {}.
== anim ==
 anim forward {&lt;value&gt;}
Starts animation forward. If the &lt;value&gt; is given, just move frames forward by the specified amount.

 anim backward {&lt;value&gt;}
Starts animation backward. If the &lt;value&gt; is given, just move frames backward by the specified amount.

 anim stop
Stops animation.

== animframe ==
 animframe &lt;frame&gt; {&lt;file_ID&gt;}
Sets the frame of all animation files for the specified value. When &lt;file_ID&gt; is given, only the specified file is processed.

== animmode ==
 animmode once
Sets the behavior of animation for 'once'. When the frame reaches the last one, animation is stopped.

 animmode loop
Sets the behavior of animation for 'loop'. When the frame reaches the last one, animation is reset to the first frame and continues playing.

 animmode swing
Sets the behavior of animation for 'swing'. When the frame reaches the last one, the direction of animation is reversed.

== animrange ==
 animrange &lt;init_frame&gt;-&lt;term_frame&gt; {&lt;file_IDs&gt;}
Sets the range of all animation files. When is given, only the specified file is processed.

== animselect ==
 animselect {-a/-r} &lt;file_IDs&gt;
Selects the specified files and makes the others not selected. More than one file IDs can be specified by putting commas as the delimiter. When the option -a or -r is specified, only the selection status of the specified files are modified, selected or not selected, respectively, and the others remain unchanged.

== animspeed ==
 animspeed &lt;speed&gt;
Sets the animation speed. The argument should be an integer value from 1 to 20.

== animstep ==
 animstep &lt;step&gt; {&lt;file_ID&gt;}
Sets the step of all animation files for the specified value. When &lt;file_ID&gt; is given, only the specified file is processed.

== backbone ==
 backbone {on/true}
Turns on the selected backbone bonds.

 backbone off/false
Turns off the selected backbone bonds.

 backbone &lt;radius&gt;
Turns on the selected backbone bonds with the specified raidus (angstrom or Rasmol unit). The maximum parameter value is 2.0.

== background ==
 background &lt;color&gt;
Changes the background color. The color may be given as RGB values [r,g,b], or predefined color names.

== cartoon ==
== center ==
== color ==
== colorvertex ==
== cpk ==
== define ==
== display ==
== displayvertex ==
== echo ==
== exit ==
== fit ==
== fselect ==
== hbonds ==
== load ==
== pause ==
== quit ==
== refresh ==
== reset ==
=== default ===
=== cartoon ===
=== line_width ===
=== pickradius ===
=== point_size ===
=== polyline_width ===
=== transparency ===
== ribbons ==
== rotate ==
== save ==
== script ==
== select ==
== selectvertex ==
== set ==
=== adjustview ===
=== background ===
=== bondmode ===
=== cartoon ===
=== center ===
=== drawlevel ===
=== hbonds ===
=== hetero ===
=== hydrogen ===
=== imagesize ===
=== line_width ===
=== loadcenter ===
=== picking ===
=== pickradius ===
=== point_size ===
=== polyline_width ===
=== projection ===
=== specular ===
=== specpower ===
=== ssbonds ===
=== stereo ===
=== transparency ===
=== viewpoint ===
== show ==
== slab ==
== spacefill ==
== ssbonds ==
== stereo ==
== structure ==
== trace ==
== translate ==
== wireframe ==
== write ==
== zap ==
== zoom ==</text>
    <sha1>8b0593cbe93b6652c4964bc64ebfd4a396b81b82</sha1>
  </revision>
  <revision>
    <id>149</id>
    <parentid>148</parentid>
    <timestamp>2009-03-09T07:51:50Z</timestamp>
    <contributor>
      <username>JVuser</username>
      <id>2</id>
    </contributor>
    <comment>/* cartoon */</comment>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="3826" xml:space="preserve"> {| style="float:right"
  |__TOC__
  |}
Command usage of jV follows that of Rasmol with some modifications. In the following part, command arguments that can take an arbitrary value are denoted as &lt;value&gt; for example, arguments restricted to several possible values are listed with / as a delimiter, and arguments that can be omitted are put in brackets {}.
== anim ==
 anim forward {&lt;value&gt;}
Starts animation forward. If the &lt;value&gt; is given, just move frames forward by the specified amount.

 anim backward {&lt;value&gt;}
Starts animation backward. If the &lt;value&gt; is given, just move frames backward by the specified amount.

 anim stop
Stops animation.

== animframe ==
 animframe &lt;frame&gt; {&lt;file_ID&gt;}
Sets the frame of all animation files for the specified value. When &lt;file_ID&gt; is given, only the specified file is processed.

== animmode ==
 animmode once
Sets the behavior of animation for 'once'. When the frame reaches the last one, animation is stopped.

 animmode loop
Sets the behavior of animation for 'loop'. When the frame reaches the last one, animation is reset to the first frame and continues playing.

 animmode swing
Sets the behavior of animation for 'swing'. When the frame reaches the last one, the direction of animation is reversed.

== animrange ==
 animrange &lt;init_frame&gt;-&lt;term_frame&gt; {&lt;file_IDs&gt;}
Sets the range of all animation files. When is given, only the specified file is processed.

== animselect ==
 animselect {-a/-r} &lt;file_IDs&gt;
Selects the specified files and makes the others not selected. More than one file IDs can be specified by putting commas as the delimiter. When the option -a or -r is specified, only the selection status of the specified files are modified, selected or not selected, respectively, and the others remain unchanged.

== animspeed ==
 animspeed &lt;speed&gt;
Sets the animation speed. The argument should be an integer value from 1 to 20.

== animstep ==
 animstep &lt;step&gt; {&lt;file_ID&gt;}
Sets the step of all animation files for the specified value. When &lt;file_ID&gt; is given, only the specified file is processed.

== backbone ==
 backbone {on/true}
Turns on the selected backbone bonds.

 backbone off/false
Turns off the selected backbone bonds.

 backbone &lt;radius&gt;
Turns on the selected backbone bonds with the specified raidus (angstrom or Rasmol unit). The maximum parameter value is 2.0.

== background ==
 background &lt;color&gt;
Changes the background color. The color may be given as RGB values [r,g,b], or predefined color names.

== cartoon ==
 cartoon {on/true}
Turns on the thick ribbons for the selected residues.

 cartoon off/false
Turns off the thick ribbons for the selected residues.

 cartoon &lt;half_width&gt;
Turns on the thick ribbons for the selected residues with the specified half width (angstrom or Rasmol unit). The maximum parameter value is 4.0.

== center ==
== color ==
== colorvertex ==
== cpk ==
== define ==
== display ==
== displayvertex ==
== echo ==
== exit ==
== fit ==
== fselect ==
== hbonds ==
== load ==
== pause ==
== quit ==
== refresh ==
== reset ==
=== default ===
=== cartoon ===
=== line_width ===
=== pickradius ===
=== point_size ===
=== polyline_width ===
=== transparency ===
== ribbons ==
== rotate ==
== save ==
== script ==
== select ==
== selectvertex ==
== set ==
=== adjustview ===
=== background ===
=== bondmode ===
=== cartoon ===
=== center ===
=== drawlevel ===
=== hbonds ===
=== hetero ===
=== hydrogen ===
=== imagesize ===
=== line_width ===
=== loadcenter ===
=== picking ===
=== pickradius ===
=== point_size ===
=== polyline_width ===
=== projection ===
=== specular ===
=== specpower ===
=== ssbonds ===
=== stereo ===
=== transparency ===
=== viewpoint ===
== show ==
== slab ==
== spacefill ==
== ssbonds ==
== stereo ==
== structure ==
== trace ==
== translate ==
== wireframe ==
== write ==
== zap ==
== zoom ==</text>
    <sha1>c6f5f3a555fc8cdc771505f38407235d4db7aa2b</sha1>
  </revision>
  <revision>
    <id>150</id>
    <parentid>149</parentid>
    <timestamp>2009-03-09T07:52:06Z</timestamp>
    <contributor>
      <username>JVuser</username>
      <id>2</id>
    </contributor>
    <comment>/* center */</comment>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="4682" xml:space="preserve"> {| style="float:right"
  |__TOC__
  |}
Command usage of jV follows that of Rasmol with some modifications. In the following part, command arguments that can take an arbitrary value are denoted as &lt;value&gt; for example, arguments restricted to several possible values are listed with / as a delimiter, and arguments that can be omitted are put in brackets {}.
== anim ==
 anim forward {&lt;value&gt;}
Starts animation forward. If the &lt;value&gt; is given, just move frames forward by the specified amount.

 anim backward {&lt;value&gt;}
Starts animation backward. If the &lt;value&gt; is given, just move frames backward by the specified amount.

 anim stop
Stops animation.

== animframe ==
 animframe &lt;frame&gt; {&lt;file_ID&gt;}
Sets the frame of all animation files for the specified value. When &lt;file_ID&gt; is given, only the specified file is processed.

== animmode ==
 animmode once
Sets the behavior of animation for 'once'. When the frame reaches the last one, animation is stopped.

 animmode loop
Sets the behavior of animation for 'loop'. When the frame reaches the last one, animation is reset to the first frame and continues playing.

 animmode swing
Sets the behavior of animation for 'swing'. When the frame reaches the last one, the direction of animation is reversed.

== animrange ==
 animrange &lt;init_frame&gt;-&lt;term_frame&gt; {&lt;file_IDs&gt;}
Sets the range of all animation files. When is given, only the specified file is processed.

== animselect ==
 animselect {-a/-r} &lt;file_IDs&gt;
Selects the specified files and makes the others not selected. More than one file IDs can be specified by putting commas as the delimiter. When the option -a or -r is specified, only the selection status of the specified files are modified, selected or not selected, respectively, and the others remain unchanged.

== animspeed ==
 animspeed &lt;speed&gt;
Sets the animation speed. The argument should be an integer value from 1 to 20.

== animstep ==
 animstep &lt;step&gt; {&lt;file_ID&gt;}
Sets the step of all animation files for the specified value. When &lt;file_ID&gt; is given, only the specified file is processed.

== backbone ==
 backbone {on/true}
Turns on the selected backbone bonds.

 backbone off/false
Turns off the selected backbone bonds.

 backbone &lt;radius&gt;
Turns on the selected backbone bonds with the specified raidus (angstrom or Rasmol unit). The maximum parameter value is 2.0.

== background ==
 background &lt;color&gt;
Changes the background color. The color may be given as RGB values [r,g,b], or predefined color names.

== cartoon ==
 cartoon {on/true}
Turns on the thick ribbons for the selected residues.

 cartoon off/false
Turns off the thick ribbons for the selected residues.

 cartoon &lt;half_width&gt;
Turns on the thick ribbons for the selected residues with the specified half width (angstrom or Rasmol unit). The maximum parameter value is 4.0.

== center ==
 center {-r/-s} {&lt;atom_expression&gt;}
Sets the center of rotation and the center of the screen to the center of a group of atoms specified by the atom expression. When the option -r or -s is specified, only the center of rotation or the center of the screen is modified, respectively.

 center {-r} [x, y, z]
Moves the center of rotation and the center of the screen from the current position by the specified amount. When the option -r is specified, only the center of rotation is modified.

 center {-r} {x, y, z}
Sets the center of rotation and the center of the screen to the specified coordinates. When the option -r is specified, only the center of rotation is modified.

 center -s [x, y]
Moves the center of the screen from the current position by the specified amount.

 center -s {x, y}
Sets the center of the screen to the specified coordinates.

== color ==
== colorvertex ==
== cpk ==
== define ==
== display ==
== displayvertex ==
== echo ==
== exit ==
== fit ==
== fselect ==
== hbonds ==
== load ==
== pause ==
== quit ==
== refresh ==
== reset ==
=== default ===
=== cartoon ===
=== line_width ===
=== pickradius ===
=== point_size ===
=== polyline_width ===
=== transparency ===
== ribbons ==
== rotate ==
== save ==
== script ==
== select ==
== selectvertex ==
== set ==
=== adjustview ===
=== background ===
=== bondmode ===
=== cartoon ===
=== center ===
=== drawlevel ===
=== hbonds ===
=== hetero ===
=== hydrogen ===
=== imagesize ===
=== line_width ===
=== loadcenter ===
=== picking ===
=== pickradius ===
=== point_size ===
=== polyline_width ===
=== projection ===
=== specular ===
=== specpower ===
=== ssbonds ===
=== stereo ===
=== transparency ===
=== viewpoint ===
== show ==
== slab ==
== spacefill ==
== ssbonds ==
== stereo ==
== structure ==
== trace ==
== translate ==
== wireframe ==
== write ==
== zap ==
== zoom ==</text>
    <sha1>607990f5a91fc1dbf7e2f69120fa2db360267a45</sha1>
  </revision>
</page>
<page arvcontinue="20090309075222|151">
  <title>Command List</title>
  <ns>0</ns>
  <id>20</id>
  <revision>
    <id>151</id>
    <parentid>150</parentid>
    <timestamp>2009-03-09T07:52:22Z</timestamp>
    <contributor>
      <username>JVuser</username>
      <id>2</id>
    </contributor>
    <comment>/* color */</comment>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="5231" xml:space="preserve"> {| style="float:right"
  |__TOC__
  |}
Command usage of jV follows that of Rasmol with some modifications. In the following part, command arguments that can take an arbitrary value are denoted as &lt;value&gt; for example, arguments restricted to several possible values are listed with / as a delimiter, and arguments that can be omitted are put in brackets {}.
== anim ==
 anim forward {&lt;value&gt;}
Starts animation forward. If the &lt;value&gt; is given, just move frames forward by the specified amount.

 anim backward {&lt;value&gt;}
Starts animation backward. If the &lt;value&gt; is given, just move frames backward by the specified amount.

 anim stop
Stops animation.

== animframe ==
 animframe &lt;frame&gt; {&lt;file_ID&gt;}
Sets the frame of all animation files for the specified value. When &lt;file_ID&gt; is given, only the specified file is processed.

== animmode ==
 animmode once
Sets the behavior of animation for 'once'. When the frame reaches the last one, animation is stopped.

 animmode loop
Sets the behavior of animation for 'loop'. When the frame reaches the last one, animation is reset to the first frame and continues playing.

 animmode swing
Sets the behavior of animation for 'swing'. When the frame reaches the last one, the direction of animation is reversed.

== animrange ==
 animrange &lt;init_frame&gt;-&lt;term_frame&gt; {&lt;file_IDs&gt;}
Sets the range of all animation files. When is given, only the specified file is processed.

== animselect ==
 animselect {-a/-r} &lt;file_IDs&gt;
Selects the specified files and makes the others not selected. More than one file IDs can be specified by putting commas as the delimiter. When the option -a or -r is specified, only the selection status of the specified files are modified, selected or not selected, respectively, and the others remain unchanged.

== animspeed ==
 animspeed &lt;speed&gt;
Sets the animation speed. The argument should be an integer value from 1 to 20.

== animstep ==
 animstep &lt;step&gt; {&lt;file_ID&gt;}
Sets the step of all animation files for the specified value. When &lt;file_ID&gt; is given, only the specified file is processed.

== backbone ==
 backbone {on/true}
Turns on the selected backbone bonds.

 backbone off/false
Turns off the selected backbone bonds.

 backbone &lt;radius&gt;
Turns on the selected backbone bonds with the specified raidus (angstrom or Rasmol unit). The maximum parameter value is 2.0.

== background ==
 background &lt;color&gt;
Changes the background color. The color may be given as RGB values [r,g,b], or predefined color names.

== cartoon ==
 cartoon {on/true}
Turns on the thick ribbons for the selected residues.

 cartoon off/false
Turns off the thick ribbons for the selected residues.

 cartoon &lt;half_width&gt;
Turns on the thick ribbons for the selected residues with the specified half width (angstrom or Rasmol unit). The maximum parameter value is 4.0.

== center ==
 center {-r/-s} {&lt;atom_expression&gt;}
Sets the center of rotation and the center of the screen to the center of a group of atoms specified by the atom expression. When the option -r or -s is specified, only the center of rotation or the center of the screen is modified, respectively.

 center {-r} [x, y, z]
Moves the center of rotation and the center of the screen from the current position by the specified amount. When the option -r is specified, only the center of rotation is modified.

 center {-r} {x, y, z}
Sets the center of rotation and the center of the screen to the specified coordinates. When the option -r is specified, only the center of rotation is modified.

 center -s [x, y]
Moves the center of the screen from the current position by the specified amount.

 center -s {x, y}
Sets the center of the screen to the specified coordinates.

== color ==
 color {atoms} &lt;color&gt;
Sets the color of the selected atoms. The color may be given as RGB values [r,g,b], predefined color names, or predefined color schemes; amino, chain, charge, cpk, group, shapely, structure, and temperature.

 color bonds/backbone/ribbons/hbonds/ssbonds &lt;color&gt;
Sets the color of the specified object. The color may be given as RGB values [r,g,b] or predefined color names. For hydrogen bonds, color scheme 'type' can be specified.

 color bonds/backbone/ribbons/hbonds/ssbonds none
Resets the color of the specified object.

== colorvertex ==
== cpk ==
== define ==
== display ==
== displayvertex ==
== echo ==
== exit ==
== fit ==
== fselect ==
== hbonds ==
== load ==
== pause ==
== quit ==
== refresh ==
== reset ==
=== default ===
=== cartoon ===
=== line_width ===
=== pickradius ===
=== point_size ===
=== polyline_width ===
=== transparency ===
== ribbons ==
== rotate ==
== save ==
== script ==
== select ==
== selectvertex ==
== set ==
=== adjustview ===
=== background ===
=== bondmode ===
=== cartoon ===
=== center ===
=== drawlevel ===
=== hbonds ===
=== hetero ===
=== hydrogen ===
=== imagesize ===
=== line_width ===
=== loadcenter ===
=== picking ===
=== pickradius ===
=== point_size ===
=== polyline_width ===
=== projection ===
=== specular ===
=== specpower ===
=== ssbonds ===
=== stereo ===
=== transparency ===
=== viewpoint ===
== show ==
== slab ==
== spacefill ==
== ssbonds ==
== stereo ==
== structure ==
== trace ==
== translate ==
== wireframe ==
== write ==
== zap ==
== zoom ==</text>
    <sha1>f42801449e3e4ff9ff6a5d1eec1b4cba79306521</sha1>
  </revision>
  <revision>
    <id>152</id>
    <parentid>151</parentid>
    <timestamp>2009-03-09T07:52:39Z</timestamp>
    <contributor>
      <username>JVuser</username>
      <id>2</id>
    </contributor>
    <comment>/* colorvertex */</comment>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="5428" xml:space="preserve"> {| style="float:right"
  |__TOC__
  |}
Command usage of jV follows that of Rasmol with some modifications. In the following part, command arguments that can take an arbitrary value are denoted as &lt;value&gt; for example, arguments restricted to several possible values are listed with / as a delimiter, and arguments that can be omitted are put in brackets {}.
== anim ==
 anim forward {&lt;value&gt;}
Starts animation forward. If the &lt;value&gt; is given, just move frames forward by the specified amount.

 anim backward {&lt;value&gt;}
Starts animation backward. If the &lt;value&gt; is given, just move frames backward by the specified amount.

 anim stop
Stops animation.

== animframe ==
 animframe &lt;frame&gt; {&lt;file_ID&gt;}
Sets the frame of all animation files for the specified value. When &lt;file_ID&gt; is given, only the specified file is processed.

== animmode ==
 animmode once
Sets the behavior of animation for 'once'. When the frame reaches the last one, animation is stopped.

 animmode loop
Sets the behavior of animation for 'loop'. When the frame reaches the last one, animation is reset to the first frame and continues playing.

 animmode swing
Sets the behavior of animation for 'swing'. When the frame reaches the last one, the direction of animation is reversed.

== animrange ==
 animrange &lt;init_frame&gt;-&lt;term_frame&gt; {&lt;file_IDs&gt;}
Sets the range of all animation files. When is given, only the specified file is processed.

== animselect ==
 animselect {-a/-r} &lt;file_IDs&gt;
Selects the specified files and makes the others not selected. More than one file IDs can be specified by putting commas as the delimiter. When the option -a or -r is specified, only the selection status of the specified files are modified, selected or not selected, respectively, and the others remain unchanged.

== animspeed ==
 animspeed &lt;speed&gt;
Sets the animation speed. The argument should be an integer value from 1 to 20.

== animstep ==
 animstep &lt;step&gt; {&lt;file_ID&gt;}
Sets the step of all animation files for the specified value. When &lt;file_ID&gt; is given, only the specified file is processed.

== backbone ==
 backbone {on/true}
Turns on the selected backbone bonds.

 backbone off/false
Turns off the selected backbone bonds.

 backbone &lt;radius&gt;
Turns on the selected backbone bonds with the specified raidus (angstrom or Rasmol unit). The maximum parameter value is 2.0.

== background ==
 background &lt;color&gt;
Changes the background color. The color may be given as RGB values [r,g,b], or predefined color names.

== cartoon ==
 cartoon {on/true}
Turns on the thick ribbons for the selected residues.

 cartoon off/false
Turns off the thick ribbons for the selected residues.

 cartoon &lt;half_width&gt;
Turns on the thick ribbons for the selected residues with the specified half width (angstrom or Rasmol unit). The maximum parameter value is 4.0.

== center ==
 center {-r/-s} {&lt;atom_expression&gt;}
Sets the center of rotation and the center of the screen to the center of a group of atoms specified by the atom expression. When the option -r or -s is specified, only the center of rotation or the center of the screen is modified, respectively.

 center {-r} [x, y, z]
Moves the center of rotation and the center of the screen from the current position by the specified amount. When the option -r is specified, only the center of rotation is modified.

 center {-r} {x, y, z}
Sets the center of rotation and the center of the screen to the specified coordinates. When the option -r is specified, only the center of rotation is modified.

 center -s [x, y]
Moves the center of the screen from the current position by the specified amount.

 center -s {x, y}
Sets the center of the screen to the specified coordinates.

== color ==
 color {atoms} &lt;color&gt;
Sets the color of the selected atoms. The color may be given as RGB values [r,g,b], predefined color names, or predefined color schemes; amino, chain, charge, cpk, group, shapely, structure, and temperature.

 color bonds/backbone/ribbons/hbonds/ssbonds &lt;color&gt;
Sets the color of the specified object. The color may be given as RGB values [r,g,b] or predefined color names. For hydrogen bonds, color scheme 'type' can be specified.

 color bonds/backbone/ribbons/hbonds/ssbonds none
Resets the color of the specified object.

== colorvertex ==
 colorvertex &lt;color&gt;
Sets the color of the selected vertices. The color may be given as RGB values [r,g,b] or predefined color names.

 colorvertex none
Resets the color of the selected vertices.

== cpk ==
== define ==
== display ==
== displayvertex ==
== echo ==
== exit ==
== fit ==
== fselect ==
== hbonds ==
== load ==
== pause ==
== quit ==
== refresh ==
== reset ==
=== default ===
=== cartoon ===
=== line_width ===
=== pickradius ===
=== point_size ===
=== polyline_width ===
=== transparency ===
== ribbons ==
== rotate ==
== save ==
== script ==
== select ==
== selectvertex ==
== set ==
=== adjustview ===
=== background ===
=== bondmode ===
=== cartoon ===
=== center ===
=== drawlevel ===
=== hbonds ===
=== hetero ===
=== hydrogen ===
=== imagesize ===
=== line_width ===
=== loadcenter ===
=== picking ===
=== pickradius ===
=== point_size ===
=== polyline_width ===
=== projection ===
=== specular ===
=== specpower ===
=== ssbonds ===
=== stereo ===
=== transparency ===
=== viewpoint ===
== show ==
== slab ==
== spacefill ==
== ssbonds ==
== stereo ==
== structure ==
== trace ==
== translate ==
== wireframe ==
== write ==
== zap ==
== zoom ==</text>
    <sha1>c32b266a9ae695f4d944853bbf29fbc6418945f1</sha1>
  </revision>
  <revision>
    <id>153</id>
    <parentid>152</parentid>
    <timestamp>2009-03-09T07:52:50Z</timestamp>
    <contributor>
      <username>JVuser</username>
      <id>2</id>
    </contributor>
    <comment>/* cpk */</comment>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="5470" xml:space="preserve"> {| style="float:right"
  |__TOC__
  |}
Command usage of jV follows that of Rasmol with some modifications. In the following part, command arguments that can take an arbitrary value are denoted as &lt;value&gt; for example, arguments restricted to several possible values are listed with / as a delimiter, and arguments that can be omitted are put in brackets {}.
== anim ==
 anim forward {&lt;value&gt;}
Starts animation forward. If the &lt;value&gt; is given, just move frames forward by the specified amount.

 anim backward {&lt;value&gt;}
Starts animation backward. If the &lt;value&gt; is given, just move frames backward by the specified amount.

 anim stop
Stops animation.

== animframe ==
 animframe &lt;frame&gt; {&lt;file_ID&gt;}
Sets the frame of all animation files for the specified value. When &lt;file_ID&gt; is given, only the specified file is processed.

== animmode ==
 animmode once
Sets the behavior of animation for 'once'. When the frame reaches the last one, animation is stopped.

 animmode loop
Sets the behavior of animation for 'loop'. When the frame reaches the last one, animation is reset to the first frame and continues playing.

 animmode swing
Sets the behavior of animation for 'swing'. When the frame reaches the last one, the direction of animation is reversed.

== animrange ==
 animrange &lt;init_frame&gt;-&lt;term_frame&gt; {&lt;file_IDs&gt;}
Sets the range of all animation files. When is given, only the specified file is processed.

== animselect ==
 animselect {-a/-r} &lt;file_IDs&gt;
Selects the specified files and makes the others not selected. More than one file IDs can be specified by putting commas as the delimiter. When the option -a or -r is specified, only the selection status of the specified files are modified, selected or not selected, respectively, and the others remain unchanged.

== animspeed ==
 animspeed &lt;speed&gt;
Sets the animation speed. The argument should be an integer value from 1 to 20.

== animstep ==
 animstep &lt;step&gt; {&lt;file_ID&gt;}
Sets the step of all animation files for the specified value. When &lt;file_ID&gt; is given, only the specified file is processed.

== backbone ==
 backbone {on/true}
Turns on the selected backbone bonds.

 backbone off/false
Turns off the selected backbone bonds.

 backbone &lt;radius&gt;
Turns on the selected backbone bonds with the specified raidus (angstrom or Rasmol unit). The maximum parameter value is 2.0.

== background ==
 background &lt;color&gt;
Changes the background color. The color may be given as RGB values [r,g,b], or predefined color names.

== cartoon ==
 cartoon {on/true}
Turns on the thick ribbons for the selected residues.

 cartoon off/false
Turns off the thick ribbons for the selected residues.

 cartoon &lt;half_width&gt;
Turns on the thick ribbons for the selected residues with the specified half width (angstrom or Rasmol unit). The maximum parameter value is 4.0.

== center ==
 center {-r/-s} {&lt;atom_expression&gt;}
Sets the center of rotation and the center of the screen to the center of a group of atoms specified by the atom expression. When the option -r or -s is specified, only the center of rotation or the center of the screen is modified, respectively.

 center {-r} [x, y, z]
Moves the center of rotation and the center of the screen from the current position by the specified amount. When the option -r is specified, only the center of rotation is modified.

 center {-r} {x, y, z}
Sets the center of rotation and the center of the screen to the specified coordinates. When the option -r is specified, only the center of rotation is modified.

 center -s [x, y]
Moves the center of the screen from the current position by the specified amount.

 center -s {x, y}
Sets the center of the screen to the specified coordinates.

== color ==
 color {atoms} &lt;color&gt;
Sets the color of the selected atoms. The color may be given as RGB values [r,g,b], predefined color names, or predefined color schemes; amino, chain, charge, cpk, group, shapely, structure, and temperature.

 color bonds/backbone/ribbons/hbonds/ssbonds &lt;color&gt;
Sets the color of the specified object. The color may be given as RGB values [r,g,b] or predefined color names. For hydrogen bonds, color scheme 'type' can be specified.

 color bonds/backbone/ribbons/hbonds/ssbonds none
Resets the color of the specified object.

== colorvertex ==
 colorvertex &lt;color&gt;
Sets the color of the selected vertices. The color may be given as RGB values [r,g,b] or predefined color names.

 colorvertex none
Resets the color of the selected vertices.

== cpk ==
 cpk
A synonym of the spacefill command.

== define ==
== display ==
== displayvertex ==
== echo ==
== exit ==
== fit ==
== fselect ==
== hbonds ==
== load ==
== pause ==
== quit ==
== refresh ==
== reset ==
=== default ===
=== cartoon ===
=== line_width ===
=== pickradius ===
=== point_size ===
=== polyline_width ===
=== transparency ===
== ribbons ==
== rotate ==
== save ==
== script ==
== select ==
== selectvertex ==
== set ==
=== adjustview ===
=== background ===
=== bondmode ===
=== cartoon ===
=== center ===
=== drawlevel ===
=== hbonds ===
=== hetero ===
=== hydrogen ===
=== imagesize ===
=== line_width ===
=== loadcenter ===
=== picking ===
=== pickradius ===
=== point_size ===
=== polyline_width ===
=== projection ===
=== specular ===
=== specpower ===
=== ssbonds ===
=== stereo ===
=== transparency ===
=== viewpoint ===
== show ==
== slab ==
== spacefill ==
== ssbonds ==
== stereo ==
== structure ==
== trace ==
== translate ==
== wireframe ==
== write ==
== zap ==
== zoom ==</text>
    <sha1>1f943db6bc5ec30dad49887c2448788690552330</sha1>
  </revision>
  <revision>
    <id>154</id>
    <parentid>153</parentid>
    <timestamp>2009-03-09T07:52:59Z</timestamp>
    <contributor>
      <username>JVuser</username>
      <id>2</id>
    </contributor>
    <comment>/* define */</comment>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="5561" xml:space="preserve"> {| style="float:right"
  |__TOC__
  |}
Command usage of jV follows that of Rasmol with some modifications. In the following part, command arguments that can take an arbitrary value are denoted as &lt;value&gt; for example, arguments restricted to several possible values are listed with / as a delimiter, and arguments that can be omitted are put in brackets {}.
== anim ==
 anim forward {&lt;value&gt;}
Starts animation forward. If the &lt;value&gt; is given, just move frames forward by the specified amount.

 anim backward {&lt;value&gt;}
Starts animation backward. If the &lt;value&gt; is given, just move frames backward by the specified amount.

 anim stop
Stops animation.

== animframe ==
 animframe &lt;frame&gt; {&lt;file_ID&gt;}
Sets the frame of all animation files for the specified value. When &lt;file_ID&gt; is given, only the specified file is processed.

== animmode ==
 animmode once
Sets the behavior of animation for 'once'. When the frame reaches the last one, animation is stopped.

 animmode loop
Sets the behavior of animation for 'loop'. When the frame reaches the last one, animation is reset to the first frame and continues playing.

 animmode swing
Sets the behavior of animation for 'swing'. When the frame reaches the last one, the direction of animation is reversed.

== animrange ==
 animrange &lt;init_frame&gt;-&lt;term_frame&gt; {&lt;file_IDs&gt;}
Sets the range of all animation files. When is given, only the specified file is processed.

== animselect ==
 animselect {-a/-r} &lt;file_IDs&gt;
Selects the specified files and makes the others not selected. More than one file IDs can be specified by putting commas as the delimiter. When the option -a or -r is specified, only the selection status of the specified files are modified, selected or not selected, respectively, and the others remain unchanged.

== animspeed ==
 animspeed &lt;speed&gt;
Sets the animation speed. The argument should be an integer value from 1 to 20.

== animstep ==
 animstep &lt;step&gt; {&lt;file_ID&gt;}
Sets the step of all animation files for the specified value. When &lt;file_ID&gt; is given, only the specified file is processed.

== backbone ==
 backbone {on/true}
Turns on the selected backbone bonds.

 backbone off/false
Turns off the selected backbone bonds.

 backbone &lt;radius&gt;
Turns on the selected backbone bonds with the specified raidus (angstrom or Rasmol unit). The maximum parameter value is 2.0.

== background ==
 background &lt;color&gt;
Changes the background color. The color may be given as RGB values [r,g,b], or predefined color names.

== cartoon ==
 cartoon {on/true}
Turns on the thick ribbons for the selected residues.

 cartoon off/false
Turns off the thick ribbons for the selected residues.

 cartoon &lt;half_width&gt;
Turns on the thick ribbons for the selected residues with the specified half width (angstrom or Rasmol unit). The maximum parameter value is 4.0.

== center ==
 center {-r/-s} {&lt;atom_expression&gt;}
Sets the center of rotation and the center of the screen to the center of a group of atoms specified by the atom expression. When the option -r or -s is specified, only the center of rotation or the center of the screen is modified, respectively.

 center {-r} [x, y, z]
Moves the center of rotation and the center of the screen from the current position by the specified amount. When the option -r is specified, only the center of rotation is modified.

 center {-r} {x, y, z}
Sets the center of rotation and the center of the screen to the specified coordinates. When the option -r is specified, only the center of rotation is modified.

 center -s [x, y]
Moves the center of the screen from the current position by the specified amount.

 center -s {x, y}
Sets the center of the screen to the specified coordinates.

== color ==
 color {atoms} &lt;color&gt;
Sets the color of the selected atoms. The color may be given as RGB values [r,g,b], predefined color names, or predefined color schemes; amino, chain, charge, cpk, group, shapely, structure, and temperature.

 color bonds/backbone/ribbons/hbonds/ssbonds &lt;color&gt;
Sets the color of the specified object. The color may be given as RGB values [r,g,b] or predefined color names. For hydrogen bonds, color scheme 'type' can be specified.

 color bonds/backbone/ribbons/hbonds/ssbonds none
Resets the color of the specified object.

== colorvertex ==
 colorvertex &lt;color&gt;
Sets the color of the selected vertices. The color may be given as RGB values [r,g,b] or predefined color names.

 colorvertex none
Resets the color of the selected vertices.

== cpk ==
 cpk
A synonym of the spacefill command.

== define ==
 define &lt;name&gt; &lt;atom_expression&gt;
Associates an arbitrary set of atoms with a unique name.

== display ==
== displayvertex ==
== echo ==
== exit ==
== fit ==
== fselect ==
== hbonds ==
== load ==
== pause ==
== quit ==
== refresh ==
== reset ==
=== default ===
=== cartoon ===
=== line_width ===
=== pickradius ===
=== point_size ===
=== polyline_width ===
=== transparency ===
== ribbons ==
== rotate ==
== save ==
== script ==
== select ==
== selectvertex ==
== set ==
=== adjustview ===
=== background ===
=== bondmode ===
=== cartoon ===
=== center ===
=== drawlevel ===
=== hbonds ===
=== hetero ===
=== hydrogen ===
=== imagesize ===
=== line_width ===
=== loadcenter ===
=== picking ===
=== pickradius ===
=== point_size ===
=== polyline_width ===
=== projection ===
=== specular ===
=== specpower ===
=== ssbonds ===
=== stereo ===
=== transparency ===
=== viewpoint ===
== show ==
== slab ==
== spacefill ==
== ssbonds ==
== stereo ==
== structure ==
== trace ==
== translate ==
== wireframe ==
== write ==
== zap ==
== zoom ==</text>
    <sha1>38077fcc6bba3e5a941be976cde52dc734bef9e2</sha1>
  </revision>
  <revision>
    <id>155</id>
    <parentid>154</parentid>
    <timestamp>2009-03-09T07:53:17Z</timestamp>
    <contributor>
      <username>JVuser</username>
      <id>2</id>
    </contributor>
    <comment>/* display */</comment>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="5966" xml:space="preserve"> {| style="float:right"
  |__TOC__
  |}
Command usage of jV follows that of Rasmol with some modifications. In the following part, command arguments that can take an arbitrary value are denoted as &lt;value&gt; for example, arguments restricted to several possible values are listed with / as a delimiter, and arguments that can be omitted are put in brackets {}.
== anim ==
 anim forward {&lt;value&gt;}
Starts animation forward. If the &lt;value&gt; is given, just move frames forward by the specified amount.

 anim backward {&lt;value&gt;}
Starts animation backward. If the &lt;value&gt; is given, just move frames backward by the specified amount.

 anim stop
Stops animation.

== animframe ==
 animframe &lt;frame&gt; {&lt;file_ID&gt;}
Sets the frame of all animation files for the specified value. When &lt;file_ID&gt; is given, only the specified file is processed.

== animmode ==
 animmode once
Sets the behavior of animation for 'once'. When the frame reaches the last one, animation is stopped.

 animmode loop
Sets the behavior of animation for 'loop'. When the frame reaches the last one, animation is reset to the first frame and continues playing.

 animmode swing
Sets the behavior of animation for 'swing'. When the frame reaches the last one, the direction of animation is reversed.

== animrange ==
 animrange &lt;init_frame&gt;-&lt;term_frame&gt; {&lt;file_IDs&gt;}
Sets the range of all animation files. When is given, only the specified file is processed.

== animselect ==
 animselect {-a/-r} &lt;file_IDs&gt;
Selects the specified files and makes the others not selected. More than one file IDs can be specified by putting commas as the delimiter. When the option -a or -r is specified, only the selection status of the specified files are modified, selected or not selected, respectively, and the others remain unchanged.

== animspeed ==
 animspeed &lt;speed&gt;
Sets the animation speed. The argument should be an integer value from 1 to 20.

== animstep ==
 animstep &lt;step&gt; {&lt;file_ID&gt;}
Sets the step of all animation files for the specified value. When &lt;file_ID&gt; is given, only the specified file is processed.

== backbone ==
 backbone {on/true}
Turns on the selected backbone bonds.

 backbone off/false
Turns off the selected backbone bonds.

 backbone &lt;radius&gt;
Turns on the selected backbone bonds with the specified raidus (angstrom or Rasmol unit). The maximum parameter value is 2.0.

== background ==
 background &lt;color&gt;
Changes the background color. The color may be given as RGB values [r,g,b], or predefined color names.

== cartoon ==
 cartoon {on/true}
Turns on the thick ribbons for the selected residues.

 cartoon off/false
Turns off the thick ribbons for the selected residues.

 cartoon &lt;half_width&gt;
Turns on the thick ribbons for the selected residues with the specified half width (angstrom or Rasmol unit). The maximum parameter value is 4.0.

== center ==
 center {-r/-s} {&lt;atom_expression&gt;}
Sets the center of rotation and the center of the screen to the center of a group of atoms specified by the atom expression. When the option -r or -s is specified, only the center of rotation or the center of the screen is modified, respectively.

 center {-r} [x, y, z]
Moves the center of rotation and the center of the screen from the current position by the specified amount. When the option -r is specified, only the center of rotation is modified.

 center {-r} {x, y, z}
Sets the center of rotation and the center of the screen to the specified coordinates. When the option -r is specified, only the center of rotation is modified.

 center -s [x, y]
Moves the center of the screen from the current position by the specified amount.

 center -s {x, y}
Sets the center of the screen to the specified coordinates.

== color ==
 color {atoms} &lt;color&gt;
Sets the color of the selected atoms. The color may be given as RGB values [r,g,b], predefined color names, or predefined color schemes; amino, chain, charge, cpk, group, shapely, structure, and temperature.

 color bonds/backbone/ribbons/hbonds/ssbonds &lt;color&gt;
Sets the color of the specified object. The color may be given as RGB values [r,g,b] or predefined color names. For hydrogen bonds, color scheme 'type' can be specified.

 color bonds/backbone/ribbons/hbonds/ssbonds none
Resets the color of the specified object.

== colorvertex ==
 colorvertex &lt;color&gt;
Sets the color of the selected vertices. The color may be given as RGB values [r,g,b] or predefined color names.

 colorvertex none
Resets the color of the selected vertices.

== cpk ==
 cpk
A synonym of the spacefill command.

== define ==
 define &lt;name&gt; &lt;atom_expression&gt;
Associates an arbitrary set of atoms with a unique name.

== display ==
 display all
Displays the image of all files.

 display none
Turns off the image of all files.

 display {-a/-r} &lt;file_IDs&gt;
Displays the image of the specified files and turns off the others. More than one file IDs can be specified by putting commas as the delimiter. When the option -a or -r is specified, turns the image of the specified files on or off, respectively, and the others remain unchanged.

== displayvertex ==
== echo ==
== exit ==
== fit ==
== fselect ==
== hbonds ==
== load ==
== pause ==
== quit ==
== refresh ==
== reset ==
=== default ===
=== cartoon ===
=== line_width ===
=== pickradius ===
=== point_size ===
=== polyline_width ===
=== transparency ===
== ribbons ==
== rotate ==
== save ==
== script ==
== select ==
== selectvertex ==
== set ==
=== adjustview ===
=== background ===
=== bondmode ===
=== cartoon ===
=== center ===
=== drawlevel ===
=== hbonds ===
=== hetero ===
=== hydrogen ===
=== imagesize ===
=== line_width ===
=== loadcenter ===
=== picking ===
=== pickradius ===
=== point_size ===
=== polyline_width ===
=== projection ===
=== specular ===
=== specpower ===
=== ssbonds ===
=== stereo ===
=== transparency ===
=== viewpoint ===
== show ==
== slab ==
== spacefill ==
== ssbonds ==
== stereo ==
== structure ==
== trace ==
== translate ==
== wireframe ==
== write ==
== zap ==
== zoom ==</text>
    <sha1>359d6f4c900b972a1679c40e385bd9747a80f3f6</sha1>
  </revision>
  <revision>
    <id>156</id>
    <parentid>155</parentid>
    <timestamp>2009-03-09T07:53:27Z</timestamp>
    <contributor>
      <username>JVuser</username>
      <id>2</id>
    </contributor>
    <comment>/* displayvertex */</comment>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="6083" xml:space="preserve"> {| style="float:right"
  |__TOC__
  |}
Command usage of jV follows that of Rasmol with some modifications. In the following part, command arguments that can take an arbitrary value are denoted as &lt;value&gt; for example, arguments restricted to several possible values are listed with / as a delimiter, and arguments that can be omitted are put in brackets {}.
== anim ==
 anim forward {&lt;value&gt;}
Starts animation forward. If the &lt;value&gt; is given, just move frames forward by the specified amount.

 anim backward {&lt;value&gt;}
Starts animation backward. If the &lt;value&gt; is given, just move frames backward by the specified amount.

 anim stop
Stops animation.

== animframe ==
 animframe &lt;frame&gt; {&lt;file_ID&gt;}
Sets the frame of all animation files for the specified value. When &lt;file_ID&gt; is given, only the specified file is processed.

== animmode ==
 animmode once
Sets the behavior of animation for 'once'. When the frame reaches the last one, animation is stopped.

 animmode loop
Sets the behavior of animation for 'loop'. When the frame reaches the last one, animation is reset to the first frame and continues playing.

 animmode swing
Sets the behavior of animation for 'swing'. When the frame reaches the last one, the direction of animation is reversed.

== animrange ==
 animrange &lt;init_frame&gt;-&lt;term_frame&gt; {&lt;file_IDs&gt;}
Sets the range of all animation files. When is given, only the specified file is processed.

== animselect ==
 animselect {-a/-r} &lt;file_IDs&gt;
Selects the specified files and makes the others not selected. More than one file IDs can be specified by putting commas as the delimiter. When the option -a or -r is specified, only the selection status of the specified files are modified, selected or not selected, respectively, and the others remain unchanged.

== animspeed ==
 animspeed &lt;speed&gt;
Sets the animation speed. The argument should be an integer value from 1 to 20.

== animstep ==
 animstep &lt;step&gt; {&lt;file_ID&gt;}
Sets the step of all animation files for the specified value. When &lt;file_ID&gt; is given, only the specified file is processed.

== backbone ==
 backbone {on/true}
Turns on the selected backbone bonds.

 backbone off/false
Turns off the selected backbone bonds.

 backbone &lt;radius&gt;
Turns on the selected backbone bonds with the specified raidus (angstrom or Rasmol unit). The maximum parameter value is 2.0.

== background ==
 background &lt;color&gt;
Changes the background color. The color may be given as RGB values [r,g,b], or predefined color names.

== cartoon ==
 cartoon {on/true}
Turns on the thick ribbons for the selected residues.

 cartoon off/false
Turns off the thick ribbons for the selected residues.

 cartoon &lt;half_width&gt;
Turns on the thick ribbons for the selected residues with the specified half width (angstrom or Rasmol unit). The maximum parameter value is 4.0.

== center ==
 center {-r/-s} {&lt;atom_expression&gt;}
Sets the center of rotation and the center of the screen to the center of a group of atoms specified by the atom expression. When the option -r or -s is specified, only the center of rotation or the center of the screen is modified, respectively.

 center {-r} [x, y, z]
Moves the center of rotation and the center of the screen from the current position by the specified amount. When the option -r is specified, only the center of rotation is modified.

 center {-r} {x, y, z}
Sets the center of rotation and the center of the screen to the specified coordinates. When the option -r is specified, only the center of rotation is modified.

 center -s [x, y]
Moves the center of the screen from the current position by the specified amount.

 center -s {x, y}
Sets the center of the screen to the specified coordinates.

== color ==
 color {atoms} &lt;color&gt;
Sets the color of the selected atoms. The color may be given as RGB values [r,g,b], predefined color names, or predefined color schemes; amino, chain, charge, cpk, group, shapely, structure, and temperature.

 color bonds/backbone/ribbons/hbonds/ssbonds &lt;color&gt;
Sets the color of the specified object. The color may be given as RGB values [r,g,b] or predefined color names. For hydrogen bonds, color scheme 'type' can be specified.

 color bonds/backbone/ribbons/hbonds/ssbonds none
Resets the color of the specified object.

== colorvertex ==
 colorvertex &lt;color&gt;
Sets the color of the selected vertices. The color may be given as RGB values [r,g,b] or predefined color names.

 colorvertex none
Resets the color of the selected vertices.

== cpk ==
 cpk
A synonym of the spacefill command.

== define ==
 define &lt;name&gt; &lt;atom_expression&gt;
Associates an arbitrary set of atoms with a unique name.

== display ==
 display all
Displays the image of all files.

 display none
Turns off the image of all files.

 display {-a/-r} &lt;file_IDs&gt;
Displays the image of the specified files and turns off the others. More than one file IDs can be specified by putting commas as the delimiter. When the option -a or -r is specified, turns the image of the specified files on or off, respectively, and the others remain unchanged.

== displayvertex ==
 displayvertex {on/true}
Displays the selected vertices.

 displayvertex off/false
Turns off the selected vertices.

== echo ==
== exit ==
== fit ==
== fselect ==
== hbonds ==
== load ==
== pause ==
== quit ==
== refresh ==
== reset ==
=== default ===
=== cartoon ===
=== line_width ===
=== pickradius ===
=== point_size ===
=== polyline_width ===
=== transparency ===
== ribbons ==
== rotate ==
== save ==
== script ==
== select ==
== selectvertex ==
== set ==
=== adjustview ===
=== background ===
=== bondmode ===
=== cartoon ===
=== center ===
=== drawlevel ===
=== hbonds ===
=== hetero ===
=== hydrogen ===
=== imagesize ===
=== line_width ===
=== loadcenter ===
=== picking ===
=== pickradius ===
=== point_size ===
=== polyline_width ===
=== projection ===
=== specular ===
=== specpower ===
=== ssbonds ===
=== stereo ===
=== transparency ===
=== viewpoint ===
== show ==
== slab ==
== spacefill ==
== ssbonds ==
== stereo ==
== structure ==
== trace ==
== translate ==
== wireframe ==
== write ==
== zap ==
== zoom ==</text>
    <sha1>492720b64340ff8fbcd97a2516ad51b5d23b2828</sha1>
  </revision>
  <revision>
    <id>157</id>
    <parentid>156</parentid>
    <timestamp>2009-03-09T07:53:39Z</timestamp>
    <contributor>
      <username>JVuser</username>
      <id>2</id>
    </contributor>
    <comment>/* echo */</comment>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="6154" xml:space="preserve"> {| style="float:right"
  |__TOC__
  |}
Command usage of jV follows that of Rasmol with some modifications. In the following part, command arguments that can take an arbitrary value are denoted as &lt;value&gt; for example, arguments restricted to several possible values are listed with / as a delimiter, and arguments that can be omitted are put in brackets {}.
== anim ==
 anim forward {&lt;value&gt;}
Starts animation forward. If the &lt;value&gt; is given, just move frames forward by the specified amount.

 anim backward {&lt;value&gt;}
Starts animation backward. If the &lt;value&gt; is given, just move frames backward by the specified amount.

 anim stop
Stops animation.

== animframe ==
 animframe &lt;frame&gt; {&lt;file_ID&gt;}
Sets the frame of all animation files for the specified value. When &lt;file_ID&gt; is given, only the specified file is processed.

== animmode ==
 animmode once
Sets the behavior of animation for 'once'. When the frame reaches the last one, animation is stopped.

 animmode loop
Sets the behavior of animation for 'loop'. When the frame reaches the last one, animation is reset to the first frame and continues playing.

 animmode swing
Sets the behavior of animation for 'swing'. When the frame reaches the last one, the direction of animation is reversed.

== animrange ==
 animrange &lt;init_frame&gt;-&lt;term_frame&gt; {&lt;file_IDs&gt;}
Sets the range of all animation files. When is given, only the specified file is processed.

== animselect ==
 animselect {-a/-r} &lt;file_IDs&gt;
Selects the specified files and makes the others not selected. More than one file IDs can be specified by putting commas as the delimiter. When the option -a or -r is specified, only the selection status of the specified files are modified, selected or not selected, respectively, and the others remain unchanged.

== animspeed ==
 animspeed &lt;speed&gt;
Sets the animation speed. The argument should be an integer value from 1 to 20.

== animstep ==
 animstep &lt;step&gt; {&lt;file_ID&gt;}
Sets the step of all animation files for the specified value. When &lt;file_ID&gt; is given, only the specified file is processed.

== backbone ==
 backbone {on/true}
Turns on the selected backbone bonds.

 backbone off/false
Turns off the selected backbone bonds.

 backbone &lt;radius&gt;
Turns on the selected backbone bonds with the specified raidus (angstrom or Rasmol unit). The maximum parameter value is 2.0.

== background ==
 background &lt;color&gt;
Changes the background color. The color may be given as RGB values [r,g,b], or predefined color names.

== cartoon ==
 cartoon {on/true}
Turns on the thick ribbons for the selected residues.

 cartoon off/false
Turns off the thick ribbons for the selected residues.

 cartoon &lt;half_width&gt;
Turns on the thick ribbons for the selected residues with the specified half width (angstrom or Rasmol unit). The maximum parameter value is 4.0.

== center ==
 center {-r/-s} {&lt;atom_expression&gt;}
Sets the center of rotation and the center of the screen to the center of a group of atoms specified by the atom expression. When the option -r or -s is specified, only the center of rotation or the center of the screen is modified, respectively.

 center {-r} [x, y, z]
Moves the center of rotation and the center of the screen from the current position by the specified amount. When the option -r is specified, only the center of rotation is modified.

 center {-r} {x, y, z}
Sets the center of rotation and the center of the screen to the specified coordinates. When the option -r is specified, only the center of rotation is modified.

 center -s [x, y]
Moves the center of the screen from the current position by the specified amount.

 center -s {x, y}
Sets the center of the screen to the specified coordinates.

== color ==
 color {atoms} &lt;color&gt;
Sets the color of the selected atoms. The color may be given as RGB values [r,g,b], predefined color names, or predefined color schemes; amino, chain, charge, cpk, group, shapely, structure, and temperature.

 color bonds/backbone/ribbons/hbonds/ssbonds &lt;color&gt;
Sets the color of the specified object. The color may be given as RGB values [r,g,b] or predefined color names. For hydrogen bonds, color scheme 'type' can be specified.

 color bonds/backbone/ribbons/hbonds/ssbonds none
Resets the color of the specified object.

== colorvertex ==
 colorvertex &lt;color&gt;
Sets the color of the selected vertices. The color may be given as RGB values [r,g,b] or predefined color names.

 colorvertex none
Resets the color of the selected vertices.

== cpk ==
 cpk
A synonym of the spacefill command.

== define ==
 define &lt;name&gt; &lt;atom_expression&gt;
Associates an arbitrary set of atoms with a unique name.

== display ==
 display all
Displays the image of all files.

 display none
Turns off the image of all files.

 display {-a/-r} &lt;file_IDs&gt;
Displays the image of the specified files and turns off the others. More than one file IDs can be specified by putting commas as the delimiter. When the option -a or -r is specified, turns the image of the specified files on or off, respectively, and the others remain unchanged.

== displayvertex ==
 displayvertex {on/true}
Displays the selected vertices.

 displayvertex off/false
Turns off the selected vertices.

== echo ==
 echo &lt;string&gt;
Echoes the specified message back to the message area.

== exit ==
== fit ==
== fselect ==
== hbonds ==
== load ==
== pause ==
== quit ==
== refresh ==
== reset ==
=== default ===
=== cartoon ===
=== line_width ===
=== pickradius ===
=== point_size ===
=== polyline_width ===
=== transparency ===
== ribbons ==
== rotate ==
== save ==
== script ==
== select ==
== selectvertex ==
== set ==
=== adjustview ===
=== background ===
=== bondmode ===
=== cartoon ===
=== center ===
=== drawlevel ===
=== hbonds ===
=== hetero ===
=== hydrogen ===
=== imagesize ===
=== line_width ===
=== loadcenter ===
=== picking ===
=== pickradius ===
=== point_size ===
=== polyline_width ===
=== projection ===
=== specular ===
=== specpower ===
=== ssbonds ===
=== stereo ===
=== transparency ===
=== viewpoint ===
== show ==
== slab ==
== spacefill ==
== ssbonds ==
== stereo ==
== structure ==
== trace ==
== translate ==
== wireframe ==
== write ==
== zap ==
== zoom ==</text>
    <sha1>6623e18802cd356f5e49f28bc2d1206f42a56096</sha1>
  </revision>
  <revision>
    <id>158</id>
    <parentid>157</parentid>
    <timestamp>2009-03-09T07:53:48Z</timestamp>
    <contributor>
      <username>JVuser</username>
      <id>2</id>
    </contributor>
    <comment>/* exit */</comment>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="6189" xml:space="preserve"> {| style="float:right"
  |__TOC__
  |}
Command usage of jV follows that of Rasmol with some modifications. In the following part, command arguments that can take an arbitrary value are denoted as &lt;value&gt; for example, arguments restricted to several possible values are listed with / as a delimiter, and arguments that can be omitted are put in brackets {}.
== anim ==
 anim forward {&lt;value&gt;}
Starts animation forward. If the &lt;value&gt; is given, just move frames forward by the specified amount.

 anim backward {&lt;value&gt;}
Starts animation backward. If the &lt;value&gt; is given, just move frames backward by the specified amount.

 anim stop
Stops animation.

== animframe ==
 animframe &lt;frame&gt; {&lt;file_ID&gt;}
Sets the frame of all animation files for the specified value. When &lt;file_ID&gt; is given, only the specified file is processed.

== animmode ==
 animmode once
Sets the behavior of animation for 'once'. When the frame reaches the last one, animation is stopped.

 animmode loop
Sets the behavior of animation for 'loop'. When the frame reaches the last one, animation is reset to the first frame and continues playing.

 animmode swing
Sets the behavior of animation for 'swing'. When the frame reaches the last one, the direction of animation is reversed.

== animrange ==
 animrange &lt;init_frame&gt;-&lt;term_frame&gt; {&lt;file_IDs&gt;}
Sets the range of all animation files. When is given, only the specified file is processed.

== animselect ==
 animselect {-a/-r} &lt;file_IDs&gt;
Selects the specified files and makes the others not selected. More than one file IDs can be specified by putting commas as the delimiter. When the option -a or -r is specified, only the selection status of the specified files are modified, selected or not selected, respectively, and the others remain unchanged.

== animspeed ==
 animspeed &lt;speed&gt;
Sets the animation speed. The argument should be an integer value from 1 to 20.

== animstep ==
 animstep &lt;step&gt; {&lt;file_ID&gt;}
Sets the step of all animation files for the specified value. When &lt;file_ID&gt; is given, only the specified file is processed.

== backbone ==
 backbone {on/true}
Turns on the selected backbone bonds.

 backbone off/false
Turns off the selected backbone bonds.

 backbone &lt;radius&gt;
Turns on the selected backbone bonds with the specified raidus (angstrom or Rasmol unit). The maximum parameter value is 2.0.

== background ==
 background &lt;color&gt;
Changes the background color. The color may be given as RGB values [r,g,b], or predefined color names.

== cartoon ==
 cartoon {on/true}
Turns on the thick ribbons for the selected residues.

 cartoon off/false
Turns off the thick ribbons for the selected residues.

 cartoon &lt;half_width&gt;
Turns on the thick ribbons for the selected residues with the specified half width (angstrom or Rasmol unit). The maximum parameter value is 4.0.

== center ==
 center {-r/-s} {&lt;atom_expression&gt;}
Sets the center of rotation and the center of the screen to the center of a group of atoms specified by the atom expression. When the option -r or -s is specified, only the center of rotation or the center of the screen is modified, respectively.

 center {-r} [x, y, z]
Moves the center of rotation and the center of the screen from the current position by the specified amount. When the option -r is specified, only the center of rotation is modified.

 center {-r} {x, y, z}
Sets the center of rotation and the center of the screen to the specified coordinates. When the option -r is specified, only the center of rotation is modified.

 center -s [x, y]
Moves the center of the screen from the current position by the specified amount.

 center -s {x, y}
Sets the center of the screen to the specified coordinates.

== color ==
 color {atoms} &lt;color&gt;
Sets the color of the selected atoms. The color may be given as RGB values [r,g,b], predefined color names, or predefined color schemes; amino, chain, charge, cpk, group, shapely, structure, and temperature.

 color bonds/backbone/ribbons/hbonds/ssbonds &lt;color&gt;
Sets the color of the specified object. The color may be given as RGB values [r,g,b] or predefined color names. For hydrogen bonds, color scheme 'type' can be specified.

 color bonds/backbone/ribbons/hbonds/ssbonds none
Resets the color of the specified object.

== colorvertex ==
 colorvertex &lt;color&gt;
Sets the color of the selected vertices. The color may be given as RGB values [r,g,b] or predefined color names.

 colorvertex none
Resets the color of the selected vertices.

== cpk ==
 cpk
A synonym of the spacefill command.

== define ==
 define &lt;name&gt; &lt;atom_expression&gt;
Associates an arbitrary set of atoms with a unique name.

== display ==
 display all
Displays the image of all files.

 display none
Turns off the image of all files.

 display {-a/-r} &lt;file_IDs&gt;
Displays the image of the specified files and turns off the others. More than one file IDs can be specified by putting commas as the delimiter. When the option -a or -r is specified, turns the image of the specified files on or off, respectively, and the others remain unchanged.

== displayvertex ==
 displayvertex {on/true}
Displays the selected vertices.

 displayvertex off/false
Turns off the selected vertices.

== echo ==
 echo &lt;string&gt;
Echoes the specified message back to the message area.

== exit ==
 exit
Terminates the application.

== fit ==
== fselect ==
== hbonds ==
== load ==
== pause ==
== quit ==
== refresh ==
== reset ==
=== default ===
=== cartoon ===
=== line_width ===
=== pickradius ===
=== point_size ===
=== polyline_width ===
=== transparency ===
== ribbons ==
== rotate ==
== save ==
== script ==
== select ==
== selectvertex ==
== set ==
=== adjustview ===
=== background ===
=== bondmode ===
=== cartoon ===
=== center ===
=== drawlevel ===
=== hbonds ===
=== hetero ===
=== hydrogen ===
=== imagesize ===
=== line_width ===
=== loadcenter ===
=== picking ===
=== pickradius ===
=== point_size ===
=== polyline_width ===
=== projection ===
=== specular ===
=== specpower ===
=== ssbonds ===
=== stereo ===
=== transparency ===
=== viewpoint ===
== show ==
== slab ==
== spacefill ==
== ssbonds ==
== stereo ==
== structure ==
== trace ==
== translate ==
== wireframe ==
== write ==
== zap ==
== zoom ==</text>
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  |__TOC__
  |}
Command usage of jV follows that of Rasmol with some modifications. In the following part, command arguments that can take an arbitrary value are denoted as &lt;value&gt; for example, arguments restricted to several possible values are listed with / as a delimiter, and arguments that can be omitted are put in brackets {}.
== anim ==
 anim forward {&lt;value&gt;}
Starts animation forward. If the &lt;value&gt; is given, just move frames forward by the specified amount.

 anim backward {&lt;value&gt;}
Starts animation backward. If the &lt;value&gt; is given, just move frames backward by the specified amount.

 anim stop
Stops animation.

== animframe ==
 animframe &lt;frame&gt; {&lt;file_ID&gt;}
Sets the frame of all animation files for the specified value. When &lt;file_ID&gt; is given, only the specified file is processed.

== animmode ==
 animmode once
Sets the behavior of animation for 'once'. When the frame reaches the last one, animation is stopped.

 animmode loop
Sets the behavior of animation for 'loop'. When the frame reaches the last one, animation is reset to the first frame and continues playing.

 animmode swing
Sets the behavior of animation for 'swing'. When the frame reaches the last one, the direction of animation is reversed.

== animrange ==
 animrange &lt;init_frame&gt;-&lt;term_frame&gt; {&lt;file_IDs&gt;}
Sets the range of all animation files. When is given, only the specified file is processed.

== animselect ==
 animselect {-a/-r} &lt;file_IDs&gt;
Selects the specified files and makes the others not selected. More than one file IDs can be specified by putting commas as the delimiter. When the option -a or -r is specified, only the selection status of the specified files are modified, selected or not selected, respectively, and the others remain unchanged.

== animspeed ==
 animspeed &lt;speed&gt;
Sets the animation speed. The argument should be an integer value from 1 to 20.

== animstep ==
 animstep &lt;step&gt; {&lt;file_ID&gt;}
Sets the step of all animation files for the specified value. When &lt;file_ID&gt; is given, only the specified file is processed.

== backbone ==
 backbone {on/true}
Turns on the selected backbone bonds.

 backbone off/false
Turns off the selected backbone bonds.

 backbone &lt;radius&gt;
Turns on the selected backbone bonds with the specified raidus (angstrom or Rasmol unit). The maximum parameter value is 2.0.

== background ==
 background &lt;color&gt;
Changes the background color. The color may be given as RGB values [r,g,b], or predefined color names.

== cartoon ==
 cartoon {on/true}
Turns on the thick ribbons for the selected residues.

 cartoon off/false
Turns off the thick ribbons for the selected residues.

 cartoon &lt;half_width&gt;
Turns on the thick ribbons for the selected residues with the specified half width (angstrom or Rasmol unit). The maximum parameter value is 4.0.

== center ==
 center {-r/-s} {&lt;atom_expression&gt;}
Sets the center of rotation and the center of the screen to the center of a group of atoms specified by the atom expression. When the option -r or -s is specified, only the center of rotation or the center of the screen is modified, respectively.

 center {-r} [x, y, z]
Moves the center of rotation and the center of the screen from the current position by the specified amount. When the option -r is specified, only the center of rotation is modified.

 center {-r} {x, y, z}
Sets the center of rotation and the center of the screen to the specified coordinates. When the option -r is specified, only the center of rotation is modified.

 center -s [x, y]
Moves the center of the screen from the current position by the specified amount.

 center -s {x, y}
Sets the center of the screen to the specified coordinates.

== color ==
 color {atoms} &lt;color&gt;
Sets the color of the selected atoms. The color may be given as RGB values [r,g,b], predefined color names, or predefined color schemes; amino, chain, charge, cpk, group, shapely, structure, and temperature.

 color bonds/backbone/ribbons/hbonds/ssbonds &lt;color&gt;
Sets the color of the specified object. The color may be given as RGB values [r,g,b] or predefined color names. For hydrogen bonds, color scheme 'type' can be specified.

 color bonds/backbone/ribbons/hbonds/ssbonds none
Resets the color of the specified object.

== colorvertex ==
 colorvertex &lt;color&gt;
Sets the color of the selected vertices. The color may be given as RGB values [r,g,b] or predefined color names.

 colorvertex none
Resets the color of the selected vertices.

== cpk ==
 cpk
A synonym of the spacefill command.

== define ==
 define &lt;name&gt; &lt;atom_expression&gt;
Associates an arbitrary set of atoms with a unique name.

== display ==
 display all
Displays the image of all files.

 display none
Turns off the image of all files.

 display {-a/-r} &lt;file_IDs&gt;
Displays the image of the specified files and turns off the others. More than one file IDs can be specified by putting commas as the delimiter. When the option -a or -r is specified, turns the image of the specified files on or off, respectively, and the others remain unchanged.

== displayvertex ==
 displayvertex {on/true}
Displays the selected vertices.

 displayvertex off/false
Turns off the selected vertices.

== echo ==
 echo &lt;string&gt;
Echoes the specified message back to the message area.

== exit ==
 exit
Terminates the application.

== fit ==
 fit &lt;file1_ID&gt; &lt;file2_ID&gt;
Sets the transform matrix of file1 identical to that of file2. 

== fselect ==
 fselect all
Selects all files.

 fselect none
Selects no files.

 fselect {-a/-r} &lt;file_IDs&gt;
Selects the specified files and makes the others not selected. More than one file IDs can be specified by putting commas as the delimiter. When the option -a or -r is specified, only the selection status of the specified files are modified, selected or not selected, respectively, and the others remain unchanged.

== hbonds ==
 hbonds {on/true}
Turns on the selected hydrogen bonds.

 hbonds off/false
Turns off the selected hydrogen bonds.

 hbonds &lt;radius&gt;
Turns on the selected hydrogen bonds with the specified raidus (angstrom or Rasmol unit). The maximum parameter value is 2.0. 

== load ==
 load {pdbml} &lt;filename&gt; {fit &lt;file_ID&gt;}
Opens a PDBML file. URL can be used to open a remote file. On loading, the transform matrix can be set identical to that of the specified file.

 load pdb &lt;filename&gt; {fit &lt;file_ID&gt;}
Opens a PDB file. URL can be used to open a remote file. On loading, the transform matrix can be set identical to that of the specified file.

 load polygon &lt;filename&gt; {fit &lt;file_ID&gt;}
Opens a polygon file. URL can be used to open a remote file. On loading, the transform matrix can be set identical to that of the specified file.

 load animation &lt;filename&gt; {fit &lt;file_ID&gt;}
Opens an animation file. URL can be used to open a remote file. On loading, the transform matrix can be set identical to that of the specified file.

 load ftp &lt;PDB_code&gt; {fit &lt;file_ID&gt;}
Retrieves a PDBML file from the PDBj FTP site and opens it. On loading, the transform matrix can be set identical to that of the specified file. 

== pause ==
 pause
Stops the execution of a script file until any key is pressed to restart. 

== quit ==
 quit
A synonym of the exit command. 

== refresh ==
 refresh
Redraws all images. 

== reset ==
=== default ===
 reset
Restores the original viewing transformation of all images, the center of rotation, and the view point. 

=== cartoon ===
 reset cartoon
Restores the thickness of the cartoon representation. 

=== line_width ===
 reset line_width
Restores the width of lines in polygon images. 

=== pickradius ===
 reset pickradius
Restores the mouse-pickable region of each atom. 

=== point_size ===
 reset point_size
Restores the size of points in polygon images. 

=== polyline_width ===
 reset polyline_width
Restores the width of polylines in polygon images. 

=== transparency ===
 reset transparency
Restores the transparency of polygon images.

 reset point_transparency
Restores the transparency of points in polygon images.

 reset line_transparency
Restores the transparency of lines in polygon images.

 reset triangle_transparency
Restores the transparency of triangles in polygon images.

 reset quad_transparency
Restores the transparency of quads in polygon images.

 reset polyline_transparency
Restores the transparency of polylines in polygon images. 

== ribbons ==
 ribbons {on/true}
Turns on the ribbon surfaces for the selected residues.

 ribbons off/false
Turns off the ribbon surfaces for the selected residues.

 ribbons &lt;half_width&gt;
Turns on the ribbon surfaces for the selected residues with the specified half width (angstrom or Rasmol unit). The maximum parameter value is 4.0. 

== rotate ==
 rotate x/y/z &lt;angle&gt;
Rotates images about the specified axis by the specified angle in degrees. 

== save ==
 save {pdb} &lt;filename&gt;
Saves the currently selected set of atoms in a PDB format file.

 save script &lt;filename&gt;
Creates a script file that reproduces the currently displayed image.

 save png &lt;filename&gt;
Creates a PNG image file of the currently displayed image.

 save jpeg &lt;filename&gt; {&lt;quality&gt;}
Creates a JPEG image file of the currently displayed image. The compression quality can be specified, 0 &lt; quality &lt;= 1, where 'quality = 1' means no compression. 

== script ==
 script &lt;filename&gt;
Opens and executes the specified script file. URL can be used to open a remote file. 

== select ==
 select
Selects all atoms. Whether hetero atoms and hydrogens are selected or not depends on the internal parameters, hetero and hydrogen, respectively.

 select all
Selects all atoms including hetero atoms and hydrogens.

 select none
Selects no atoms.

 select &lt;atom_expression&gt;
Selects a group of atoms specified by the atom expression. 

== selectvertex ==
 selectvertex {all}
Selects all vertices.

 selectvertex none
Selects no vertices.

 selectvertex &lt;vertex_expression&gt;
Selects a group of vertices specified by the vertex expression. 

== set ==
=== adjustview ===
 set adjustview on
The view point is automatically adjusted when a new file is loaded.

 set adjustview off
The view point is kept unchanged when a new file is loaded. 

=== background ===
 set background &lt;color&gt;
Changes the background color. The color may be given as RGB values [r,g,b], or predefined color names. 

=== bondmode ===
 set bondmode and
Specifies how to select an individual bonds. A bond is selected when both atoms connected by the bond are selected.

 set bondmode or
Specifies how to select an individual bonds. A bond is selected when either of the connected atoms is selected. 

=== cartoon ===
 set cartoon {&lt;value&gt;}
Specifies the thickness of the cartoon representation (angstrom or Rasmol unit). The maximum parameter value is 2.0. When the parameter is not specified, it is restored to the default value. 

=== center ===
 set center &lt;atom_expression&gt;
Sets the default center of the selected files to the center of the specified atoms.

 set center [x, y, z]
Sets the default center of the selected files to the specified coordinates. 

=== drawlevel ===
 set drawlevel &lt;value&gt;
Specifies precision of the rendering of spheres and cylinders. The value may be given as an integer (minimum 5) that stands for the number of straight line segments to represent an arc of 180 degrees. 

=== hbonds ===
 set hbonds backbone
Hydrogen bonds are displayed between backbones.

 set hbonds sidechain
Hydrogen bonds are displayed between sidechains. 

=== hetero ===
 set hetero on
Sets the default behavior of the select command such that hetero atoms are selected.

 set hetero off
Sets the default behavior of the select command such that hetero atoms are not selected. 

=== hydrogen ===
 set hydrogen on
Sets the default behavior of the select command such that hydrogens are selected.

 set hydrogen off
Sets the default behavior of the select command such that hydrogens are not selected. 

=== imagesize ===
 set imagesize &lt;width&gt; &lt;height&gt;
Sets the size of the 3D-rendering panel in pixels. The size will be set within the screen size with the width being an even integer. 

=== line_width ===
 set line_width &lt;value&gt;
Sets the width of lines in polygon images. The &lt;value&gt; should be larger than 0. 

=== loadcenter ===
 set loadcenter on
When a file is opened, sets the default center of that file to the center of all files that have already opened.

 set loadcenter off
When a file is opened, sets the default center of that file according to its own coordiantes. 

=== picking ===
 set picking off
Turns off the mouse picking.

 set picking ident
Sets the mouse picking behavior to show atom identification.

 set picking coord
Sets the mouse picking behavior to show atom coordinates with identification.

 set picking distance
Sets the mouse picking behavior to show the distance between atoms successively picked.

 set picking center
Sets the mouse picking behavior to specify the center of rotation and center of the screen.

 set picking select
Sets the mouse picking behavior to select the file that contains the atom picked. 

=== pickradius ===
 set pickradius &lt;value&gt;
Sets the mouse-pickable region of each atom to be the sphere centered to each atom with the specified radius (angstrom or Rasmol unit). 

=== point_size ===
 set point_size &lt;value&gt;
Sets the size of points in polygon images. The &lt;value&gt; should be larger than 0. 

=== polyline_width ===
 set polyline_width &lt;value&gt;
Sets the width of polylines in polygon images. The &lt;value&gt; should be larger than 0. 

=== projection ===
 set projection perspective
Sets the projection mode for a perspective projection.

 set projection parallel {&lt;size&gt;}
Sets the projection mode for a parallel projection. The size of image (fit to the height of the screen) can be specified (angstrom or Rasmol unit). 

=== specular ===
 set specular on/true
Enables the display of specular highlights on solid objects.

 set specular off/false
Disables the display of specular highlights on solid objects.

 set specular &lt;value&gt;
Enables the display of specular highlights on solid objects. The value between 0 and 100 specifies the specular color in gray scale with 0 and 100 being black and white, respectively. The default value is 50.0. 

=== specpower ===
 set specpower &lt;value&gt;
Sets the shininess of solid objects. The value between 0 and 100 specifies a material reflection coefficient with 0 being diffuse surfaces and 100 being shiny surfaces. 

=== ssbonds ===
 set ssbonds backbone
Disulfide bonds are displayed between backbones.

 set ssbonds sidechain
Disulfide bonds are displayed between sidechains. 

=== stereo ===
 set stereo
A synonym of the stereo command. 

=== transparency ===
 set transparency &lt;value&gt;
Sets the transparency of polygon images.

 set point_transparency &lt;value&gt;
Sets the transparency of points in polygon images.

 set line_transparency &lt;value&gt;
Sets the transparency of lines in polygon images.

 set triangle_transparency &lt;value&gt;
Sets the transparency of triangles in polygon images.

 set quad_transparency &lt;value&gt;
Sets the transparency of quads in polygon images.

 set polyline_transparency &lt;value&gt;
Sets the transparency of polylines in polygon images. 

=== viewpoint ===
 set viewpoint {x, y, z}
Sets the viewpoint to the specified coordinates. 

== show ==
 show godata
Displays gene ontology data of molecules.

 show imagesize
Displays the size of the 3D-rendering panel.

 show information
Displays a detail discription of molecules.

 show site {&lt;prefix&gt;:&lt;db&gt;:&lt;category&gt;}
Displays site information in an external database.

 show transform
Displays the transform matrix of molecules.

 show viewpoint
Displays the current viewpoint.

 show xps3
Displays keywords available in xps3 selection. 

== slab ==
 slab {on/true}
Enables the z-clipping plane of molecules and polygons.

 slab off/false
Disables the z-clipping plane of molecules and polygons.

 slab &lt;ratio&gt;
Sets the position of the z-clipping plane of molecules and polygons. The parameter may be given as a number from 0 to 100. The values 0 and 100 represent that image as a whole is completely invisible and visible, respectively.

 slab -v &lt;value&gt;
Sets the position of the z-clipping plane of molecules and polygons by specifying the z coordinate value. 

== spacefill ==
 spacefill {on/true}
Turns on the ball image of the selected atoms.

 spacefill off/false
Turns off the ball image of the selected atoms.

 spacefill &lt;radius&gt;
Turns on the ball image of the selected atoms with the specified radius (angstrom or Rasmol unit). The maximum parameter value is 3.0.

 spacefill temperature
Turns on the ball image of the selected atoms using the temperature factor as radius. 

== ssbonds ==
 ssbonds {on/true}
Turns on the selected disulfide bonds.

 ssbonds off/false
Turns off the selected disulfide bonds.

 ssbonds &lt;radius&gt;
Turns on the selected disulfide bonds with the specified raidus (angstrom or Rasmol unit). The maximum parameter value is 2.0. 

== stereo ==
 stereo {on/true}
Enables stereo display. This command without arguments cycles three state; 'stereo off', 'stereo on' in cross-eyed mode and 'stereo on' in parallel-eyed mode.

 stereo off/false
Disables stereo display.

 stereo &lt;angle&gt;
Enables stereo display with the specified separation angle. Positive and negative values represent cross-eyed and parallel-eyed viewing, respectively.


== structure ==
 structure
Estimates the secondary structure using Kabsch and Sander's DSSP algorithm. 

== trace ==
 trace {on/true}
Turns on a tube representation for the selected residues.

 trace off/false
Turns off a tube representation for the selected residues.

 trace &lt;radius&gt;
Turns on a tube representation for the selected residues with the specified radius (angstrom or Rasmol unit). The maximum parameter value is 2.0.


== translate ==
 translate x/y/z &lt;value&gt;
Moves images along the specified axis by the specified amount (angstrom). 

== wireframe ==
 wireframe {on/true}
Turns on the selected bonds.

 wireframe off/false
Turns off the selected bonds.

 wireframe &lt;radius&gt;
Turns on the selected bonds with the specified raidus (angstrom or Rasmol unit). The maximum parameter value is 2.0. 

== write ==
 write
A synonym of the save command. 

== zap ==
 zap {&lt;file_IDs&gt;}
Closes the specified files. More than one file IDs can be specified by putting commas as the delimiter. When the paraneter is absent, all files are closed. 

== zoom ==
 zoom {&lt;value&gt;}
Sets the magnification of the image as a whole. The value stands for the magnification as a percentage of the current scale. The minimum parameter value is 10.0.</text>
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<page arvcontinue="20090309075222|151">
  <title>Atom Expression</title>
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    </contributor>
    <comment>Created page with '{| style="float:right"  |__TOC__  |} In order to specify a group of atoms in a molecule, the following five expressions are available.  The standard boolean connectives 'and', 'o...'</comment>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="1799" xml:space="preserve">{| style="float:right"
 |__TOC__
 |}
In order to specify a group of atoms in a molecule, the following five expressions are available.

The standard boolean connectives 'and', 'or' and 'not', and brackets can be used to construct a complex expression. The boolean connectives may be abbreviated as '&amp;', '|', and '|', respectively. 

== predefined set ==
=== element name ===
Element names, such as carbon or nitrogen, can be used to select atoms. 
=== set based on residue property ===
# amino acids in protein molecule

# nucleotides

# others

=== others ===


== comparison operators ==
Parts of a molecule can be selected using equality, inequality and ordering operators on their properties. Possible operators are =, ==, &lt;&gt;, !=, /=, &lt;, &lt;=, &gt; and &gt;=, and possible property names are as follows.
{| border="1"
 |-
 | AtomNo || atom ID in PDB files.
 |-
 | ElemNo || atomic number.
 |-
 | ResNo || residue ID in PDB files.
 |}
!!!!!!!!!!

== residue range ==
A group of atoms in a molecule can be selected by the residue ID. For example, command 'select 3' selects atoms whose residue ID is 3, and 'select 3-10' selects atoms whose residue ID is larger than or equal to 3 and smaller than or equal to 10. 

== within expression ==
A within expression selects atoms that exist within a specified distance from another set of atoms. For example, 'select within(3.0, backbone) selects atoms within a 3.0 Angstrom radius of any atom in a protein or nucleic acid backbone. 

== xPSSS expression ==


== primitive expression ==
A xPSSS expression selects a group of atoms according to molecule's properties defined in the 'PDBML plus' file. It takes the following form;
 xps3:keyword.
For example, 'select xps3:binding'. The keywords available for each molecule are obtained by the 'show xps3' command.</text>
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    <comment>/* comparison operators */</comment>
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    <text bytes="1952" xml:space="preserve">{| style="float:right"
 |__TOC__
 |}
In order to specify a group of atoms in a molecule, the following five expressions are available.

The standard boolean connectives 'and', 'or' and 'not', and brackets can be used to construct a complex expression. The boolean connectives may be abbreviated as '&amp;', '|', and '|', respectively. 

== predefined set ==
=== element name ===
Element names, such as carbon or nitrogen, can be used to select atoms. 
=== set based on residue property ===
# amino acids in protein molecule

# nucleotides

# others

=== others ===


== comparison operators ==
Parts of a molecule can be selected using equality, inequality and ordering operators on their properties. Possible operators are =, ==, &lt;&gt;, !=, /=, &lt;, &lt;=, &gt; and &gt;=, and possible property names are as follows.
{| border="1"
 |-
 | AtomNo || atom ID in PDB files.
 |-
 | ElemNo || atomic number.
 |-
 | ResNo || residue ID in PDB files.
 |-
 | Radius || radius of a ball image of atoms.
 |-
 | Temperature || temperature factor of atoms.
 |-
 | Model || model ID in PDB files.
 |-
 | File || File ID.
 |}

== residue range ==
A group of atoms in a molecule can be selected by the residue ID. For example, command 'select 3' selects atoms whose residue ID is 3, and 'select 3-10' selects atoms whose residue ID is larger than or equal to 3 and smaller than or equal to 10. 

== within expression ==
A within expression selects atoms that exist within a specified distance from another set of atoms. For example, 'select within(3.0, backbone) selects atoms within a 3.0 Angstrom radius of any atom in a protein or nucleic acid backbone. 

== xPSSS expression ==


== primitive expression ==
A xPSSS expression selects a group of atoms according to molecule's properties defined in the 'PDBML plus' file. It takes the following form;
 xps3:keyword.
For example, 'select xps3:binding'. The keywords available for each molecule are obtained by the 'show xps3' command.</text>
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    <comment>/* set based on residue property */</comment>
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    <text bytes="8733" xml:space="preserve">{| style="float:right"
 |__TOC__
 |}
In order to specify a group of atoms in a molecule, the following five expressions are available.

The standard boolean connectives 'and', 'or' and 'not', and brackets can be used to construct a complex expression. The boolean connectives may be abbreviated as '&amp;', '|', and '|', respectively. 

== predefined set ==
=== element name ===
Element names, such as carbon or nitrogen, can be used to select atoms. 
=== set based on residue property ===
a) amino acids in protein molecule
&lt;table border="1"&gt;
&lt;tr&gt;
&lt;td&gt;&lt;/td&gt;
&lt;td&gt;ALA&lt;/td&gt;&lt;td&gt;ARG&lt;/td&gt;&lt;td&gt;ASN&lt;/td&gt;&lt;td&gt;ASP&lt;/td&gt;&lt;td&gt;CYS&lt;/td&gt;
&lt;td&gt;GLU&lt;/td&gt;&lt;td&gt;GLN&lt;/td&gt;&lt;td&gt;GLY&lt;/td&gt;&lt;td&gt;HIS&lt;/td&gt;&lt;td&gt;ILE&lt;/td&gt;
&lt;td&gt;LEU&lt;/td&gt;&lt;td&gt;LYS&lt;/td&gt;&lt;td&gt;MET&lt;/td&gt;&lt;td&gt;PHE&lt;/td&gt;&lt;td&gt;PRO&lt;/td&gt;
&lt;td&gt;SER&lt;/td&gt;&lt;td&gt;THR&lt;/td&gt;&lt;td&gt;TRP&lt;/td&gt;&lt;td&gt;TYR&lt;/td&gt;&lt;td&gt;VAL&lt;/td&gt;
&lt;/tr&gt;
&lt;tr&gt;
&lt;td&gt;Acidic&lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;/tr&gt;
&lt;tr&gt;
&lt;td&gt;Acyclic&lt;/td&gt;
&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;
&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;
&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;&lt;/td&gt;&lt;td&gt;&lt;/td&gt;
&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;&lt;/td&gt;&lt;td&gt;&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;
&lt;/tr&gt;
&lt;tr&gt;
&lt;td&gt;Aliphatic&lt;/td&gt;
&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;
&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;
&lt;/tr&gt;
&lt;tr&gt;
&lt;td&gt;Aromatic&lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;/tr&gt;
&lt;tr&gt;
&lt;td&gt;Basic&lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;/tr&gt;
&lt;tr&gt;
&lt;td&gt;Buried&lt;/td&gt;
&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;
&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;
&lt;/tr&gt;
&lt;tr&gt;
&lt;td&gt;Charged&lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;/tr&gt;
&lt;tr&gt;
&lt;td&gt;Cyclic&lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;/tr&gt;
&lt;tr&gt;
&lt;td&gt;Hydrophobic&lt;/td&gt;
&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;
&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;
&lt;/tr&gt;
&lt;tr&gt;
&lt;td&gt;Large&lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;
&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;/tr&gt;
&lt;tr&gt;
&lt;td&gt;Medium&lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;
&lt;/tr&gt;
&lt;tr&gt;
&lt;td&gt;Negative&lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;/tr&gt;
&lt;tr&gt;
&lt;td&gt;Neutral&lt;/td&gt;
&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;
&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;
&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;
&lt;/tr&gt;
&lt;tr&gt;
&lt;td&gt;Polar&lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;
&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;/tr&gt;
&lt;tr&gt;
&lt;td&gt;Positive&lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;/tr&gt;
&lt;tr&gt;
&lt;td&gt;Small&lt;/td&gt;
&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;/tr&gt;
&lt;tr&gt;
&lt;td&gt;Surface&lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;
&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;/tr&gt;
&lt;tr&gt;
&lt;td&gt;Cysteine&lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;/tr&gt;
&lt;tr&gt;
&lt;td&gt;Amino&lt;/td&gt;
&lt;td colspan="20"&gt;above 20 amino acids + ASX, GLX, PCA, HYP&lt;/td&gt;
&lt;/tr&gt;
&lt;tr&gt;
&lt;td&gt;Protein&lt;/td&gt;
&lt;td colspan="20"&gt;above 20 amino acids + ASX, GLX, PCA, HYP, UNK, ACE, FOR&lt;/td&gt;
&lt;/tr&gt;
&lt;/table&gt;

b) nucleotides
&lt;table border="1"&gt;
&lt;tr&gt;
&lt;td&gt;&lt;/td&gt;
&lt;td&gt;  A&lt;/td&gt;&lt;td&gt;  C&lt;/td&gt;&lt;td&gt;  G&lt;/td&gt;&lt;td&gt;  T&lt;/td&gt;&lt;td&gt;  U&lt;/td&gt;
&lt;td&gt; +U&lt;/td&gt;&lt;td&gt;  I&lt;/td&gt;&lt;td&gt;1MA&lt;/td&gt;&lt;td&gt;5MC&lt;/td&gt;&lt;td&gt;OMC&lt;/td&gt;
&lt;td&gt;1MG&lt;/td&gt;&lt;td&gt;2MG&lt;/td&gt;&lt;td&gt;M2G&lt;/td&gt;&lt;td&gt;7MG&lt;/td&gt;&lt;td&gt;OMG&lt;/td&gt;
&lt;td&gt; YG&lt;/td&gt;&lt;td&gt;H2U&lt;/td&gt;&lt;td&gt;5MU&lt;/td&gt;&lt;td&gt;PSU&lt;/td&gt;
&lt;/tr&gt;
&lt;tr&gt;
&lt;td&gt;AT&lt;/td&gt;
&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;/tr&gt;
&lt;tr&gt;
&lt;td&gt;CG&lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;/tr&gt;
&lt;tr&gt;
&lt;td&gt;Purine&lt;/td&gt;
&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;/tr&gt;
&lt;tr&gt;
&lt;td&gt;Pyrimidine&lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;/tr&gt;
&lt;tr&gt;
&lt;td&gt;DNA&lt;/td&gt;
&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;/tr&gt;
&lt;tr&gt;
&lt;td&gt;RNA&lt;/td&gt;
&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;
&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;
&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;
&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;
&lt;/tr&gt;
&lt;tr&gt;
&lt;td&gt;Nucleic&lt;/td&gt;
&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;
&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;
&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;
&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;
&lt;/tr&gt;
&lt;/table&gt;

c) others
&lt;table border="1"&gt;
&lt;tr&gt;
&lt;td&gt;&lt;/td&gt;
&lt;td&gt;HOH&lt;/td&gt;&lt;td&gt;DOD&lt;/td&gt;&lt;td&gt;SO4&lt;/td&gt;&lt;td&gt;PO4&lt;/td&gt;
&lt;/tr&gt;
&lt;tr&gt;
&lt;td&gt;Water&lt;/td&gt;
&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;/tr&gt;
&lt;tr&gt;
&lt;td&gt;Ions&lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;
&lt;/tr&gt;
&lt;tr&gt;
&lt;td&gt;Solvent&lt;/td&gt;
&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;
&lt;/tr&gt;
&lt;/table&gt;

=== others ===


== comparison operators ==
Parts of a molecule can be selected using equality, inequality and ordering operators on their properties. Possible operators are =, ==, &lt;&gt;, !=, /=, &lt;, &lt;=, &gt; and &gt;=, and possible property names are as follows.
{| border="1"
 |-
 | AtomNo || atom ID in PDB files.
 |-
 | ElemNo || atomic number.
 |-
 | ResNo || residue ID in PDB files.
 |-
 | Radius || radius of a ball image of atoms.
 |-
 | Temperature || temperature factor of atoms.
 |-
 | Model || model ID in PDB files.
 |-
 | File || File ID.
 |}

== residue range ==
A group of atoms in a molecule can be selected by the residue ID. For example, command 'select 3' selects atoms whose residue ID is 3, and 'select 3-10' selects atoms whose residue ID is larger than or equal to 3 and smaller than or equal to 10. 

== within expression ==
A within expression selects atoms that exist within a specified distance from another set of atoms. For example, 'select within(3.0, backbone) selects atoms within a 3.0 Angstrom radius of any atom in a protein or nucleic acid backbone. 

== xPSSS expression ==


== primitive expression ==
A xPSSS expression selects a group of atoms according to molecule's properties defined in the 'PDBML plus' file. It takes the following form;
 xps3:keyword.
For example, 'select xps3:binding'. The keywords available for each molecule are obtained by the 'show xps3' command.</text>
    <sha1>8273500f472c85f002603171065d7c3496ce9bb6</sha1>
  </revision>
</page>
<page arvcontinue="20090309075222|151">
  <title>Vertex Expression</title>
  <ns>0</ns>
  <id>22</id>
  <revision>
    <id>163</id>
    <timestamp>2009-03-09T08:17:38Z</timestamp>
    <contributor>
      <username>JVuser</username>
      <id>2</id>
    </contributor>
    <comment>Created page with 'In order to specify a group of vertices in a polygon, the following three expressions are available.  The standard boolean connectives 'and', 'or' and 'not', and brackets can be ...'</comment>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="1775" xml:space="preserve">In order to specify a group of vertices in a polygon, the following three expressions are available.

The standard boolean connectives 'and', 'or' and 'not', and brackets can be used to construct a complex expression. The boolean connectives may be abbreviated as '&amp;', '|', and '|', respectively. 

== comparison operators ==
Parts of a polygon can be selected using equality and inequality operators on the ID numbers assigned to each vertex; for example, id &gt;= 100. Possible operators are =, ==, &lt;&gt;, !=, /=, &lt;, &lt;=, &gt; and &gt;=. When each vertex element has a user_data element, every attributes in the user_data element can be used to select vertices with equality and inequality operators. 

== within expression ==
A within expression selects vertices that exist within a specified distance from a set of atoms.
# within( &lt;distance&gt;, &lt;atom_expression&gt; )&lt;br /&gt;Instead of a set of atoms, a single point coordinates, from which the distance is measured, can be specified.
# within( &lt;distance&gt;, [x, y, z] )
# within( &lt;distance&gt;, {x, y, z} )
In case 2), vertices are selected according to their current coordinates displayed in the screen. On the other hand, coordinates written in the original polygon file are used in case 3). 

== box expression ==
A box expression selects vertices that exist in some cubes, where each cube is centered to each atom in a specified set of atoms. The syntax is similar to that of the within expression.
# box( &lt;size&gt;, &lt;atom_expression&gt; )&lt;br /&gt;When a single point coordinates is given in the second argument, vertices that exist in a single cube, whose center is set to the passed coordinates, are selected.
# box( &lt;size&gt;, [x, y, z] )
# box( &lt;size&gt;, {x, y, z} )
In every cases, the length of an edge of the cubes is twice as the specified value.</text>
    <sha1>f4500a9ce969323ef489ce21c4d79477e280a528</sha1>
  </revision>
  <revision>
    <id>164</id>
    <parentid>163</parentid>
    <timestamp>2009-03-09T08:18:01Z</timestamp>
    <contributor>
      <username>JVuser</username>
      <id>2</id>
    </contributor>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="1812" xml:space="preserve">{| style="float:right"
 |__TOC__
 |}
In order to specify a group of vertices in a polygon, the following three expressions are available.

The standard boolean connectives 'and', 'or' and 'not', and brackets can be used to construct a complex expression. The boolean connectives may be abbreviated as '&amp;', '|', and '|', respectively. 

== comparison operators ==
Parts of a polygon can be selected using equality and inequality operators on the ID numbers assigned to each vertex; for example, id &gt;= 100. Possible operators are =, ==, &lt;&gt;, !=, /=, &lt;, &lt;=, &gt; and &gt;=. When each vertex element has a user_data element, every attributes in the user_data element can be used to select vertices with equality and inequality operators. 

== within expression ==
A within expression selects vertices that exist within a specified distance from a set of atoms.
# within( &lt;distance&gt;, &lt;atom_expression&gt; )&lt;br /&gt;Instead of a set of atoms, a single point coordinates, from which the distance is measured, can be specified.
# within( &lt;distance&gt;, [x, y, z] )
# within( &lt;distance&gt;, {x, y, z} )
In case 2), vertices are selected according to their current coordinates displayed in the screen. On the other hand, coordinates written in the original polygon file are used in case 3). 

== box expression ==
A box expression selects vertices that exist in some cubes, where each cube is centered to each atom in a specified set of atoms. The syntax is similar to that of the within expression.
# box( &lt;size&gt;, &lt;atom_expression&gt; )&lt;br /&gt;When a single point coordinates is given in the second argument, vertices that exist in a single cube, whose center is set to the passed coordinates, are selected.
# box( &lt;size&gt;, [x, y, z] )
# box( &lt;size&gt;, {x, y, z} )
In every cases, the length of an edge of the cubes is twice as the specified value.</text>
    <sha1>28c74cd3fb3e2296fc1e1b022808fa153e3e4320</sha1>
  </revision>
</page>
<page arvcontinue="20090309075222|151">
  <title>How to use</title>
  <ns>0</ns>
  <id>11</id>
  <revision>
    <id>165</id>
    <parentid>139</parentid>
    <timestamp>2009-03-09T08:19:32Z</timestamp>
    <contributor>
      <username>JVuser</username>
      <id>2</id>
    </contributor>
    <comment>/* How to use */</comment>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="3044" xml:space="preserve">jV is an interactive 3D viewer program to visualize protein and nucleic acid molecules. The program reads in a PDBML file that is an XML format for PDB. Usual PDB format files are also accepted. More than one molecule files can be opened and displayed at the same time and their display models and transforms can be operated separately. In addition to molecule files, a polygon file written in XML can be read and displayed. More than one polygon files can be opened at the same time and superposed on molecule images. The [http://ef-site.hgc.jp/eF-site/schema/polygon12.xsd XML schema] of the polygon file is available. jV can perform an animation of molecules. The animation file is a PDB format file in which each frame is separated by a MODEL line.

jV runs on Java Runtime Environment ([http://java.sun.com/javase/index.jsp JRE]) and can be used both as a standalone program and an applet. The 3D rendering is performed with the use of [https://jogl.dev.java.net/ JOGL] API. The version requirements are as follows.

* JRE (includes Java Plug-in) 1.4.2 or later
* JOGL 1.1.1 or JSR-231

Here, [http://java.sun.com/products/plugin/ Java Plug-in] is required in order to use the program as an applet.

The program allows an interactive mouse control and command execution. The commnad syntax follows that of [http://www.rasmol.org/ Rasmol] with some modifications. In order to handle the transform of each molecule and polygon separately, every files are set to be either selected or not selected. The transform operation commands, such as rotate or translate, act only on selected files. On the other hand, every atoms in a molecule are also set to be either selected or not selected independently of whether the molecule itself is selected or not selected. Only selected atoms are the target of display model operations, such as wireframe or spacefill commands, and coloring operations.

[[Release note]]
== How to use ==
The following table shows hot to do the minimum things with jV.&lt;br /&gt;
{| class="wikitable" border="1" style="margin:0 auto" 
 ! Action !! Window, Linux !! Mac OS X 
 |-
 ! style="text-align:left" | rotate around X,Y axes
 | left drag || mouse drag
 |-
 ! style="text-align:left" | rotate around Z axis
 | Shift + right drag || Shift + command + drag
 |-
 ! style="text-align:left" | translate along X,Y axes
 | right drag || command + drag
 |-
 ! style="text-align:left" | translate along Z axis (zoom in/out)
 | Shift + left drag || Shift + drag
 |}
For the detail,&lt;br /&gt;
PDF Document: &amp;nbsp;&amp;nbsp;[[Media:JV3_User'sGuide.pdf|User's Guide]](30 October 2006) &amp;nbsp;&amp;nbsp;|&amp;nbsp;&amp;nbsp; [[Media:JV_manual.pdf|jV Manual]](30 Octover 2006)
* The install manual [[Installaion of jV3]]
* The reference manual
 ** Manual
# [[Tutorials]]
# [[GUI]]
# [[Document type of the polygon file]]
# [[Functional site information for molecules]]
 ** User's Guide
# [[Command List]]
# [[Atom Expression]]
# [[Vertex Expression]]
# [[Color Expression]]
# [[Use as Applet]]
Some examples
# [[Animation]]
# [[User jV with applet launcher]]</text>
    <sha1>76623ae8cfcc12097fc4dd6fd1444178900041bb</sha1>
  </revision>
  <revision>
    <id>166</id>
    <parentid>165</parentid>
    <timestamp>2009-03-09T08:19:59Z</timestamp>
    <contributor>
      <username>JVuser</username>
      <id>2</id>
    </contributor>
    <comment>/* How to use */</comment>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="3042" xml:space="preserve">jV is an interactive 3D viewer program to visualize protein and nucleic acid molecules. The program reads in a PDBML file that is an XML format for PDB. Usual PDB format files are also accepted. More than one molecule files can be opened and displayed at the same time and their display models and transforms can be operated separately. In addition to molecule files, a polygon file written in XML can be read and displayed. More than one polygon files can be opened at the same time and superposed on molecule images. The [http://ef-site.hgc.jp/eF-site/schema/polygon12.xsd XML schema] of the polygon file is available. jV can perform an animation of molecules. The animation file is a PDB format file in which each frame is separated by a MODEL line.

jV runs on Java Runtime Environment ([http://java.sun.com/javase/index.jsp JRE]) and can be used both as a standalone program and an applet. The 3D rendering is performed with the use of [https://jogl.dev.java.net/ JOGL] API. The version requirements are as follows.

* JRE (includes Java Plug-in) 1.4.2 or later
* JOGL 1.1.1 or JSR-231

Here, [http://java.sun.com/products/plugin/ Java Plug-in] is required in order to use the program as an applet.

The program allows an interactive mouse control and command execution. The commnad syntax follows that of [http://www.rasmol.org/ Rasmol] with some modifications. In order to handle the transform of each molecule and polygon separately, every files are set to be either selected or not selected. The transform operation commands, such as rotate or translate, act only on selected files. On the other hand, every atoms in a molecule are also set to be either selected or not selected independently of whether the molecule itself is selected or not selected. Only selected atoms are the target of display model operations, such as wireframe or spacefill commands, and coloring operations.

[[Release note]]
== How to use ==
The following table shows hot to do the minimum things with jV.&lt;br /&gt;
{| class="wikitable" border="1" style="margin:0 auto" 
 ! Action !! Window, Linux !! Mac OS X 
 |-
 ! style="text-align:left" | rotate around X,Y axes
 | left drag || mouse drag
 |-
 ! style="text-align:left" | rotate around Z axis
 | Shift + right drag || Shift + command + drag
 |-
 ! style="text-align:left" | translate along X,Y axes
 | right drag || command + drag
 |-
 ! style="text-align:left" | translate along Z axis (zoom in/out)
 | Shift + left drag || Shift + drag
 |}
For the detail,&lt;br /&gt;
PDF Document: &amp;nbsp;&amp;nbsp;[[Media:JV3_User'sGuide.pdf|User's Guide]](30 October 2006) &amp;nbsp;&amp;nbsp;|&amp;nbsp;&amp;nbsp; [[Media:JV_manual.pdf|jV Manual]](30 Octover 2006)
* The install manual [[Installaion of jV3]]
* The reference manual
** User's Guide
# [[Tutorials]]
# [[GUI]]
# [[Document type of the polygon file]]
# [[Functional site information for molecules]]
** Manual
# [[Command List]]
# [[Atom Expression]]
# [[Vertex Expression]]
# [[Color Expression]]
# [[Use as Applet]]
Some examples
# [[Animation]]
# [[User jV with applet launcher]]</text>
    <sha1>baf22dcad8722d747dce847f327e29a410412d8b</sha1>
  </revision>
  <revision>
    <id>167</id>
    <parentid>166</parentid>
    <timestamp>2009-03-09T08:23:57Z</timestamp>
    <contributor>
      <username>JVuser</username>
      <id>2</id>
    </contributor>
    <comment>/* How to use */</comment>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="3044" xml:space="preserve">jV is an interactive 3D viewer program to visualize protein and nucleic acid molecules. The program reads in a PDBML file that is an XML format for PDB. Usual PDB format files are also accepted. More than one molecule files can be opened and displayed at the same time and their display models and transforms can be operated separately. In addition to molecule files, a polygon file written in XML can be read and displayed. More than one polygon files can be opened at the same time and superposed on molecule images. The [http://ef-site.hgc.jp/eF-site/schema/polygon12.xsd XML schema] of the polygon file is available. jV can perform an animation of molecules. The animation file is a PDB format file in which each frame is separated by a MODEL line.

jV runs on Java Runtime Environment ([http://java.sun.com/javase/index.jsp JRE]) and can be used both as a standalone program and an applet. The 3D rendering is performed with the use of [https://jogl.dev.java.net/ JOGL] API. The version requirements are as follows.

* JRE (includes Java Plug-in) 1.4.2 or later
* JOGL 1.1.1 or JSR-231

Here, [http://java.sun.com/products/plugin/ Java Plug-in] is required in order to use the program as an applet.

The program allows an interactive mouse control and command execution. The commnad syntax follows that of [http://www.rasmol.org/ Rasmol] with some modifications. In order to handle the transform of each molecule and polygon separately, every files are set to be either selected or not selected. The transform operation commands, such as rotate or translate, act only on selected files. On the other hand, every atoms in a molecule are also set to be either selected or not selected independently of whether the molecule itself is selected or not selected. Only selected atoms are the target of display model operations, such as wireframe or spacefill commands, and coloring operations.

[[Release note]]
== How to use ==
The following table shows hot to do the minimum things with jV.&lt;br /&gt;
{| class="wikitable" border="1" style="margin:0 auto" 
 ! Action !! Window, Linux !! Mac OS X 
 |-
 ! style="text-align:left" | rotate around X,Y axes
 | left drag || mouse drag
 |-
 ! style="text-align:left" | rotate around Z axis
 | Shift + right drag || Shift + command + drag
 |-
 ! style="text-align:left" | translate along X,Y axes
 | right drag || command + drag
 |-
 ! style="text-align:left" | translate along Z axis (zoom in/out)
 | Shift + left drag || Shift + drag
 |}
For the detail,&lt;br /&gt;
PDF Document: &amp;nbsp;&amp;nbsp;[[Media:JV3_User'sGuide.pdf|User's Guide]](30 October 2006) &amp;nbsp;&amp;nbsp;|&amp;nbsp;&amp;nbsp; [[Media:JV_manual.pdf|jV Manual]](30 Octover 2006)
* The install manual [[Installaion of jV3]]
* The reference manual
:** User's Guide
# [[Tutorials]]
# [[GUI]]
# [[Document type of the polygon file]]
# [[Functional site information for molecules]]
:** Manual
# [[Command List]]
# [[Atom Expression]]
# [[Vertex Expression]]
# [[Color Expression]]
# [[Use as Applet]]
Some examples
# [[Animation]]
# [[User jV with applet launcher]]</text>
    <sha1>3c67f58a26e3a63bfc96ba6493a8b913d7e1c00f</sha1>
  </revision>
  <revision>
    <id>168</id>
    <parentid>167</parentid>
    <timestamp>2009-03-09T08:24:14Z</timestamp>
    <contributor>
      <username>JVuser</username>
      <id>2</id>
    </contributor>
    <comment>/* How to use */</comment>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="3042" xml:space="preserve">jV is an interactive 3D viewer program to visualize protein and nucleic acid molecules. The program reads in a PDBML file that is an XML format for PDB. Usual PDB format files are also accepted. More than one molecule files can be opened and displayed at the same time and their display models and transforms can be operated separately. In addition to molecule files, a polygon file written in XML can be read and displayed. More than one polygon files can be opened at the same time and superposed on molecule images. The [http://ef-site.hgc.jp/eF-site/schema/polygon12.xsd XML schema] of the polygon file is available. jV can perform an animation of molecules. The animation file is a PDB format file in which each frame is separated by a MODEL line.

jV runs on Java Runtime Environment ([http://java.sun.com/javase/index.jsp JRE]) and can be used both as a standalone program and an applet. The 3D rendering is performed with the use of [https://jogl.dev.java.net/ JOGL] API. The version requirements are as follows.

* JRE (includes Java Plug-in) 1.4.2 or later
* JOGL 1.1.1 or JSR-231

Here, [http://java.sun.com/products/plugin/ Java Plug-in] is required in order to use the program as an applet.

The program allows an interactive mouse control and command execution. The commnad syntax follows that of [http://www.rasmol.org/ Rasmol] with some modifications. In order to handle the transform of each molecule and polygon separately, every files are set to be either selected or not selected. The transform operation commands, such as rotate or translate, act only on selected files. On the other hand, every atoms in a molecule are also set to be either selected or not selected independently of whether the molecule itself is selected or not selected. Only selected atoms are the target of display model operations, such as wireframe or spacefill commands, and coloring operations.

[[Release note]]
== How to use ==
The following table shows hot to do the minimum things with jV.&lt;br /&gt;
{| class="wikitable" border="1" style="margin:0 auto" 
 ! Action !! Window, Linux !! Mac OS X 
 |-
 ! style="text-align:left" | rotate around X,Y axes
 | left drag || mouse drag
 |-
 ! style="text-align:left" | rotate around Z axis
 | Shift + right drag || Shift + command + drag
 |-
 ! style="text-align:left" | translate along X,Y axes
 | right drag || command + drag
 |-
 ! style="text-align:left" | translate along Z axis (zoom in/out)
 | Shift + left drag || Shift + drag
 |}
For the detail,&lt;br /&gt;
PDF Document: &amp;nbsp;&amp;nbsp;[[Media:JV3_User'sGuide.pdf|User's Guide]](30 October 2006) &amp;nbsp;&amp;nbsp;|&amp;nbsp;&amp;nbsp; [[Media:JV_manual.pdf|jV Manual]](30 Octover 2006)
* The install manual [[Installaion of jV3]]
* The reference manual
:* User's Guide
# [[Tutorials]]
# [[GUI]]
# [[Document type of the polygon file]]
# [[Functional site information for molecules]]
:* Manual
# [[Command List]]
# [[Atom Expression]]
# [[Vertex Expression]]
# [[Color Expression]]
# [[Use as Applet]]
Some examples
# [[Animation]]
# [[User jV with applet launcher]]</text>
    <sha1>8f34f9ed8ca7321e1f049cf569c36140101adb4b</sha1>
  </revision>
  <revision>
    <id>169</id>
    <parentid>168</parentid>
    <timestamp>2009-03-09T08:25:07Z</timestamp>
    <contributor>
      <username>JVuser</username>
      <id>2</id>
    </contributor>
    <comment>/* How to use */</comment>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="3042" xml:space="preserve">jV is an interactive 3D viewer program to visualize protein and nucleic acid molecules. The program reads in a PDBML file that is an XML format for PDB. Usual PDB format files are also accepted. More than one molecule files can be opened and displayed at the same time and their display models and transforms can be operated separately. In addition to molecule files, a polygon file written in XML can be read and displayed. More than one polygon files can be opened at the same time and superposed on molecule images. The [http://ef-site.hgc.jp/eF-site/schema/polygon12.xsd XML schema] of the polygon file is available. jV can perform an animation of molecules. The animation file is a PDB format file in which each frame is separated by a MODEL line.

jV runs on Java Runtime Environment ([http://java.sun.com/javase/index.jsp JRE]) and can be used both as a standalone program and an applet. The 3D rendering is performed with the use of [https://jogl.dev.java.net/ JOGL] API. The version requirements are as follows.

* JRE (includes Java Plug-in) 1.4.2 or later
* JOGL 1.1.1 or JSR-231

Here, [http://java.sun.com/products/plugin/ Java Plug-in] is required in order to use the program as an applet.

The program allows an interactive mouse control and command execution. The commnad syntax follows that of [http://www.rasmol.org/ Rasmol] with some modifications. In order to handle the transform of each molecule and polygon separately, every files are set to be either selected or not selected. The transform operation commands, such as rotate or translate, act only on selected files. On the other hand, every atoms in a molecule are also set to be either selected or not selected independently of whether the molecule itself is selected or not selected. Only selected atoms are the target of display model operations, such as wireframe or spacefill commands, and coloring operations.

[[Release note]]
== How to use ==
The following table shows hot to do the minimum things with jV.&lt;br /&gt;
{| class="wikitable" border="1" style="margin:0 auto" 
 ! Action !! Window, Linux !! Mac OS X 
 |-
 ! style="text-align:left" | rotate around X,Y axes
 | left drag || mouse drag
 |-
 ! style="text-align:left" | rotate around Z axis
 | Shift + right drag || Shift + command + drag
 |-
 ! style="text-align:left" | translate along X,Y axes
 | right drag || command + drag
 |-
 ! style="text-align:left" | translate along Z axis (zoom in/out)
 | Shift + left drag || Shift + drag
 |}
For the detail,&lt;br /&gt;
PDF Document: &amp;nbsp;&amp;nbsp;[[Media:JV3_User'sGuide.pdf|User's Guide]](30 October 2006) &amp;nbsp;&amp;nbsp;|&amp;nbsp;&amp;nbsp; [[Media:JV_manual.pdf|jV Manual]](30 Octover 2006)
; The install manual [[Installaion of jV3]]
; The reference manual
:* User's Guide
# [[Tutorials]]
# [[GUI]]
# [[Document type of the polygon file]]
# [[Functional site information for molecules]]
:* Manual
# [[Command List]]
# [[Atom Expression]]
# [[Vertex Expression]]
# [[Color Expression]]
# [[Use as Applet]]
Some examples
# [[Animation]]
# [[User jV with applet launcher]]</text>
    <sha1>d32e426df1bff26905e4716039b22f994b9b056c</sha1>
  </revision>
  <revision>
    <id>170</id>
    <parentid>169</parentid>
    <timestamp>2009-03-09T08:25:47Z</timestamp>
    <contributor>
      <username>JVuser</username>
      <id>2</id>
    </contributor>
    <comment>/* How to use */</comment>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="3043" xml:space="preserve">jV is an interactive 3D viewer program to visualize protein and nucleic acid molecules. The program reads in a PDBML file that is an XML format for PDB. Usual PDB format files are also accepted. More than one molecule files can be opened and displayed at the same time and their display models and transforms can be operated separately. In addition to molecule files, a polygon file written in XML can be read and displayed. More than one polygon files can be opened at the same time and superposed on molecule images. The [http://ef-site.hgc.jp/eF-site/schema/polygon12.xsd XML schema] of the polygon file is available. jV can perform an animation of molecules. The animation file is a PDB format file in which each frame is separated by a MODEL line.

jV runs on Java Runtime Environment ([http://java.sun.com/javase/index.jsp JRE]) and can be used both as a standalone program and an applet. The 3D rendering is performed with the use of [https://jogl.dev.java.net/ JOGL] API. The version requirements are as follows.

* JRE (includes Java Plug-in) 1.4.2 or later
* JOGL 1.1.1 or JSR-231

Here, [http://java.sun.com/products/plugin/ Java Plug-in] is required in order to use the program as an applet.

The program allows an interactive mouse control and command execution. The commnad syntax follows that of [http://www.rasmol.org/ Rasmol] with some modifications. In order to handle the transform of each molecule and polygon separately, every files are set to be either selected or not selected. The transform operation commands, such as rotate or translate, act only on selected files. On the other hand, every atoms in a molecule are also set to be either selected or not selected independently of whether the molecule itself is selected or not selected. Only selected atoms are the target of display model operations, such as wireframe or spacefill commands, and coloring operations.

[[Release note]]
== How to use ==
The following table shows hot to do the minimum things with jV.&lt;br /&gt;
{| class="wikitable" border="1" style="margin:0 auto" 
 ! Action !! Window, Linux !! Mac OS X 
 |-
 ! style="text-align:left" | rotate around X,Y axes
 | left drag || mouse drag
 |-
 ! style="text-align:left" | rotate around Z axis
 | Shift + right drag || Shift + command + drag
 |-
 ! style="text-align:left" | translate along X,Y axes
 | right drag || command + drag
 |-
 ! style="text-align:left" | translate along Z axis (zoom in/out)
 | Shift + left drag || Shift + drag
 |}
For the detail,&lt;br /&gt;
PDF Document: &amp;nbsp;&amp;nbsp;[[Media:JV3_User'sGuide.pdf|User's Guide]](30 October 2006) &amp;nbsp;&amp;nbsp;|&amp;nbsp;&amp;nbsp; [[Media:JV_manual.pdf|jV Manual]](30 Octover 2006)
; The install manual 
* [[Installaion of jV3]]
; The reference manual
* User's Guide
# [[Tutorials]]
# [[GUI]]
# [[Document type of the polygon file]]
# [[Functional site information for molecules]]
* Manual
# [[Command List]]
# [[Atom Expression]]
# [[Vertex Expression]]
# [[Color Expression]]
# [[Use as Applet]]
Some examples
# [[Animation]]
# [[User jV with applet launcher]]</text>
    <sha1>549e9a47aa78afe7e2b2cfccf46e68b152babc9d</sha1>
  </revision>
  <revision>
    <id>171</id>
    <parentid>170</parentid>
    <timestamp>2009-03-09T08:26:41Z</timestamp>
    <contributor>
      <username>JVuser</username>
      <id>2</id>
    </contributor>
    <comment>/* How to use */</comment>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="2992" xml:space="preserve">jV is an interactive 3D viewer program to visualize protein and nucleic acid molecules. The program reads in a PDBML file that is an XML format for PDB. Usual PDB format files are also accepted. More than one molecule files can be opened and displayed at the same time and their display models and transforms can be operated separately. In addition to molecule files, a polygon file written in XML can be read and displayed. More than one polygon files can be opened at the same time and superposed on molecule images. The [http://ef-site.hgc.jp/eF-site/schema/polygon12.xsd XML schema] of the polygon file is available. jV can perform an animation of molecules. The animation file is a PDB format file in which each frame is separated by a MODEL line.

jV runs on Java Runtime Environment ([http://java.sun.com/javase/index.jsp JRE]) and can be used both as a standalone program and an applet. The 3D rendering is performed with the use of [https://jogl.dev.java.net/ JOGL] API. The version requirements are as follows.

* JRE (includes Java Plug-in) 1.4.2 or later
* JOGL 1.1.1 or JSR-231

Here, [http://java.sun.com/products/plugin/ Java Plug-in] is required in order to use the program as an applet.

The program allows an interactive mouse control and command execution. The commnad syntax follows that of [http://www.rasmol.org/ Rasmol] with some modifications. In order to handle the transform of each molecule and polygon separately, every files are set to be either selected or not selected. The transform operation commands, such as rotate or translate, act only on selected files. On the other hand, every atoms in a molecule are also set to be either selected or not selected independently of whether the molecule itself is selected or not selected. Only selected atoms are the target of display model operations, such as wireframe or spacefill commands, and coloring operations.

[[Release note]]
== How to use ==
The following table shows hot to do the minimum things with jV.&lt;br /&gt;
{| class="wikitable" border="1" style="margin:0 auto" 
 ! Action !! Window, Linux !! Mac OS X 
 |-
 ! style="text-align:left" | rotate around X,Y axes
 | left drag || mouse drag
 |-
 ! style="text-align:left" | rotate around Z axis
 | Shift + right drag || Shift + command + drag
 |-
 ! style="text-align:left" | translate along X,Y axes
 | right drag || command + drag
 |-
 ! style="text-align:left" | translate along Z axis (zoom in/out)
 | Shift + left drag || Shift + drag
 |}
For the detail,&lt;br /&gt;

; The install manual 
* [[Installaion of jV3]]
; The reference manual
* User's Guide [[Media:JV3_User'sGuide.pdf|User's Guide]](30 October 2006)
# [[Tutorials]]
# [[GUI]]
# [[Document type of the polygon file]]
# [[Functional site information for molecules]]
* Manual [[Media:JV_manual.pdf|jV Manual]](30 Octover 2006)
# [[Command List]]
# [[Atom Expression]]
# [[Vertex Expression]]
# [[Color Expression]]
# [[Use as Applet]]
Some examples
# [[Animation]]
# [[User jV with applet launcher]]</text>
    <sha1>71a5efc89b1b05391c343086aa63c25104af647b</sha1>
  </revision>
  <revision>
    <id>172</id>
    <parentid>171</parentid>
    <timestamp>2009-03-09T08:27:08Z</timestamp>
    <contributor>
      <username>JVuser</username>
      <id>2</id>
    </contributor>
    <comment>/* How to use */</comment>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="2977" xml:space="preserve">jV is an interactive 3D viewer program to visualize protein and nucleic acid molecules. The program reads in a PDBML file that is an XML format for PDB. Usual PDB format files are also accepted. More than one molecule files can be opened and displayed at the same time and their display models and transforms can be operated separately. In addition to molecule files, a polygon file written in XML can be read and displayed. More than one polygon files can be opened at the same time and superposed on molecule images. The [http://ef-site.hgc.jp/eF-site/schema/polygon12.xsd XML schema] of the polygon file is available. jV can perform an animation of molecules. The animation file is a PDB format file in which each frame is separated by a MODEL line.

jV runs on Java Runtime Environment ([http://java.sun.com/javase/index.jsp JRE]) and can be used both as a standalone program and an applet. The 3D rendering is performed with the use of [https://jogl.dev.java.net/ JOGL] API. The version requirements are as follows.

* JRE (includes Java Plug-in) 1.4.2 or later
* JOGL 1.1.1 or JSR-231

Here, [http://java.sun.com/products/plugin/ Java Plug-in] is required in order to use the program as an applet.

The program allows an interactive mouse control and command execution. The commnad syntax follows that of [http://www.rasmol.org/ Rasmol] with some modifications. In order to handle the transform of each molecule and polygon separately, every files are set to be either selected or not selected. The transform operation commands, such as rotate or translate, act only on selected files. On the other hand, every atoms in a molecule are also set to be either selected or not selected independently of whether the molecule itself is selected or not selected. Only selected atoms are the target of display model operations, such as wireframe or spacefill commands, and coloring operations.

[[Release note]]
== How to use ==
The following table shows hot to do the minimum things with jV.&lt;br /&gt;
{| class="wikitable" border="1" style="margin:0 auto" 
 ! Action !! Window, Linux !! Mac OS X 
 |-
 ! style="text-align:left" | rotate around X,Y axes
 | left drag || mouse drag
 |-
 ! style="text-align:left" | rotate around Z axis
 | Shift + right drag || Shift + command + drag
 |-
 ! style="text-align:left" | translate along X,Y axes
 | right drag || command + drag
 |-
 ! style="text-align:left" | translate along Z axis (zoom in/out)
 | Shift + left drag || Shift + drag
 |}
For the detail,&lt;br /&gt;

; The install manual 
* [[Installaion of jV3]]
; The reference manual
* User's Guide [[Media:JV3_User'sGuide.pdf|pdf]](30 October 2006)
# [[Tutorials]]
# [[GUI]]
# [[Document type of the polygon file]]
# [[Functional site information for molecules]]
* Manual [[Media:JV_manual.pdf|pdf]](30 Octover 2006)
# [[Command List]]
# [[Atom Expression]]
# [[Vertex Expression]]
# [[Color Expression]]
# [[Use as Applet]]
Some examples
# [[Animation]]
# [[User jV with applet launcher]]</text>
    <sha1>7c981a474c6874a5de7acd659bf6e732cda6d6b0</sha1>
  </revision>
  <revision>
    <id>173</id>
    <parentid>172</parentid>
    <timestamp>2009-03-09T08:28:25Z</timestamp>
    <contributor>
      <username>JVuser</username>
      <id>2</id>
    </contributor>
    <comment>/* How to use */</comment>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="2989" xml:space="preserve">jV is an interactive 3D viewer program to visualize protein and nucleic acid molecules. The program reads in a PDBML file that is an XML format for PDB. Usual PDB format files are also accepted. More than one molecule files can be opened and displayed at the same time and their display models and transforms can be operated separately. In addition to molecule files, a polygon file written in XML can be read and displayed. More than one polygon files can be opened at the same time and superposed on molecule images. The [http://ef-site.hgc.jp/eF-site/schema/polygon12.xsd XML schema] of the polygon file is available. jV can perform an animation of molecules. The animation file is a PDB format file in which each frame is separated by a MODEL line.

jV runs on Java Runtime Environment ([http://java.sun.com/javase/index.jsp JRE]) and can be used both as a standalone program and an applet. The 3D rendering is performed with the use of [https://jogl.dev.java.net/ JOGL] API. The version requirements are as follows.

* JRE (includes Java Plug-in) 1.4.2 or later
* JOGL 1.1.1 or JSR-231

Here, [http://java.sun.com/products/plugin/ Java Plug-in] is required in order to use the program as an applet.

The program allows an interactive mouse control and command execution. The commnad syntax follows that of [http://www.rasmol.org/ Rasmol] with some modifications. In order to handle the transform of each molecule and polygon separately, every files are set to be either selected or not selected. The transform operation commands, such as rotate or translate, act only on selected files. On the other hand, every atoms in a molecule are also set to be either selected or not selected independently of whether the molecule itself is selected or not selected. Only selected atoms are the target of display model operations, such as wireframe or spacefill commands, and coloring operations.

[[Release note]]
== How to use ==
The following table shows hot to do the minimum things with jV.&lt;br /&gt;
{| class="wikitable" border="1" style="margin:0 auto" 
 ! Action !! Window, Linux !! Mac OS X 
 |-
 ! style="text-align:left" | rotate around X,Y axes
 | left drag || mouse drag
 |-
 ! style="text-align:left" | rotate around Z axis
 | Shift + right drag || Shift + command + drag
 |-
 ! style="text-align:left" | translate along X,Y axes
 | right drag || command + drag
 |-
 ! style="text-align:left" | translate along Z axis (zoom in/out)
 | Shift + left drag || Shift + drag
 |}
For the detail,&lt;br /&gt;

; The install manual 
* [[Installaion of jV3]]
; The reference manual
* User's Guide &amp;nbsp;[[Media:JV3_User'sGuide.pdf|pdf]](30 October 2006)
# [[Tutorials]]
# [[GUI]]
# [[Document type of the polygon file]]
# [[Functional site information for molecules]]
* Manual &amp;nbsp;[[Media:JV_manual.pdf|pdf]](30 Octover 2006)
# [[Command List]]
# [[Atom Expression]]
# [[Vertex Expression]]
# [[Color Expression]]
# [[Use as Applet]]
Some examples
# [[Animation]]
# [[User jV with applet launcher]]</text>
    <sha1>47801ddb88475afc575823eb74f173f55460d9e4</sha1>
  </revision>
  <revision>
    <id>174</id>
    <parentid>173</parentid>
    <timestamp>2009-03-09T08:28:56Z</timestamp>
    <contributor>
      <username>JVuser</username>
      <id>2</id>
    </contributor>
    <comment>/* How to use */</comment>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="2989" xml:space="preserve">jV is an interactive 3D viewer program to visualize protein and nucleic acid molecules. The program reads in a PDBML file that is an XML format for PDB. Usual PDB format files are also accepted. More than one molecule files can be opened and displayed at the same time and their display models and transforms can be operated separately. In addition to molecule files, a polygon file written in XML can be read and displayed. More than one polygon files can be opened at the same time and superposed on molecule images. The [http://ef-site.hgc.jp/eF-site/schema/polygon12.xsd XML schema] of the polygon file is available. jV can perform an animation of molecules. The animation file is a PDB format file in which each frame is separated by a MODEL line.

jV runs on Java Runtime Environment ([http://java.sun.com/javase/index.jsp JRE]) and can be used both as a standalone program and an applet. The 3D rendering is performed with the use of [https://jogl.dev.java.net/ JOGL] API. The version requirements are as follows.

* JRE (includes Java Plug-in) 1.4.2 or later
* JOGL 1.1.1 or JSR-231

Here, [http://java.sun.com/products/plugin/ Java Plug-in] is required in order to use the program as an applet.

The program allows an interactive mouse control and command execution. The commnad syntax follows that of [http://www.rasmol.org/ Rasmol] with some modifications. In order to handle the transform of each molecule and polygon separately, every files are set to be either selected or not selected. The transform operation commands, such as rotate or translate, act only on selected files. On the other hand, every atoms in a molecule are also set to be either selected or not selected independently of whether the molecule itself is selected or not selected. Only selected atoms are the target of display model operations, such as wireframe or spacefill commands, and coloring operations.

[[Release note]]
== How to use ==
The following table shows hot to do the minimum things with jV.&lt;br /&gt;
{| class="wikitable" border="1" style="margin:0 auto" 
 ! Action !! Window, Linux !! Mac OS X 
 |-
 ! style="text-align:left" | rotate around X,Y axes
 | left drag || mouse drag
 |-
 ! style="text-align:left" | rotate around Z axis
 | Shift + right drag || Shift + command + drag
 |-
 ! style="text-align:left" | translate along X,Y axes
 | right drag || command + drag
 |-
 ! style="text-align:left" | translate along Z axis (zoom in/out)
 | Shift + left drag || Shift + drag
 |}
For the detail,&lt;br /&gt;

; The install manual 
* [[Installaion of jV3]]
; The reference manual
* User's Guide &amp;nbsp;[[Media:JV3_User'sGuide.pdf|pdf(30 October 2006)]]
# [[Tutorials]]
# [[GUI]]
# [[Document type of the polygon file]]
# [[Functional site information for molecules]]
* Manual &amp;nbsp;[[Media:JV_manual.pdf|pdf]](30 Octover 2006)
# [[Command List]]
# [[Atom Expression]]
# [[Vertex Expression]]
# [[Color Expression]]
# [[Use as Applet]]
Some examples
# [[Animation]]
# [[User jV with applet launcher]]</text>
    <sha1>185962b97b6a3c63947da01a814cc6739ffaa177</sha1>
  </revision>
  <revision>
    <id>175</id>
    <parentid>174</parentid>
    <timestamp>2009-03-09T08:29:18Z</timestamp>
    <contributor>
      <username>JVuser</username>
      <id>2</id>
    </contributor>
    <comment>/* How to use */</comment>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="2989" xml:space="preserve">jV is an interactive 3D viewer program to visualize protein and nucleic acid molecules. The program reads in a PDBML file that is an XML format for PDB. Usual PDB format files are also accepted. More than one molecule files can be opened and displayed at the same time and their display models and transforms can be operated separately. In addition to molecule files, a polygon file written in XML can be read and displayed. More than one polygon files can be opened at the same time and superposed on molecule images. The [http://ef-site.hgc.jp/eF-site/schema/polygon12.xsd XML schema] of the polygon file is available. jV can perform an animation of molecules. The animation file is a PDB format file in which each frame is separated by a MODEL line.

jV runs on Java Runtime Environment ([http://java.sun.com/javase/index.jsp JRE]) and can be used both as a standalone program and an applet. The 3D rendering is performed with the use of [https://jogl.dev.java.net/ JOGL] API. The version requirements are as follows.

* JRE (includes Java Plug-in) 1.4.2 or later
* JOGL 1.1.1 or JSR-231

Here, [http://java.sun.com/products/plugin/ Java Plug-in] is required in order to use the program as an applet.

The program allows an interactive mouse control and command execution. The commnad syntax follows that of [http://www.rasmol.org/ Rasmol] with some modifications. In order to handle the transform of each molecule and polygon separately, every files are set to be either selected or not selected. The transform operation commands, such as rotate or translate, act only on selected files. On the other hand, every atoms in a molecule are also set to be either selected or not selected independently of whether the molecule itself is selected or not selected. Only selected atoms are the target of display model operations, such as wireframe or spacefill commands, and coloring operations.

[[Release note]]
== How to use ==
The following table shows hot to do the minimum things with jV.&lt;br /&gt;
{| class="wikitable" border="1" style="margin:0 auto" 
 ! Action !! Window, Linux !! Mac OS X 
 |-
 ! style="text-align:left" | rotate around X,Y axes
 | left drag || mouse drag
 |-
 ! style="text-align:left" | rotate around Z axis
 | Shift + right drag || Shift + command + drag
 |-
 ! style="text-align:left" | translate along X,Y axes
 | right drag || command + drag
 |-
 ! style="text-align:left" | translate along Z axis (zoom in/out)
 | Shift + left drag || Shift + drag
 |}
For the detail,&lt;br /&gt;

; The install manual 
* [[Installaion of jV3]]
; The reference manual
* User's Guide &amp;nbsp;[[Media:JV3_User'sGuide.pdf|pdf(30 October 2006)]]
# [[Tutorials]]
# [[GUI]]
# [[Document type of the polygon file]]
# [[Functional site information for molecules]]
* Manual &amp;nbsp;[[Media:JV_manual.pdf|pdf(30 Octover 2006)]]
# [[Command List]]
# [[Atom Expression]]
# [[Vertex Expression]]
# [[Color Expression]]
# [[Use as Applet]]
Some examples
# [[Animation]]
# [[User jV with applet launcher]]</text>
    <sha1>7012d86c2c4ae4d8f5a12194f5a572928d2c7d8f</sha1>
  </revision>
  <revision>
    <id>181</id>
    <parentid>175</parentid>
    <timestamp>2009-03-09T08:49:52Z</timestamp>
    <contributor>
      <username>JVuser</username>
      <id>2</id>
    </contributor>
    <comment>/* How to use */</comment>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="2991" xml:space="preserve">jV is an interactive 3D viewer program to visualize protein and nucleic acid molecules. The program reads in a PDBML file that is an XML format for PDB. Usual PDB format files are also accepted. More than one molecule files can be opened and displayed at the same time and their display models and transforms can be operated separately. In addition to molecule files, a polygon file written in XML can be read and displayed. More than one polygon files can be opened at the same time and superposed on molecule images. The [http://ef-site.hgc.jp/eF-site/schema/polygon12.xsd XML schema] of the polygon file is available. jV can perform an animation of molecules. The animation file is a PDB format file in which each frame is separated by a MODEL line.

jV runs on Java Runtime Environment ([http://java.sun.com/javase/index.jsp JRE]) and can be used both as a standalone program and an applet. The 3D rendering is performed with the use of [https://jogl.dev.java.net/ JOGL] API. The version requirements are as follows.

* JRE (includes Java Plug-in) 1.4.2 or later
* JOGL 1.1.1 or JSR-231

Here, [http://java.sun.com/products/plugin/ Java Plug-in] is required in order to use the program as an applet.

The program allows an interactive mouse control and command execution. The commnad syntax follows that of [http://www.rasmol.org/ Rasmol] with some modifications. In order to handle the transform of each molecule and polygon separately, every files are set to be either selected or not selected. The transform operation commands, such as rotate or translate, act only on selected files. On the other hand, every atoms in a molecule are also set to be either selected or not selected independently of whether the molecule itself is selected or not selected. Only selected atoms are the target of display model operations, such as wireframe or spacefill commands, and coloring operations.

[[Release note]]
== How to use ==
The following table shows hot to do the minimum things with jV.&lt;br /&gt;
{| class="wikitable" border="1" style="margin:0 auto" 
 ! Action !! Window, Linux !! Mac OS X 
 |-
 ! style="text-align:left" | rotate around X,Y axes
 | left drag || mouse drag
 |-
 ! style="text-align:left" | rotate around Z axis
 | Shift + right drag || Shift + command + drag
 |-
 ! style="text-align:left" | translate along X,Y axes
 | right drag || command + drag
 |-
 ! style="text-align:left" | translate along Z axis (zoom in/out)
 | Shift + left drag || Shift + drag
 |}
For the detail,&lt;br /&gt;

; The install manual 
* [[Installaion of jV3]]
; The reference manual
* User's Guide &amp;nbsp;[[Media:JV3_User'sGuide.pdf|pdf(30 October 2006)]]
# [[Tutorials]]
# [[GUI]]
# [[Document type of the polygon file]]
# [[Functional site information for molecules]]
* Manual &amp;nbsp;[[Media:JV_manual.pdf|pdf(30 Octover 2006)]]
# [[Command List]]
# [[Atom Expression]]
# [[Vertex Expression]]
# [[Color Expression]]
# [[Use as Applet]]

;Some examples
# [[Animation]]
# [[User jV with applet launcher]]</text>
    <sha1>3baecc91cb87372d478c1ae8531f314b21c6fc46</sha1>
  </revision>
</page>
<page arvcontinue="20090309075222|151">
  <title>Color Expression</title>
  <ns>0</ns>
  <id>23</id>
  <revision>
    <id>176</id>
    <timestamp>2009-03-09T08:37:31Z</timestamp>
    <contributor>
      <username>JVuser</username>
      <id>2</id>
    </contributor>
    <comment>Created page with '== RGB values == A color can be specified by a comma separated triple of Red, Green and Blue (RGB) components enclosed in square brackets, where RGB values are from 0 to 255, res...'</comment>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="11512" xml:space="preserve">== RGB values ==
A color can be specified by a comma separated triple of Red, Green and Blue (RGB) components enclosed in square brackets, where RGB values are from 0 to 255, respectively. 

== Predefined Color ==
The following 24 colors can be specified by their name.

&lt;table border="1"&gt;
 &lt;tr&gt;
  &lt;td&gt;color name&lt;/td&gt;
  &lt;td&gt;RGB values&lt;/td&gt;
  &lt;td&gt;color&lt;/td&gt;
 &lt;/tr&gt;
 &lt;tr&gt;
  &lt;td&gt;BLACK&lt;/td&gt;
  &lt;td&gt;[0, 0, 0]&lt;/td&gt;
  &lt;td width=100 style="background: #000000"&gt;&lt;/td&gt;
 &lt;/tr&gt;
 &lt;tr&gt;
  &lt;td&gt;BLUE&lt;/td&gt;
  &lt;td&gt;[0, 0, 255]&lt;/td&gt;
  &lt;td width=100 style="background: #0000FF"&gt;&lt;/td&gt;
 &lt;/tr&gt;
 &lt;tr&gt;
  &lt;td&gt;BLUETINT&lt;/td&gt;
  &lt;td&gt;[175, 214, 255]&lt;/td&gt;
  &lt;td width=100 style="background: #AFD6FF"&gt;&lt;/td&gt;
 &lt;/tr&gt;
 &lt;tr&gt;
  &lt;td&gt;BROWN&lt;/td&gt;
  &lt;td&gt;[175, 117, 89]&lt;/td&gt;
  &lt;td width=100 style="background: #AF7559"&gt;&lt;/td&gt;
 &lt;/tr&gt;
 &lt;tr&gt;
  &lt;td&gt;CYAN&lt;/td&gt;
  &lt;td&gt;[0, 255, 255]&lt;/td&gt;
  &lt;td width=100 style="background: #00FFFF"&gt;&lt;/td&gt;
 &lt;/tr&gt;
 &lt;tr&gt;
  &lt;td&gt;GOLD&lt;/td&gt;
  &lt;td&gt;[255, 156, 0]&lt;/td&gt;
  &lt;td width=100 style="background: #FF9C00"&gt;&lt;/td&gt;
 &lt;/tr&gt;
 &lt;tr&gt;
  &lt;td&gt;GREY&lt;/td&gt;
  &lt;td&gt;[125, 125, 125]&lt;/td&gt;
  &lt;td width=100 style="background: #7D7D7D"&gt;&lt;/td&gt;
 &lt;/tr&gt;
 &lt;tr&gt;
  &lt;td&gt;GREEN&lt;/td&gt;
  &lt;td&gt;[0, 255, 0]&lt;/td&gt;
  &lt;td width=100 style="background: #00FF00"&gt;&lt;/td&gt;
 &lt;/tr&gt;
 &lt;tr&gt;
  &lt;td&gt;GREENBLUE&lt;/td&gt;
  &lt;td&gt;[46, 139, 87]&lt;/td&gt;
  &lt;td width=100 style="background: #2E8B57"&gt;&lt;/td&gt;
 &lt;/tr&gt;
 &lt;tr&gt;
  &lt;td&gt;GreenTint&lt;/td&gt;
  &lt;td&gt;[152, 255, 179]&lt;/td&gt;
  &lt;td width=100 style="background: #98FFB3"&gt;&lt;/td&gt;
 &lt;/tr&gt;
 &lt;tr&gt;
  &lt;td&gt;HOTPINK&lt;/td&gt;
  &lt;td&gt;[255, 0, 101]&lt;/td&gt;
  &lt;td width=100 style="background: #FF0065"&gt;&lt;/td&gt;
 &lt;/tr&gt;
 &lt;tr&gt;
  &lt;td&gt;MAGENTA&lt;/td&gt;
  &lt;td&gt;[255, 0, 255]&lt;/td&gt;
  &lt;td width=100 style="background: #FF00FF"&gt;&lt;/td&gt;
 &lt;/tr&gt;
 &lt;tr&gt;
  &lt;td&gt;ORANGE&lt;/td&gt;
  &lt;td&gt;[255, 165, 0]&lt;/td&gt;
  &lt;td width=100 style="background: #FFA500"&gt;&lt;/td&gt;
 &lt;/tr&gt;
 &lt;tr&gt;
  &lt;td&gt;PINK&lt;/td&gt;
  &lt;td&gt;[255, 101, 117]&lt;/td&gt;
  &lt;td width=100 style="background: #FF6575"&gt;&lt;/td&gt;
 &lt;/tr&gt;
 &lt;tr&gt;
  &lt;td&gt;PINKTINT&lt;/td&gt;
  &lt;td&gt;[255, 171, 187]&lt;/td&gt;
  &lt;td width=100 style="background: #FFABBB"&gt;&lt;/td&gt;
 &lt;/tr&gt;
 &lt;tr&gt;
  &lt;td&gt;PURPLE&lt;/td&gt;
  &lt;td&gt;[160, 32, 240]&lt;/td&gt;
  &lt;td width=100 style="background: #A020F0"&gt;&lt;/td&gt;
 &lt;/tr&gt;
 &lt;tr&gt;
  &lt;td&gt;RED&lt;/td&gt;
  &lt;td&gt;[255, 0, 0]&lt;/td&gt;
  &lt;td width=100 style="background: #FF0000"&gt;&lt;/td&gt;
 &lt;/tr&gt;
 &lt;tr&gt;
  &lt;td&gt;REDORANGE&lt;/td&gt;
  &lt;td&gt;[255, 69, 0]&lt;/td&gt;
  &lt;td width=100 style="background: #FF4500"&gt;&lt;/td&gt;
 &lt;/tr&gt;
 &lt;tr&gt;
  &lt;td&gt;SEAGREEN&lt;/td&gt;
  &lt;td&gt;[0, 250, 109]&lt;/td&gt;
  &lt;td width=100 style="background: #00FA6D"&gt;&lt;/td&gt;
 &lt;/tr&gt;
 &lt;tr&gt;
  &lt;td&gt;SKYBLUE&lt;/td&gt;
  &lt;td&gt;[58, 144, 255]&lt;/td&gt;
  &lt;td width=100 style="background: #3A90FF"&gt;&lt;/td&gt;
 &lt;/tr&gt;
 &lt;tr&gt;
  &lt;td&gt;VIOLET&lt;/td&gt;
  &lt;td&gt;[238, 130, 238]&lt;/td&gt;
  &lt;td width=100 style="background: #EE82EE"&gt;&lt;/td&gt;
 &lt;/tr&gt;
 &lt;tr&gt;
  &lt;td&gt;WHITE&lt;/td&gt;
  &lt;td&gt;[255, 255, 255]&lt;/td&gt;
  &lt;td width=100 style="background: #FFFFFF"&gt;&lt;/td&gt;
 &lt;/tr&gt;
 &lt;tr&gt;
  &lt;td&gt;YELLOW&lt;/td&gt;
  &lt;td&gt;[255, 255, 0]&lt;/td&gt;
  &lt;td width=100 style="background: #FFFF00"&gt;&lt;/td&gt;
 &lt;/tr&gt;
 &lt;tr&gt;
  &lt;td&gt;YELLOWTINT&lt;/td&gt;
  &lt;td&gt;[246, 246, 117]&lt;/td&gt;
  &lt;td width=100 style="background: #F6F675"&gt;&lt;/td&gt;
 &lt;/tr&gt;
&lt;/table&gt;

== Color Scheme ==

=== amino ===
The color scheme 'amino' colors amino acids as follows.

&lt;table border="1"&gt;
 &lt;tr&gt;
  &lt;td&gt;amino acids&lt;/td&gt;
  &lt;td&gt;RGB values&lt;/td&gt;
  &lt;td&gt;color&lt;/td&gt;
 &lt;/tr&gt;
 &lt;tr&gt;
  &lt;td&gt;ASP, GLU&lt;/td&gt;
  &lt;td&gt;[230,230, 10]&lt;/td&gt;
  &lt;td width=100 style="background: #E60A0A"&gt;&lt;/td&gt;
 &lt;/tr&gt;
 &lt;tr&gt;
  &lt;td&gt;CYS, MET&lt;/td&gt;
  &lt;td&gt;[230,230, 0]&lt;/td&gt;
  &lt;td width=100 style="background: #E6E600"&gt;&lt;/td&gt;
 &lt;/tr&gt;
 &lt;tr&gt;
  &lt;td&gt;LYS, ARG&lt;/td&gt;
  &lt;td&gt;[20, 90,255]&lt;/td&gt;
  &lt;td width=100 style="background: #145AFF"&gt;&lt;/td&gt;
 &lt;/tr&gt;
 &lt;tr&gt;
  &lt;td&gt;SER, THR&lt;/td&gt;
  &lt;td&gt;[250,150, 0]&lt;/td&gt;
  &lt;td width=100 style="background: #FA9600"&gt;&lt;/td&gt;
 &lt;/tr&gt;
 &lt;tr&gt;
  &lt;td&gt;PHE, TYR&lt;/td&gt;
  &lt;td&gt;[50, 50,170]&lt;/td&gt;
  &lt;td width=100 style="background: #3232AA"&gt;&lt;/td&gt;
 &lt;/tr&gt;
 &lt;tr&gt;
  &lt;td&gt;ASN, GLN&lt;/td&gt;
  &lt;td&gt;[0,220,220]&lt;/td&gt;
  &lt;td width=100 style="background: #00DCDC"&gt;&lt;/td&gt;
 &lt;/tr&gt;
 &lt;tr&gt;
  &lt;td&gt;GLY&lt;/td&gt;
  &lt;td&gt;[235,235,235]&lt;/td&gt;
  &lt;td width=100 style="background: #EBEBEB"&gt;&lt;/td&gt;
 &lt;/tr&gt;
 &lt;tr&gt;
  &lt;td&gt;LEU, VAL, ILE&lt;/td&gt;
  &lt;td&gt;[15,130, 15]&lt;/td&gt;
  &lt;td width=100 style="background: #0F820F"&gt;&lt;/td&gt;
 &lt;/tr&gt;
 &lt;tr&gt;
  &lt;td&gt;ALA&lt;/td&gt;
  &lt;td&gt;[200,200,200]&lt;/td&gt;
  &lt;td width=100 style="background: #C8C8C8"&gt;&lt;/td&gt;
 &lt;/tr&gt;
 &lt;tr&gt;
  &lt;td&gt;TRP&lt;/td&gt;
  &lt;td&gt;[180, 90,180]&lt;/td&gt;
  &lt;td width=100 style="background: #B45AB4"&gt;&lt;/td&gt;
 &lt;/tr&gt;
 &lt;tr&gt;
  &lt;td&gt;HIS&lt;/td&gt;
  &lt;td&gt;[130,130,210]&lt;/td&gt;
  &lt;td width=100 style="background: #8282D2"&gt;&lt;/td&gt;
 &lt;/tr&gt;
 &lt;tr&gt;
  &lt;td&gt;PRO&lt;/td&gt;
  &lt;td&gt;[220,150,130]&lt;/td&gt;
  &lt;td width=100 style="background: #DC9682"&gt;&lt;/td&gt;
 &lt;/tr&gt;
 &lt;tr&gt;
  &lt;td&gt;Others&lt;/td&gt;
  &lt;td&gt;[190,160,110]&lt;/td&gt;
  &lt;td width=100 style="background: #BEA06E"&gt;&lt;/td&gt;
 &lt;/tr&gt;
&lt;/table&gt;

=== chain ===
The color scheme 'chain' assigns each macromolecular chain a unique colour.

=== charge ===
The color scheme 'charge' colors atoms according to their temperature factor. High values are coloured in blue and lower values coloured in red. 

=== cpk ===
The color scheme 'cpk' colors atoms according to the element type as follows. 

&lt;table border="1"&gt;
 &lt;tr&gt;
  &lt;td&gt;element&lt;/td&gt;
  &lt;td&gt;RGB values&lt;/td&gt;
  &lt;td&gt;color&lt;/td&gt;
 &lt;/tr&gt;
 &lt;tr&gt;
  &lt;td&gt;C&lt;/td&gt;
  &lt;td&gt;[200, 200, 200]&lt;/td&gt;
  &lt;td width=100 style="background: #C8C8C8"&gt;&lt;/td&gt;
 &lt;/tr&gt;
 &lt;tr&gt;
  &lt;td&gt;N&lt;/td&gt;
  &lt;td&gt;[143, 143, 255]&lt;/td&gt;
  &lt;td width=100 style="background: #8F8FFF"&gt;&lt;/td&gt;
 &lt;/tr&gt;
 &lt;tr&gt;
  &lt;td&gt;O&lt;/td&gt;
  &lt;td&gt;[240, 0, 0]&lt;/td&gt;
  &lt;td width=100 style="background: #F00000"&gt;&lt;/td&gt;
 &lt;/tr&gt;
 &lt;tr&gt;
  &lt;td&gt;S&lt;/td&gt;
  &lt;td&gt;[255, 200, 50]&lt;/td&gt;
  &lt;td width=100 style="background: #FFC832"&gt;&lt;/td&gt;
 &lt;/tr&gt;
 &lt;tr&gt;
  &lt;td&gt;H&lt;/td&gt;
  &lt;td&gt;[255, 255, 255]&lt;/td&gt;
  &lt;td width=100 style="background: #FFFFFF"&gt;&lt;/td&gt;
 &lt;/tr&gt;
 &lt;tr&gt;
  &lt;td&gt;He&lt;/td&gt;
  &lt;td&gt;[255, 192, 203]&lt;/td&gt;
  &lt;td width=100 style="background: #FFC0CB"&gt;&lt;/td&gt;
 &lt;/tr&gt;
 &lt;tr&gt;
  &lt;td&gt;F, Si, Au&lt;/td&gt;
  &lt;td&gt;[218, 165, 32]&lt;/td&gt;
  &lt;td width=100 style="background: #DAA520"&gt;&lt;/td&gt;
 &lt;/tr&gt;
 &lt;tr&gt;
  &lt;td&gt;Na&lt;/td&gt;
  &lt;td&gt;[0, 0, 255]&lt;/td&gt;
  &lt;td width=100 style="background: #0000FF"&gt;&lt;/td&gt;
 &lt;/tr&gt;
 &lt;tr&gt;
  &lt;td&gt;P, Fe, Ba&lt;/td&gt;
  &lt;td&gt;[255, 165, 0]&lt;/td&gt;
  &lt;td width=100 style="background: #FFA500"&gt;&lt;/td&gt;
 &lt;/tr&gt;
 &lt;tr&gt;
  &lt;td&gt;Al, Ca, Ti, Cr, Mn, Ag&lt;/td&gt;
  &lt;td&gt;[128, 128, 144]&lt;/td&gt;
  &lt;td width=100 style="background: #808090"&gt;&lt;/td&gt;
 &lt;/tr&gt;
 &lt;tr&gt;
  &lt;td&gt;Ni, Cu, Zn, Br&lt;/td&gt;
  &lt;td&gt;[165, 42, 42]&lt;/td&gt;
  &lt;td width=100 style="background: #A52A2A"&gt;&lt;/td&gt;
 &lt;/tr&gt;
 &lt;tr&gt;
  &lt;td&gt;I&lt;/td&gt;
  &lt;td&gt;[160, 32, 240]&lt;/td&gt;
  &lt;td width=100 style="background: #A020F0"&gt;&lt;/td&gt;
 &lt;/tr&gt;
 &lt;tr&gt;
  &lt;td&gt;B, Cl&lt;/td&gt;
  &lt;td&gt;[0, 255, 0]&lt;/td&gt;
  &lt;td width=100 style="background: #00FF00"&gt;&lt;/td&gt;
 &lt;/tr&gt;
 &lt;tr&gt;
  &lt;td&gt;Li&lt;/td&gt;
  &lt;td&gt;[178, 34, 34]&lt;/td&gt;
  &lt;td width=100 style="background: #B22222"&gt;&lt;/td&gt;
 &lt;/tr&gt;
 &lt;tr&gt;
  &lt;td&gt;Mg&lt;/td&gt;
  &lt;td&gt;[34, 139, 34]&lt;/td&gt;
  &lt;td width=100 style="background: #228B22"&gt;&lt;/td&gt;
 &lt;/tr&gt;
 &lt;tr&gt;
  &lt;td&gt;Others&lt;/td&gt;
  &lt;td&gt;[255, 20, 147]&lt;/td&gt;
  &lt;td width=100 style="background: #FF1493"&gt;&lt;/td&gt;
 &lt;/tr&gt;
&lt;/table&gt;

=== group ===
The color scheme 'group' colors residues by their position in a macromolecular chain. Each chain is drawn as a smooth spectrum from blue to red. The N terminus of proteins and 5' terminus of nucleic acids are colored red and the C terminus of proteins and 3' terminus of nucleic acids are drawn in blue. 

=== shapely ===
The color scheme 'shapely' colors residues as follows.

&lt;table border="1"&gt;
 &lt;tr&gt;
  &lt;td&gt;residue&lt;/td&gt;
  &lt;td&gt;RGB values&lt;/td&gt;
  &lt;td&gt;color&lt;/td&gt;
 &lt;/tr&gt;
 &lt;tr&gt;
  &lt;td&gt;ALA&lt;/td&gt;
  &lt;td&gt;[140, 255, 140]&lt;/td&gt;
  &lt;td width=100 style="background: #8CFF8C"&gt;&lt;/td&gt;
 &lt;/tr&gt;
 &lt;tr&gt;
  &lt;td&gt;GLY&lt;/td&gt;
  &lt;td&gt;[255, 255, 255]&lt;/td&gt;
  &lt;td width=100 style="background: #FFFFFF"&gt;&lt;/td&gt;
 &lt;/tr&gt;
 &lt;tr&gt;
  &lt;td&gt;LEU&lt;/td&gt;
  &lt;td&gt;[69, 94, 69]&lt;/td&gt;
  &lt;td width=100 style="background: #455E45"&gt;&lt;/td&gt;
 &lt;/tr&gt;
 &lt;tr&gt;
  &lt;td&gt;SER&lt;/td&gt;
  &lt;td&gt;[255, 112, 66]&lt;/td&gt;
  &lt;td width=100 style="background: #FF7042"&gt;&lt;/td&gt;
 &lt;/tr&gt;
 &lt;tr&gt;
  &lt;td&gt;VAL&lt;/td&gt;
  &lt;td&gt;[255, 140, 255]&lt;/td&gt;
  &lt;td width=100 style="background: #FF8CFF"&gt;&lt;/td&gt;
 &lt;/tr&gt;
 &lt;tr&gt;
  &lt;td&gt;THR&lt;/td&gt;
  &lt;td&gt;[184, 76, 0]&lt;/td&gt;
  &lt;td width=100 style="background: #B84C00"&gt;&lt;/td&gt;
 &lt;/tr&gt;
 &lt;tr&gt;
  &lt;td&gt;LYS&lt;/td&gt;
  &lt;td&gt;[71, 71, 184]&lt;/td&gt;
  &lt;td width=100 style="background: #4747B8"&gt;&lt;/td&gt;
 &lt;/tr&gt;
 &lt;tr&gt;
  &lt;td&gt;ASP&lt;/td&gt;
  &lt;td&gt;[160, 0, 66]&lt;/td&gt;
  &lt;td width=100 style="background: #A00042"&gt;&lt;/td&gt;
 &lt;/tr&gt;
 &lt;tr&gt;
  &lt;td&gt;ILE&lt;/td&gt;
  &lt;td&gt;[0, 76, 0]&lt;/td&gt;
  &lt;td width=100 style="background: #004C00"&gt;&lt;/td&gt;
 &lt;/tr&gt;
 &lt;tr&gt;
  &lt;td&gt;ASN&lt;/td&gt;
  &lt;td&gt;[255, 124, 112]&lt;/td&gt;
  &lt;td width=100 style="background: #FF7C70"&gt;&lt;/td&gt;
 &lt;/tr&gt;
 &lt;tr&gt;
  &lt;td&gt;GLU&lt;/td&gt;
  &lt;td&gt;[102, 0, 0]&lt;/td&gt;
  &lt;td width=100 style="background: #660000"&gt;&lt;/td&gt;
 &lt;/tr&gt;
 &lt;tr&gt;
  &lt;td&gt;PRO&lt;/td&gt;
  &lt;td&gt;[82, 82, 82]&lt;/td&gt;
  &lt;td width=100 style="background: #525252"&gt;&lt;/td&gt;
 &lt;/tr&gt;
 &lt;tr&gt;
  &lt;td&gt;ARG&lt;/td&gt;
  &lt;td&gt;[0, 0, 124]&lt;/td&gt;
  &lt;td width=100 style="background: #00007C"&gt;&lt;/td&gt;
 &lt;/tr&gt;
 &lt;tr&gt;
  &lt;td&gt;PHE&lt;/td&gt;
  &lt;td&gt;[83, 76, 66]&lt;/td&gt;
  &lt;td width=100 style="background: #534C42"&gt;&lt;/td&gt;
 &lt;/tr&gt;
 &lt;tr&gt;
  &lt;td&gt;GLN&lt;/td&gt;
  &lt;td&gt;[255, 76, 76]&lt;/td&gt;
  &lt;td width=100 style="background: #FF4C4C"&gt;&lt;/td&gt;
 &lt;/tr&gt;
 &lt;tr&gt;
  &lt;td&gt;TYR&lt;/td&gt;
  &lt;td&gt;[140, 112, 76]&lt;/td&gt;
  &lt;td width=100 style="background: #8C704C"&gt;&lt;/td&gt;
 &lt;/tr&gt;
 &lt;tr&gt;
  &lt;td&gt;HIS&lt;/td&gt;
  &lt;td&gt;[112, 112, 255]&lt;/td&gt;
  &lt;td width=100 style="background: #7070FF"&gt;&lt;/td&gt;
 &lt;/tr&gt;
 &lt;tr&gt;
  &lt;td&gt;CYS&lt;/td&gt;
  &lt;td&gt;[255, 255, 112]&lt;/td&gt;
  &lt;td width=100 style="background: #FFFF70"&gt;&lt;/td&gt;
 &lt;/tr&gt;
 &lt;tr&gt;
  &lt;td&gt;MET&lt;/td&gt;
  &lt;td&gt;[184, 160, 66]&lt;/td&gt;
  &lt;td width=100 style="background: #B8A042"&gt;&lt;/td&gt;
 &lt;/tr&gt;
 &lt;tr&gt;
  &lt;td&gt;TRP&lt;/td&gt;
  &lt;td&gt;[79, 70, 0]&lt;/td&gt;
  &lt;td width=100 style="background: #4F4600"&gt;&lt;/td&gt;
 &lt;/tr&gt;
 &lt;tr&gt;
  &lt;td&gt;A&lt;/td&gt;
  &lt;td&gt;[160, 160, 255]&lt;/td&gt;
  &lt;td width=100 style="background: #A0A0FF"&gt;&lt;/td&gt;
 &lt;/tr&gt;
 &lt;tr&gt;
  &lt;td&gt;C&lt;/td&gt;
  &lt;td&gt;[255, 140, 75]&lt;/td&gt;
  &lt;td width=100 style="background: #FF8C4B"&gt;&lt;/td&gt;
 &lt;/tr&gt;
 &lt;tr&gt;
  &lt;td&gt;G&lt;/td&gt;
  &lt;td&gt;[255, 112, 112]&lt;/td&gt;
  &lt;td width=100 style="background: #FF7070"&gt;&lt;/td&gt;
 &lt;/tr&gt;
 &lt;tr&gt;
  &lt;td&gt;T&lt;/td&gt;
  &lt;td&gt;[160, 255, 160]&lt;/td&gt;
  &lt;td width=100 style="background: #A0FFA0"&gt;&lt;/td&gt;
 &lt;/tr&gt;
 &lt;tr&gt;
  &lt;td&gt;Others&lt;/td&gt;
  &lt;td&gt;[255, 0, 255]&lt;/td&gt;
  &lt;td width=100 style="background: #FF00FF"&gt;&lt;/td&gt;
 &lt;/tr&gt;
&lt;/table&gt;

=== structure ===
The color scheme 'structure' colors residues according to the secondary structure as follows.

&lt;table border="1"&gt;
 &lt;tr&gt;
  &lt;td&gt;secondary structure&lt;/td&gt;
  &lt;td&gt;RGB values&lt;/td&gt;
  &lt;td&gt;color&lt;/td&gt;
 &lt;/tr&gt;
 &lt;tr&gt;
  &lt;td&gt;alpha helix&lt;/td&gt;
  &lt;td&gt;[255, 0, 128]&lt;/td&gt;
  &lt;td width=100 style="background: #FF0080"&gt;&lt;/td&gt;
 &lt;/tr&gt;
 &lt;tr&gt;
  &lt;td&gt;beta sheet&lt;/td&gt;
  &lt;td&gt;[255, 200, 0]&lt;/td&gt;
  &lt;td width=100 style="background: #FFC800"&gt;&lt;/td&gt;
 &lt;/tr&gt;
 &lt;tr&gt;
  &lt;td&gt;turn&lt;/td&gt;
  &lt;td&gt;[96, 128, 255]&lt;/td&gt;
  &lt;td width=100 style="background: #6080FF"&gt;&lt;/td&gt;
 &lt;/tr&gt;
 &lt;tr&gt;
  &lt;td&gt;none&lt;/td&gt;
  &lt;td&gt;[255, 255, 255]&lt;/td&gt;
  &lt;td width=100 style="background: #FFFFFF"&gt;&lt;/td&gt;
 &lt;/tr&gt;
&lt;/table&gt;

=== temperature ===
The color scheme 'temperature' colors atoms according to their temperature factor. High values are coloured in red and lower values coloured in blue. 

=== type ===
This color scheme 'type' colors each hydrogen bond according to the distance along a protein chain between hydrogen bond donor and acceptor as follows. 

&lt;table border="1"&gt;
 &lt;tr&gt;
  &lt;td&gt;offset&lt;/td&gt;
  &lt;td&gt;RGB values&lt;/td&gt;
  &lt;td&gt;color&lt;/td&gt;
 &lt;/tr&gt;
 &lt;tr&gt;
  &lt;td&gt;+2&lt;/td&gt;
  &lt;td&gt;[255, 255, 255]&lt;/td&gt;
  &lt;td width=100 style="background: #FFFFFF"&gt;&lt;/td&gt;
 &lt;/tr&gt;
 &lt;tr&gt;
  &lt;td&gt;+3&lt;/td&gt;
  &lt;td&gt;[255, 0, 255]&lt;/td&gt;
  &lt;td width=100 style="background: #FF00FF"&gt;&lt;/td&gt;
 &lt;/tr&gt;
 &lt;tr&gt;
  &lt;td&gt;+4&lt;/td&gt;
  &lt;td&gt;[255, 0, 0]&lt;/td&gt;
  &lt;td width=100 style="background: #FF0000"&gt;&lt;/td&gt;
 &lt;/tr&gt;
 &lt;tr&gt;
  &lt;td&gt;+5&lt;/td&gt;
  &lt;td&gt;[255, 165, 0]&lt;/td&gt;
  &lt;td width=100 style="background: #FFA500"&gt;&lt;/td&gt;
 &lt;/tr&gt;
 &lt;tr&gt;
  &lt;td&gt;-3&lt;/td&gt;
  &lt;td&gt;[0, 255, 255]&lt;/td&gt;
  &lt;td width=100 style="background: #00FFFF"&gt;&lt;/td&gt;
 &lt;/tr&gt;
 &lt;tr&gt;
  &lt;td&gt;-4&lt;/td&gt;
  &lt;td&gt;[0, 255, 0]&lt;/td&gt;
  &lt;td width=100 style="background: #00FF00"&gt;&lt;/td&gt;
 &lt;/tr&gt;
 &lt;tr&gt;
  &lt;td&gt;Others&lt;/td&gt;
  &lt;td&gt;[255, 255, 0]&lt;/td&gt;
  &lt;td width=100 style="background: #FFFF00"&gt;&lt;/td&gt;
 &lt;/tr&gt;
&lt;/table&gt;</text>
    <sha1>1618c74e7a558dc5b9b6bde897971bd5c246b6a5</sha1>
  </revision>
  <revision>
    <id>177</id>
    <parentid>176</parentid>
    <timestamp>2009-03-09T08:38:02Z</timestamp>
    <contributor>
      <username>JVuser</username>
      <id>2</id>
    </contributor>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="11549" xml:space="preserve">{| style="float:right"
 |__TOC__
 |}
== RGB values ==
A color can be specified by a comma separated triple of Red, Green and Blue (RGB) components enclosed in square brackets, where RGB values are from 0 to 255, respectively. 

== Predefined Color ==
The following 24 colors can be specified by their name.

&lt;table border="1"&gt;
 &lt;tr&gt;
  &lt;td&gt;color name&lt;/td&gt;
  &lt;td&gt;RGB values&lt;/td&gt;
  &lt;td&gt;color&lt;/td&gt;
 &lt;/tr&gt;
 &lt;tr&gt;
  &lt;td&gt;BLACK&lt;/td&gt;
  &lt;td&gt;[0, 0, 0]&lt;/td&gt;
  &lt;td width=100 style="background: #000000"&gt;&lt;/td&gt;
 &lt;/tr&gt;
 &lt;tr&gt;
  &lt;td&gt;BLUE&lt;/td&gt;
  &lt;td&gt;[0, 0, 255]&lt;/td&gt;
  &lt;td width=100 style="background: #0000FF"&gt;&lt;/td&gt;
 &lt;/tr&gt;
 &lt;tr&gt;
  &lt;td&gt;BLUETINT&lt;/td&gt;
  &lt;td&gt;[175, 214, 255]&lt;/td&gt;
  &lt;td width=100 style="background: #AFD6FF"&gt;&lt;/td&gt;
 &lt;/tr&gt;
 &lt;tr&gt;
  &lt;td&gt;BROWN&lt;/td&gt;
  &lt;td&gt;[175, 117, 89]&lt;/td&gt;
  &lt;td width=100 style="background: #AF7559"&gt;&lt;/td&gt;
 &lt;/tr&gt;
 &lt;tr&gt;
  &lt;td&gt;CYAN&lt;/td&gt;
  &lt;td&gt;[0, 255, 255]&lt;/td&gt;
  &lt;td width=100 style="background: #00FFFF"&gt;&lt;/td&gt;
 &lt;/tr&gt;
 &lt;tr&gt;
  &lt;td&gt;GOLD&lt;/td&gt;
  &lt;td&gt;[255, 156, 0]&lt;/td&gt;
  &lt;td width=100 style="background: #FF9C00"&gt;&lt;/td&gt;
 &lt;/tr&gt;
 &lt;tr&gt;
  &lt;td&gt;GREY&lt;/td&gt;
  &lt;td&gt;[125, 125, 125]&lt;/td&gt;
  &lt;td width=100 style="background: #7D7D7D"&gt;&lt;/td&gt;
 &lt;/tr&gt;
 &lt;tr&gt;
  &lt;td&gt;GREEN&lt;/td&gt;
  &lt;td&gt;[0, 255, 0]&lt;/td&gt;
  &lt;td width=100 style="background: #00FF00"&gt;&lt;/td&gt;
 &lt;/tr&gt;
 &lt;tr&gt;
  &lt;td&gt;GREENBLUE&lt;/td&gt;
  &lt;td&gt;[46, 139, 87]&lt;/td&gt;
  &lt;td width=100 style="background: #2E8B57"&gt;&lt;/td&gt;
 &lt;/tr&gt;
 &lt;tr&gt;
  &lt;td&gt;GreenTint&lt;/td&gt;
  &lt;td&gt;[152, 255, 179]&lt;/td&gt;
  &lt;td width=100 style="background: #98FFB3"&gt;&lt;/td&gt;
 &lt;/tr&gt;
 &lt;tr&gt;
  &lt;td&gt;HOTPINK&lt;/td&gt;
  &lt;td&gt;[255, 0, 101]&lt;/td&gt;
  &lt;td width=100 style="background: #FF0065"&gt;&lt;/td&gt;
 &lt;/tr&gt;
 &lt;tr&gt;
  &lt;td&gt;MAGENTA&lt;/td&gt;
  &lt;td&gt;[255, 0, 255]&lt;/td&gt;
  &lt;td width=100 style="background: #FF00FF"&gt;&lt;/td&gt;
 &lt;/tr&gt;
 &lt;tr&gt;
  &lt;td&gt;ORANGE&lt;/td&gt;
  &lt;td&gt;[255, 165, 0]&lt;/td&gt;
  &lt;td width=100 style="background: #FFA500"&gt;&lt;/td&gt;
 &lt;/tr&gt;
 &lt;tr&gt;
  &lt;td&gt;PINK&lt;/td&gt;
  &lt;td&gt;[255, 101, 117]&lt;/td&gt;
  &lt;td width=100 style="background: #FF6575"&gt;&lt;/td&gt;
 &lt;/tr&gt;
 &lt;tr&gt;
  &lt;td&gt;PINKTINT&lt;/td&gt;
  &lt;td&gt;[255, 171, 187]&lt;/td&gt;
  &lt;td width=100 style="background: #FFABBB"&gt;&lt;/td&gt;
 &lt;/tr&gt;
 &lt;tr&gt;
  &lt;td&gt;PURPLE&lt;/td&gt;
  &lt;td&gt;[160, 32, 240]&lt;/td&gt;
  &lt;td width=100 style="background: #A020F0"&gt;&lt;/td&gt;
 &lt;/tr&gt;
 &lt;tr&gt;
  &lt;td&gt;RED&lt;/td&gt;
  &lt;td&gt;[255, 0, 0]&lt;/td&gt;
  &lt;td width=100 style="background: #FF0000"&gt;&lt;/td&gt;
 &lt;/tr&gt;
 &lt;tr&gt;
  &lt;td&gt;REDORANGE&lt;/td&gt;
  &lt;td&gt;[255, 69, 0]&lt;/td&gt;
  &lt;td width=100 style="background: #FF4500"&gt;&lt;/td&gt;
 &lt;/tr&gt;
 &lt;tr&gt;
  &lt;td&gt;SEAGREEN&lt;/td&gt;
  &lt;td&gt;[0, 250, 109]&lt;/td&gt;
  &lt;td width=100 style="background: #00FA6D"&gt;&lt;/td&gt;
 &lt;/tr&gt;
 &lt;tr&gt;
  &lt;td&gt;SKYBLUE&lt;/td&gt;
  &lt;td&gt;[58, 144, 255]&lt;/td&gt;
  &lt;td width=100 style="background: #3A90FF"&gt;&lt;/td&gt;
 &lt;/tr&gt;
 &lt;tr&gt;
  &lt;td&gt;VIOLET&lt;/td&gt;
  &lt;td&gt;[238, 130, 238]&lt;/td&gt;
  &lt;td width=100 style="background: #EE82EE"&gt;&lt;/td&gt;
 &lt;/tr&gt;
 &lt;tr&gt;
  &lt;td&gt;WHITE&lt;/td&gt;
  &lt;td&gt;[255, 255, 255]&lt;/td&gt;
  &lt;td width=100 style="background: #FFFFFF"&gt;&lt;/td&gt;
 &lt;/tr&gt;
 &lt;tr&gt;
  &lt;td&gt;YELLOW&lt;/td&gt;
  &lt;td&gt;[255, 255, 0]&lt;/td&gt;
  &lt;td width=100 style="background: #FFFF00"&gt;&lt;/td&gt;
 &lt;/tr&gt;
 &lt;tr&gt;
  &lt;td&gt;YELLOWTINT&lt;/td&gt;
  &lt;td&gt;[246, 246, 117]&lt;/td&gt;
  &lt;td width=100 style="background: #F6F675"&gt;&lt;/td&gt;
 &lt;/tr&gt;
&lt;/table&gt;

== Color Scheme ==

=== amino ===
The color scheme 'amino' colors amino acids as follows.

&lt;table border="1"&gt;
 &lt;tr&gt;
  &lt;td&gt;amino acids&lt;/td&gt;
  &lt;td&gt;RGB values&lt;/td&gt;
  &lt;td&gt;color&lt;/td&gt;
 &lt;/tr&gt;
 &lt;tr&gt;
  &lt;td&gt;ASP, GLU&lt;/td&gt;
  &lt;td&gt;[230,230, 10]&lt;/td&gt;
  &lt;td width=100 style="background: #E60A0A"&gt;&lt;/td&gt;
 &lt;/tr&gt;
 &lt;tr&gt;
  &lt;td&gt;CYS, MET&lt;/td&gt;
  &lt;td&gt;[230,230, 0]&lt;/td&gt;
  &lt;td width=100 style="background: #E6E600"&gt;&lt;/td&gt;
 &lt;/tr&gt;
 &lt;tr&gt;
  &lt;td&gt;LYS, ARG&lt;/td&gt;
  &lt;td&gt;[20, 90,255]&lt;/td&gt;
  &lt;td width=100 style="background: #145AFF"&gt;&lt;/td&gt;
 &lt;/tr&gt;
 &lt;tr&gt;
  &lt;td&gt;SER, THR&lt;/td&gt;
  &lt;td&gt;[250,150, 0]&lt;/td&gt;
  &lt;td width=100 style="background: #FA9600"&gt;&lt;/td&gt;
 &lt;/tr&gt;
 &lt;tr&gt;
  &lt;td&gt;PHE, TYR&lt;/td&gt;
  &lt;td&gt;[50, 50,170]&lt;/td&gt;
  &lt;td width=100 style="background: #3232AA"&gt;&lt;/td&gt;
 &lt;/tr&gt;
 &lt;tr&gt;
  &lt;td&gt;ASN, GLN&lt;/td&gt;
  &lt;td&gt;[0,220,220]&lt;/td&gt;
  &lt;td width=100 style="background: #00DCDC"&gt;&lt;/td&gt;
 &lt;/tr&gt;
 &lt;tr&gt;
  &lt;td&gt;GLY&lt;/td&gt;
  &lt;td&gt;[235,235,235]&lt;/td&gt;
  &lt;td width=100 style="background: #EBEBEB"&gt;&lt;/td&gt;
 &lt;/tr&gt;
 &lt;tr&gt;
  &lt;td&gt;LEU, VAL, ILE&lt;/td&gt;
  &lt;td&gt;[15,130, 15]&lt;/td&gt;
  &lt;td width=100 style="background: #0F820F"&gt;&lt;/td&gt;
 &lt;/tr&gt;
 &lt;tr&gt;
  &lt;td&gt;ALA&lt;/td&gt;
  &lt;td&gt;[200,200,200]&lt;/td&gt;
  &lt;td width=100 style="background: #C8C8C8"&gt;&lt;/td&gt;
 &lt;/tr&gt;
 &lt;tr&gt;
  &lt;td&gt;TRP&lt;/td&gt;
  &lt;td&gt;[180, 90,180]&lt;/td&gt;
  &lt;td width=100 style="background: #B45AB4"&gt;&lt;/td&gt;
 &lt;/tr&gt;
 &lt;tr&gt;
  &lt;td&gt;HIS&lt;/td&gt;
  &lt;td&gt;[130,130,210]&lt;/td&gt;
  &lt;td width=100 style="background: #8282D2"&gt;&lt;/td&gt;
 &lt;/tr&gt;
 &lt;tr&gt;
  &lt;td&gt;PRO&lt;/td&gt;
  &lt;td&gt;[220,150,130]&lt;/td&gt;
  &lt;td width=100 style="background: #DC9682"&gt;&lt;/td&gt;
 &lt;/tr&gt;
 &lt;tr&gt;
  &lt;td&gt;Others&lt;/td&gt;
  &lt;td&gt;[190,160,110]&lt;/td&gt;
  &lt;td width=100 style="background: #BEA06E"&gt;&lt;/td&gt;
 &lt;/tr&gt;
&lt;/table&gt;

=== chain ===
The color scheme 'chain' assigns each macromolecular chain a unique colour.

=== charge ===
The color scheme 'charge' colors atoms according to their temperature factor. High values are coloured in blue and lower values coloured in red. 

=== cpk ===
The color scheme 'cpk' colors atoms according to the element type as follows. 

&lt;table border="1"&gt;
 &lt;tr&gt;
  &lt;td&gt;element&lt;/td&gt;
  &lt;td&gt;RGB values&lt;/td&gt;
  &lt;td&gt;color&lt;/td&gt;
 &lt;/tr&gt;
 &lt;tr&gt;
  &lt;td&gt;C&lt;/td&gt;
  &lt;td&gt;[200, 200, 200]&lt;/td&gt;
  &lt;td width=100 style="background: #C8C8C8"&gt;&lt;/td&gt;
 &lt;/tr&gt;
 &lt;tr&gt;
  &lt;td&gt;N&lt;/td&gt;
  &lt;td&gt;[143, 143, 255]&lt;/td&gt;
  &lt;td width=100 style="background: #8F8FFF"&gt;&lt;/td&gt;
 &lt;/tr&gt;
 &lt;tr&gt;
  &lt;td&gt;O&lt;/td&gt;
  &lt;td&gt;[240, 0, 0]&lt;/td&gt;
  &lt;td width=100 style="background: #F00000"&gt;&lt;/td&gt;
 &lt;/tr&gt;
 &lt;tr&gt;
  &lt;td&gt;S&lt;/td&gt;
  &lt;td&gt;[255, 200, 50]&lt;/td&gt;
  &lt;td width=100 style="background: #FFC832"&gt;&lt;/td&gt;
 &lt;/tr&gt;
 &lt;tr&gt;
  &lt;td&gt;H&lt;/td&gt;
  &lt;td&gt;[255, 255, 255]&lt;/td&gt;
  &lt;td width=100 style="background: #FFFFFF"&gt;&lt;/td&gt;
 &lt;/tr&gt;
 &lt;tr&gt;
  &lt;td&gt;He&lt;/td&gt;
  &lt;td&gt;[255, 192, 203]&lt;/td&gt;
  &lt;td width=100 style="background: #FFC0CB"&gt;&lt;/td&gt;
 &lt;/tr&gt;
 &lt;tr&gt;
  &lt;td&gt;F, Si, Au&lt;/td&gt;
  &lt;td&gt;[218, 165, 32]&lt;/td&gt;
  &lt;td width=100 style="background: #DAA520"&gt;&lt;/td&gt;
 &lt;/tr&gt;
 &lt;tr&gt;
  &lt;td&gt;Na&lt;/td&gt;
  &lt;td&gt;[0, 0, 255]&lt;/td&gt;
  &lt;td width=100 style="background: #0000FF"&gt;&lt;/td&gt;
 &lt;/tr&gt;
 &lt;tr&gt;
  &lt;td&gt;P, Fe, Ba&lt;/td&gt;
  &lt;td&gt;[255, 165, 0]&lt;/td&gt;
  &lt;td width=100 style="background: #FFA500"&gt;&lt;/td&gt;
 &lt;/tr&gt;
 &lt;tr&gt;
  &lt;td&gt;Al, Ca, Ti, Cr, Mn, Ag&lt;/td&gt;
  &lt;td&gt;[128, 128, 144]&lt;/td&gt;
  &lt;td width=100 style="background: #808090"&gt;&lt;/td&gt;
 &lt;/tr&gt;
 &lt;tr&gt;
  &lt;td&gt;Ni, Cu, Zn, Br&lt;/td&gt;
  &lt;td&gt;[165, 42, 42]&lt;/td&gt;
  &lt;td width=100 style="background: #A52A2A"&gt;&lt;/td&gt;
 &lt;/tr&gt;
 &lt;tr&gt;
  &lt;td&gt;I&lt;/td&gt;
  &lt;td&gt;[160, 32, 240]&lt;/td&gt;
  &lt;td width=100 style="background: #A020F0"&gt;&lt;/td&gt;
 &lt;/tr&gt;
 &lt;tr&gt;
  &lt;td&gt;B, Cl&lt;/td&gt;
  &lt;td&gt;[0, 255, 0]&lt;/td&gt;
  &lt;td width=100 style="background: #00FF00"&gt;&lt;/td&gt;
 &lt;/tr&gt;
 &lt;tr&gt;
  &lt;td&gt;Li&lt;/td&gt;
  &lt;td&gt;[178, 34, 34]&lt;/td&gt;
  &lt;td width=100 style="background: #B22222"&gt;&lt;/td&gt;
 &lt;/tr&gt;
 &lt;tr&gt;
  &lt;td&gt;Mg&lt;/td&gt;
  &lt;td&gt;[34, 139, 34]&lt;/td&gt;
  &lt;td width=100 style="background: #228B22"&gt;&lt;/td&gt;
 &lt;/tr&gt;
 &lt;tr&gt;
  &lt;td&gt;Others&lt;/td&gt;
  &lt;td&gt;[255, 20, 147]&lt;/td&gt;
  &lt;td width=100 style="background: #FF1493"&gt;&lt;/td&gt;
 &lt;/tr&gt;
&lt;/table&gt;

=== group ===
The color scheme 'group' colors residues by their position in a macromolecular chain. Each chain is drawn as a smooth spectrum from blue to red. The N terminus of proteins and 5' terminus of nucleic acids are colored red and the C terminus of proteins and 3' terminus of nucleic acids are drawn in blue. 

=== shapely ===
The color scheme 'shapely' colors residues as follows.

&lt;table border="1"&gt;
 &lt;tr&gt;
  &lt;td&gt;residue&lt;/td&gt;
  &lt;td&gt;RGB values&lt;/td&gt;
  &lt;td&gt;color&lt;/td&gt;
 &lt;/tr&gt;
 &lt;tr&gt;
  &lt;td&gt;ALA&lt;/td&gt;
  &lt;td&gt;[140, 255, 140]&lt;/td&gt;
  &lt;td width=100 style="background: #8CFF8C"&gt;&lt;/td&gt;
 &lt;/tr&gt;
 &lt;tr&gt;
  &lt;td&gt;GLY&lt;/td&gt;
  &lt;td&gt;[255, 255, 255]&lt;/td&gt;
  &lt;td width=100 style="background: #FFFFFF"&gt;&lt;/td&gt;
 &lt;/tr&gt;
 &lt;tr&gt;
  &lt;td&gt;LEU&lt;/td&gt;
  &lt;td&gt;[69, 94, 69]&lt;/td&gt;
  &lt;td width=100 style="background: #455E45"&gt;&lt;/td&gt;
 &lt;/tr&gt;
 &lt;tr&gt;
  &lt;td&gt;SER&lt;/td&gt;
  &lt;td&gt;[255, 112, 66]&lt;/td&gt;
  &lt;td width=100 style="background: #FF7042"&gt;&lt;/td&gt;
 &lt;/tr&gt;
 &lt;tr&gt;
  &lt;td&gt;VAL&lt;/td&gt;
  &lt;td&gt;[255, 140, 255]&lt;/td&gt;
  &lt;td width=100 style="background: #FF8CFF"&gt;&lt;/td&gt;
 &lt;/tr&gt;
 &lt;tr&gt;
  &lt;td&gt;THR&lt;/td&gt;
  &lt;td&gt;[184, 76, 0]&lt;/td&gt;
  &lt;td width=100 style="background: #B84C00"&gt;&lt;/td&gt;
 &lt;/tr&gt;
 &lt;tr&gt;
  &lt;td&gt;LYS&lt;/td&gt;
  &lt;td&gt;[71, 71, 184]&lt;/td&gt;
  &lt;td width=100 style="background: #4747B8"&gt;&lt;/td&gt;
 &lt;/tr&gt;
 &lt;tr&gt;
  &lt;td&gt;ASP&lt;/td&gt;
  &lt;td&gt;[160, 0, 66]&lt;/td&gt;
  &lt;td width=100 style="background: #A00042"&gt;&lt;/td&gt;
 &lt;/tr&gt;
 &lt;tr&gt;
  &lt;td&gt;ILE&lt;/td&gt;
  &lt;td&gt;[0, 76, 0]&lt;/td&gt;
  &lt;td width=100 style="background: #004C00"&gt;&lt;/td&gt;
 &lt;/tr&gt;
 &lt;tr&gt;
  &lt;td&gt;ASN&lt;/td&gt;
  &lt;td&gt;[255, 124, 112]&lt;/td&gt;
  &lt;td width=100 style="background: #FF7C70"&gt;&lt;/td&gt;
 &lt;/tr&gt;
 &lt;tr&gt;
  &lt;td&gt;GLU&lt;/td&gt;
  &lt;td&gt;[102, 0, 0]&lt;/td&gt;
  &lt;td width=100 style="background: #660000"&gt;&lt;/td&gt;
 &lt;/tr&gt;
 &lt;tr&gt;
  &lt;td&gt;PRO&lt;/td&gt;
  &lt;td&gt;[82, 82, 82]&lt;/td&gt;
  &lt;td width=100 style="background: #525252"&gt;&lt;/td&gt;
 &lt;/tr&gt;
 &lt;tr&gt;
  &lt;td&gt;ARG&lt;/td&gt;
  &lt;td&gt;[0, 0, 124]&lt;/td&gt;
  &lt;td width=100 style="background: #00007C"&gt;&lt;/td&gt;
 &lt;/tr&gt;
 &lt;tr&gt;
  &lt;td&gt;PHE&lt;/td&gt;
  &lt;td&gt;[83, 76, 66]&lt;/td&gt;
  &lt;td width=100 style="background: #534C42"&gt;&lt;/td&gt;
 &lt;/tr&gt;
 &lt;tr&gt;
  &lt;td&gt;GLN&lt;/td&gt;
  &lt;td&gt;[255, 76, 76]&lt;/td&gt;
  &lt;td width=100 style="background: #FF4C4C"&gt;&lt;/td&gt;
 &lt;/tr&gt;
 &lt;tr&gt;
  &lt;td&gt;TYR&lt;/td&gt;
  &lt;td&gt;[140, 112, 76]&lt;/td&gt;
  &lt;td width=100 style="background: #8C704C"&gt;&lt;/td&gt;
 &lt;/tr&gt;
 &lt;tr&gt;
  &lt;td&gt;HIS&lt;/td&gt;
  &lt;td&gt;[112, 112, 255]&lt;/td&gt;
  &lt;td width=100 style="background: #7070FF"&gt;&lt;/td&gt;
 &lt;/tr&gt;
 &lt;tr&gt;
  &lt;td&gt;CYS&lt;/td&gt;
  &lt;td&gt;[255, 255, 112]&lt;/td&gt;
  &lt;td width=100 style="background: #FFFF70"&gt;&lt;/td&gt;
 &lt;/tr&gt;
 &lt;tr&gt;
  &lt;td&gt;MET&lt;/td&gt;
  &lt;td&gt;[184, 160, 66]&lt;/td&gt;
  &lt;td width=100 style="background: #B8A042"&gt;&lt;/td&gt;
 &lt;/tr&gt;
 &lt;tr&gt;
  &lt;td&gt;TRP&lt;/td&gt;
  &lt;td&gt;[79, 70, 0]&lt;/td&gt;
  &lt;td width=100 style="background: #4F4600"&gt;&lt;/td&gt;
 &lt;/tr&gt;
 &lt;tr&gt;
  &lt;td&gt;A&lt;/td&gt;
  &lt;td&gt;[160, 160, 255]&lt;/td&gt;
  &lt;td width=100 style="background: #A0A0FF"&gt;&lt;/td&gt;
 &lt;/tr&gt;
 &lt;tr&gt;
  &lt;td&gt;C&lt;/td&gt;
  &lt;td&gt;[255, 140, 75]&lt;/td&gt;
  &lt;td width=100 style="background: #FF8C4B"&gt;&lt;/td&gt;
 &lt;/tr&gt;
 &lt;tr&gt;
  &lt;td&gt;G&lt;/td&gt;
  &lt;td&gt;[255, 112, 112]&lt;/td&gt;
  &lt;td width=100 style="background: #FF7070"&gt;&lt;/td&gt;
 &lt;/tr&gt;
 &lt;tr&gt;
  &lt;td&gt;T&lt;/td&gt;
  &lt;td&gt;[160, 255, 160]&lt;/td&gt;
  &lt;td width=100 style="background: #A0FFA0"&gt;&lt;/td&gt;
 &lt;/tr&gt;
 &lt;tr&gt;
  &lt;td&gt;Others&lt;/td&gt;
  &lt;td&gt;[255, 0, 255]&lt;/td&gt;
  &lt;td width=100 style="background: #FF00FF"&gt;&lt;/td&gt;
 &lt;/tr&gt;
&lt;/table&gt;

=== structure ===
The color scheme 'structure' colors residues according to the secondary structure as follows.

&lt;table border="1"&gt;
 &lt;tr&gt;
  &lt;td&gt;secondary structure&lt;/td&gt;
  &lt;td&gt;RGB values&lt;/td&gt;
  &lt;td&gt;color&lt;/td&gt;
 &lt;/tr&gt;
 &lt;tr&gt;
  &lt;td&gt;alpha helix&lt;/td&gt;
  &lt;td&gt;[255, 0, 128]&lt;/td&gt;
  &lt;td width=100 style="background: #FF0080"&gt;&lt;/td&gt;
 &lt;/tr&gt;
 &lt;tr&gt;
  &lt;td&gt;beta sheet&lt;/td&gt;
  &lt;td&gt;[255, 200, 0]&lt;/td&gt;
  &lt;td width=100 style="background: #FFC800"&gt;&lt;/td&gt;
 &lt;/tr&gt;
 &lt;tr&gt;
  &lt;td&gt;turn&lt;/td&gt;
  &lt;td&gt;[96, 128, 255]&lt;/td&gt;
  &lt;td width=100 style="background: #6080FF"&gt;&lt;/td&gt;
 &lt;/tr&gt;
 &lt;tr&gt;
  &lt;td&gt;none&lt;/td&gt;
  &lt;td&gt;[255, 255, 255]&lt;/td&gt;
  &lt;td width=100 style="background: #FFFFFF"&gt;&lt;/td&gt;
 &lt;/tr&gt;
&lt;/table&gt;

=== temperature ===
The color scheme 'temperature' colors atoms according to their temperature factor. High values are coloured in red and lower values coloured in blue. 

=== type ===
This color scheme 'type' colors each hydrogen bond according to the distance along a protein chain between hydrogen bond donor and acceptor as follows. 

&lt;table border="1"&gt;
 &lt;tr&gt;
  &lt;td&gt;offset&lt;/td&gt;
  &lt;td&gt;RGB values&lt;/td&gt;
  &lt;td&gt;color&lt;/td&gt;
 &lt;/tr&gt;
 &lt;tr&gt;
  &lt;td&gt;+2&lt;/td&gt;
  &lt;td&gt;[255, 255, 255]&lt;/td&gt;
  &lt;td width=100 style="background: #FFFFFF"&gt;&lt;/td&gt;
 &lt;/tr&gt;
 &lt;tr&gt;
  &lt;td&gt;+3&lt;/td&gt;
  &lt;td&gt;[255, 0, 255]&lt;/td&gt;
  &lt;td width=100 style="background: #FF00FF"&gt;&lt;/td&gt;
 &lt;/tr&gt;
 &lt;tr&gt;
  &lt;td&gt;+4&lt;/td&gt;
  &lt;td&gt;[255, 0, 0]&lt;/td&gt;
  &lt;td width=100 style="background: #FF0000"&gt;&lt;/td&gt;
 &lt;/tr&gt;
 &lt;tr&gt;
  &lt;td&gt;+5&lt;/td&gt;
  &lt;td&gt;[255, 165, 0]&lt;/td&gt;
  &lt;td width=100 style="background: #FFA500"&gt;&lt;/td&gt;
 &lt;/tr&gt;
 &lt;tr&gt;
  &lt;td&gt;-3&lt;/td&gt;
  &lt;td&gt;[0, 255, 255]&lt;/td&gt;
  &lt;td width=100 style="background: #00FFFF"&gt;&lt;/td&gt;
 &lt;/tr&gt;
 &lt;tr&gt;
  &lt;td&gt;-4&lt;/td&gt;
  &lt;td&gt;[0, 255, 0]&lt;/td&gt;
  &lt;td width=100 style="background: #00FF00"&gt;&lt;/td&gt;
 &lt;/tr&gt;
 &lt;tr&gt;
  &lt;td&gt;Others&lt;/td&gt;
  &lt;td&gt;[255, 255, 0]&lt;/td&gt;
  &lt;td width=100 style="background: #FFFF00"&gt;&lt;/td&gt;
 &lt;/tr&gt;
&lt;/table&gt;</text>
    <sha1>9d3a8a138c97d3020ccc7e261dceb8df45f75537</sha1>
  </revision>
</page>
<page arvcontinue="20090309075222|151">
  <title>Use as Applet</title>
  <ns>0</ns>
  <id>24</id>
  <revision>
    <id>178</id>
    <timestamp>2009-03-09T08:46:40Z</timestamp>
    <contributor>
      <username>JVuser</username>
      <id>2</id>
    </contributor>
    <comment>Created page with '== Introduction == In order to use jV as an applet, [http://java.sun.com/products/plugin/ Java Plug-in] must be installed on client computers. The applet is called from usual APP...'</comment>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="3247" xml:space="preserve">== Introduction ==
In order to use jV as an applet, [http://java.sun.com/products/plugin/ Java Plug-in] must be installed on client computers. The applet is called from usual APPLET tags, or OBJECT and EMBED tags in HTML (see [http://java.sun.com/products/plugin/ Java Plug-in] homepage), where class name that should be called is "org.pdbj.viewer.gui.ViewerApplet" class. The program has following features.
* whether to use the command line interface or not can be specified
* whether to use the file control panel or not can be specified
* whether to use the popup menu or not can be specified
* witihin applets in the same web page, mouse events can be shared
* applet can receive a command string from JaveScript
* applet can send information about mouse-picked atoms to JavaScript.

== Parameters ==
To initialize the applet, the following parameters can be specified in HTML.
{| class="wikitable"
 ! parameter !! value 
 |-
 | pdbmlURL || URL of the PDBML files to be loaded (delimited by comma for more than one files).
 |-
 | pdbURL || URL of the PDB files to be loaded (delimited by comma for more than one files).
 |-
 | polygonURL || URL of the polygon files to be loaded (delimited by comma for more than one files).
 |-
 | animURL || URL of the animation files to be loaded (delimited by comma for more than one files).
 |-
 | command_area || whether to use the command line interface or not (true or false).
 |-
 | file_control || whether to use the file control panel or not (true or false).
 |-
 | popup_menu || whether to use the popup menu or not (true or false).
 |-
 | mouse_send_to || name property of applets with which mouse events are shared (delimited by comma for more than one applets).
 |-
 | commands || initial commands that are executed when the applet starts (delimited by semicolon for more than one commands).
 |-
 | report_picking || whether to send information about mouse-picked atoms to JavaScript or not (true or false).
|}

== JavaScript-to-Applet Communication ==
The ViewerApplet class has some public methods, which can be called from JavaScript.

 void executeCommand(String commands)

Through this method, the applet can receive some arbitrary commands (delimited by semicolon).

 void loadPDB(String fileLocation)
 void loadPDBML(String fileLocation)
 void loadPolygon(String fileLocation)
 void loadAnim(String fileLocation)

Using these methods, PDB file, PDBML file, polygon file, and animation file specified by URL can be loaded respectively.

 void loadPDB(String fileLocation, int fitTo)
 void loadPDBML(String fileLocation, int fitTo)
 void loadPolygon(String fileLocation, int fitTo)
 void loadAnim(String fileLocation, int fitTo)

When these methods are used, the transform matrix of the loaded file is set identical to that of the specified file. 

== Applet-to-JavaScript Communication ==
In order to send the result of mouse-picking to JavaScript, the following function must be defined in JavaScript.

 function receiveMousePick(file, model, chain, res, atom, altloc, resName, atomName, x, y, z)

In addition, a new attribute 'MAYSCRIPT' is required in APPLET or OBJECT/EMBED tags (see [http://java.sun.com/j2se/1.4.2/docs/guide/plugin/developer_guide/java_js.html Java Plug-in guide]).</text>
    <sha1>95f1adcc141e34de761e948e3f42a19c51cf1ea6</sha1>
  </revision>
  <revision>
    <id>179</id>
    <parentid>178</parentid>
    <timestamp>2009-03-09T08:47:21Z</timestamp>
    <contributor>
      <username>JVuser</username>
      <id>2</id>
    </contributor>
    <comment>/* Parameters */</comment>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="3258" xml:space="preserve">== Introduction ==
In order to use jV as an applet, [http://java.sun.com/products/plugin/ Java Plug-in] must be installed on client computers. The applet is called from usual APPLET tags, or OBJECT and EMBED tags in HTML (see [http://java.sun.com/products/plugin/ Java Plug-in] homepage), where class name that should be called is "org.pdbj.viewer.gui.ViewerApplet" class. The program has following features.
* whether to use the command line interface or not can be specified
* whether to use the file control panel or not can be specified
* whether to use the popup menu or not can be specified
* witihin applets in the same web page, mouse events can be shared
* applet can receive a command string from JaveScript
* applet can send information about mouse-picked atoms to JavaScript.

== Parameters ==
To initialize the applet, the following parameters can be specified in HTML.
{| class="wikitable" border="1"
 ! parameter !! value 
 |-
 | pdbmlURL || URL of the PDBML files to be loaded (delimited by comma for more than one files).
 |-
 | pdbURL || URL of the PDB files to be loaded (delimited by comma for more than one files).
 |-
 | polygonURL || URL of the polygon files to be loaded (delimited by comma for more than one files).
 |-
 | animURL || URL of the animation files to be loaded (delimited by comma for more than one files).
 |-
 | command_area || whether to use the command line interface or not (true or false).
 |-
 | file_control || whether to use the file control panel or not (true or false).
 |-
 | popup_menu || whether to use the popup menu or not (true or false).
 |-
 | mouse_send_to || name property of applets with which mouse events are shared (delimited by comma for more than one applets).
 |-
 | commands || initial commands that are executed when the applet starts (delimited by semicolon for more than one commands).
 |-
 | report_picking || whether to send information about mouse-picked atoms to JavaScript or not (true or false).
|}

== JavaScript-to-Applet Communication ==
The ViewerApplet class has some public methods, which can be called from JavaScript.

 void executeCommand(String commands)

Through this method, the applet can receive some arbitrary commands (delimited by semicolon).

 void loadPDB(String fileLocation)
 void loadPDBML(String fileLocation)
 void loadPolygon(String fileLocation)
 void loadAnim(String fileLocation)

Using these methods, PDB file, PDBML file, polygon file, and animation file specified by URL can be loaded respectively.

 void loadPDB(String fileLocation, int fitTo)
 void loadPDBML(String fileLocation, int fitTo)
 void loadPolygon(String fileLocation, int fitTo)
 void loadAnim(String fileLocation, int fitTo)

When these methods are used, the transform matrix of the loaded file is set identical to that of the specified file. 

== Applet-to-JavaScript Communication ==
In order to send the result of mouse-picking to JavaScript, the following function must be defined in JavaScript.

 function receiveMousePick(file, model, chain, res, atom, altloc, resName, atomName, x, y, z)

In addition, a new attribute 'MAYSCRIPT' is required in APPLET or OBJECT/EMBED tags (see [http://java.sun.com/j2se/1.4.2/docs/guide/plugin/developer_guide/java_js.html Java Plug-in guide]).</text>
    <sha1>bb81db8fbf78b4373558d50f16358542f81fe175</sha1>
  </revision>
  <revision>
    <id>180</id>
    <parentid>179</parentid>
    <timestamp>2009-03-09T08:47:42Z</timestamp>
    <contributor>
      <username>JVuser</username>
      <id>2</id>
    </contributor>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="3296" xml:space="preserve">{| style="float:right"
 |__TOC__
 |}

== Introduction ==
In order to use jV as an applet, [http://java.sun.com/products/plugin/ Java Plug-in] must be installed on client computers. The applet is called from usual APPLET tags, or OBJECT and EMBED tags in HTML (see [http://java.sun.com/products/plugin/ Java Plug-in] homepage), where class name that should be called is "org.pdbj.viewer.gui.ViewerApplet" class. The program has following features.
* whether to use the command line interface or not can be specified
* whether to use the file control panel or not can be specified
* whether to use the popup menu or not can be specified
* witihin applets in the same web page, mouse events can be shared
* applet can receive a command string from JaveScript
* applet can send information about mouse-picked atoms to JavaScript.

== Parameters ==
To initialize the applet, the following parameters can be specified in HTML.
{| class="wikitable" border="1"
 ! parameter !! value 
 |-
 | pdbmlURL || URL of the PDBML files to be loaded (delimited by comma for more than one files).
 |-
 | pdbURL || URL of the PDB files to be loaded (delimited by comma for more than one files).
 |-
 | polygonURL || URL of the polygon files to be loaded (delimited by comma for more than one files).
 |-
 | animURL || URL of the animation files to be loaded (delimited by comma for more than one files).
 |-
 | command_area || whether to use the command line interface or not (true or false).
 |-
 | file_control || whether to use the file control panel or not (true or false).
 |-
 | popup_menu || whether to use the popup menu or not (true or false).
 |-
 | mouse_send_to || name property of applets with which mouse events are shared (delimited by comma for more than one applets).
 |-
 | commands || initial commands that are executed when the applet starts (delimited by semicolon for more than one commands).
 |-
 | report_picking || whether to send information about mouse-picked atoms to JavaScript or not (true or false).
|}

== JavaScript-to-Applet Communication ==
The ViewerApplet class has some public methods, which can be called from JavaScript.

 void executeCommand(String commands)

Through this method, the applet can receive some arbitrary commands (delimited by semicolon).

 void loadPDB(String fileLocation)
 void loadPDBML(String fileLocation)
 void loadPolygon(String fileLocation)
 void loadAnim(String fileLocation)

Using these methods, PDB file, PDBML file, polygon file, and animation file specified by URL can be loaded respectively.

 void loadPDB(String fileLocation, int fitTo)
 void loadPDBML(String fileLocation, int fitTo)
 void loadPolygon(String fileLocation, int fitTo)
 void loadAnim(String fileLocation, int fitTo)

When these methods are used, the transform matrix of the loaded file is set identical to that of the specified file. 

== Applet-to-JavaScript Communication ==
In order to send the result of mouse-picking to JavaScript, the following function must be defined in JavaScript.

 function receiveMousePick(file, model, chain, res, atom, altloc, resName, atomName, x, y, z)

In addition, a new attribute 'MAYSCRIPT' is required in APPLET or OBJECT/EMBED tags (see [http://java.sun.com/j2se/1.4.2/docs/guide/plugin/developer_guide/java_js.html Java Plug-in guide]).</text>
    <sha1>e611907d84acbd9a45a7737728c1d2bb508bee4d</sha1>
  </revision>
</page>
<page arvcontinue="20090309075222|151">
  <title>Tutorials</title>
  <ns>0</ns>
  <id>25</id>
  <revision>
    <id>182</id>
    <timestamp>2009-03-09T09:10:51Z</timestamp>
    <contributor>
      <username>JVuser</username>
      <id>2</id>
    </contributor>
    <comment>Created page with '== Starting up == It is assumed that Java Runtime Environment and JOGL have been appropriately installed. Once you extract the binary distribution file of jV3, the directory of t...'</comment>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="12054" xml:space="preserve">== Starting up ==
It is assumed that Java Runtime Environment and JOGL have been appropriately installed. Once you extract the binary distribution file of jV3, the directory of the name, jV_(version), is generated (Ex. jV_3_6_2). The version is assumed to be 3_6_x hereafter. The application starts up by double-clicking the file ‘jv_3_6_x.jar’ in the jV_3_6_x directory or executing the following command from the command line interface.
 java –jar jv_3_6_x.jar
Figure 1 shows the start-up screen. The window has a 3-panel structure, and the upper-left panel with the black background is a 3D image display area. The status of files that have been loaded to the application is shown in the upper-right panel and the lower panel is a command-input and a message-output area.
[[File:Fig1.jpg|Figure 1 Start-up screen]]

== Displaying molecules ==
If you are working in the environment that is getting on the Internet and know the PDB ID of the molecule that you want to display, the simplest way is as follows. A dialog shown in Figure 2 is opened by selecting the [File] – [Open – Remote] – [PDB ID] menu item. Enter a PDB ID '12as', for example, to the text field and click the 'OK' button, then the PDBML file is read through the Internet and the molecule is displayed. The URL where the PDBML file is retrieved from is specified in the 'properties.txt' file in the jV_3_3_x directory. A molecule is displayed in a wire frame model with colored by atom type in the initial state.
[[File:Fig2.jpg|Dialog to open the molecule specified by PDB ID]]
Let us next attempt to load an arbitrary file on the Internet. Here we use 'http://ef-site.hgc.jp/eF-site/jV/1yec.pdb' as an example. The file is a conventional PDB file whose PDB ID is 1yec. In this case we choose the [File] – [Open – Remote] – [PDB] menu item. Then the open-remote dialog is appeared. Enter the above URL to the text field at the top of the dialog and click the 'OK' button and the molecule is read in and displayed. In jV3, each molecule is displayed according to the space coordination described in its file. Therefore, when loading and displaying more than one molecule together, they can be viewed with an appropriate separation in some cases; however, they may be displayed far separately or may be overlapped depending on the combination. In any case, when adding a new file, the position of the viewpoint is automatically controlled for the whole to be displayed.
The coordinate system is the right hand system with the x-y plane being on the screen (the x-axis is a horizontal line with positive values to the right and the y-axis is a vertical line with positive values up). Although, the above examples are about operations for remote files, a PDB file on your local hard disk can also be opened from the [File] – [Open – Local] – [PDB] menu item.

== Operating molecules ==
Interactive mouse operations are possible for 3D images. By left-dragging the mouse on the 3D-display panel, molecules are rotated around the x-axis or y-axis. By left-dragging the mouse while holding the Shift key or Alt key on the keyboard, molecules are translated along the z-axis. All mouse operations are as follows (as for the Macintosh environment, the Command key + left-drag substitutes for the right-drag).

{|
 ! Mouse operations !! Actions
 |-
 | Left-drag || The image is rotated around the x (for a vertical motion) and y (for a horizontal motion) axes.
 |-
 | Right-drag || The image is translated on the x-y plane.
 |-
 | [Alt or Shift] + left-drag || The image is translated along the z-axis.
 |-
 | [Alt or Shift] + right-drag || The image is rotated around the z-axis.
 |-
 | [Ctrl] + left-drag || The z-clipping plane is shifted when [Option]-[Slab] is checked.
 |-
 | Left-click || An atom of the molecule displayed on the screen is picked.
 |}

In the upper-right panel in the application window (see Figure 3), the file names that have been loaded to the application are listed, where sequential integers are automatically assigned to the individual file. Each integer is a file ID that can be used to specify the file in the command line interface. In addition, two checkboxes are attached to each file. If you change the status of a ‘display’ checkbox, the corresponding molecule is switched to be displayed or not to be displayed. If you change the status of a ‘select’ checkbox, the corresponding molecule is switched to be a target of the mouse operations or not. For example, set the both ‘display’ checkboxes on, and the both ‘select’ checkboxes off. In this case, either molecule does not move against mouse operations. 
Subsequently set the ‘select’ checkbox of file 1 on. In this case, mouse operations work for the molecule 1. Thus, each file is assigned either selected or not selected, and transform operations, such as rotation or translation, act only on selected files. On the other hand, every atom in a molecule is also assigned either selected or not selected, independently of whether the molecule itself is selected or not. Operations that modify display models or colors work for selected atoms. To see this, choose the [Display] – [Spacefill] menu item. Then the both molecules are displayed with the space fill model because all atoms are initially selected. In the same way, if you choose the [Colors] – [Monochrome] menu item, the both molecules are colored white. These operations are independent of the status of ‘select’ checkboxes mentioned above. 
Let us next try a more detailed operation. Type ‘select *@2’ in the command line area and press Enter key. This command means to select all atoms contained in the file 2 (the usage of the select command is summarized in the reference manual included in the binary distribution of jV3). Subsequently, choose the [Display] – [Cartoon] menu item. As a result, only the molecule 2 is displayed in the cartoon model. Furthermore select the [Colors] – [Structure] menu item, and each residue of the molecule 2 is colored according to its secondary structure type (see Figure 3). 
In order to reproduce the same view as that in Figure 3, first execute ‘reset’ command. It restores the position of the viewpoint and the transform of every file to the initial state. Note that the command line interface tries to complement a command word when the Tab key is pressed. If you enter ‘res’ to the command line and subsequently press the Tab key, the command ‘reset’ is automatically entered. Next set the both ‘select’ checkboxes on, and execute ‘translate z 100’ command. This command means to translate the molecules along the z-axis by 100 angstroms.
[[File:Fig3.jpg|An example of molecular images.]]

== Displaying polygons ==
In addition to molecules, arbitrary shapes described by polygons can be read in and displayed together, where the polygon file is an XML file, whose document type is described in the section 6. Here, we use ’http://ef-site.hgc.jp/eF-site/jV/1yec.surface.gz’ as an example. This polygon file represents a molecular surface of the molecule 2 (1yec) and the surface is colored according to the electrostatic potential and the hydrophobicity. It is assumed that the current image is the same as that in Figure 3. Then, open the open-remote dialog by choosing the [File] – [Open – Remote] – [Polygon] menu item, enter the above URL to the text field at the top of the dialog, and click the 'OK' button. As a result, the polygon is loaded, displayed and assigned file ID 3. 
Note that the polygon is displayed at the different position from the molecule 2 since the molecule 2 is translated. However, because the polygon and the molecule 2 are described by the same coordinates in their files, their images can be exactly superposed by executing ‘fit 3 2’ from the command line, where the ‘fit’ command performs the copy of the transform matrix. Finally, the image in Figure 4 appears.
[[File:Fig4.jpg|An example of polygon images.]]
You can control the transparency rate of polygons. Try ’set transparency 0.5’ from the command line, where 0.5 stands for 50% transparency. To restore the image, execute ‘reset transparency’ or ‘set transparency 0’. In the same sense as each atom of a molecule, each vertex of a polygon is assigned either selected or not selected. All vertices are selected in the initial state. Execute a command ’displayvertex off’ and all vertices become invisible. Next execute ’selectvertex within(10.0, 1&amp;*H@2)’, where this means to select vertices that exist within 10 angstroms from each atom that belongs to the first residue of the ‘H’ chain of the molecule 2. Subsequently execute ’displayvertex on’. As a result, only the selected vertices are appeared. The usage of the selectvertex command is summarized in the reference manual. 

== Working with xPSSS ==
Functional site information on a molecule stored at xPSSS (xml-based Protein Structure Search Service) is available in jV3. Before trying this, let us close the molecule 2 and the polygon 3 to make the situation simple. Select the [File] – [Close] – [2. 1yec.pdb] and [File] – [Close] – [3. 1yec.surface.gz] menu items sequentially. Then execute a ‘reset’ command and the transform of the molecule 1 and the position of the viewpoint are initialized. 
Next, confirm that the ‘select’ checkbox of the file 1 is checked, and try a ‘show xps3’ command. The functional site information of the molecule ‘12as’ is read from the xPSSS and ‘type’ and ‘subtype’ keywords for each functional site are listed. These keywords can be used to select a set of atoms. For example, if a keyword ‘CATRES’ exists (probably it does), the command ‘select xps3:CATRES’ selects the corresponding atoms. 
In addition, gene ontology information can be obtained from the xPSSS. The gene ontology information for the molecule 12as is displayed by the command ’show godata’. Similar operations can be applied to other external databases on the Internet provided that the external database supports the interface that jV3 requires. See the section 7 for details.

== Animation ==
The animation of molecules can be performed in jV3. The animation file takes the PDB format, where the MODEL line divides each frame. Let us open an animation file ’http://ef-site.hgc.jp/eF-site/jV/anim.pdb.gz’ as an example from the open-remote dialog shown by selecting the [File] – [Open – Remote] – [Animation] menu item. When an animation file is loaded to the application, the first frame is automatically displayed in the wire frame model. You can start the animation by using the animation-control dialog that is shown by choosing the [Options] – [Animation] menu item. The dialog provides operations such as start and stop of the animation, selection of the animation mode, and adjustment of the speed. Some sample figures of the dialog are shown in the [[GUI]]

== Saving your work ==
While in your work, you can create a script file that contains a set of commands that reproduces the current work by using the [File] – [Save] – [Script] menu item. The script file can be loaded by the [File] – [Open – Local] – [Script] menu item. On the other hand, the [File] – [Save] – [PDB] menu item enables to save a molecule to a PDB format file with the coordinates of the atoms being transformed according to the current image. Here, only one molecule must be selected and only selected atoms in the molecule are saved. The other two menu items in the [File] – [Save] menu, [PNG] and [JPEG], save the current screen image to an image file in the PNG and JPEG format, respectively. The created image file has the same size as that of the 3D-display panel in the application.

== Terminating the application ==
The application is terminated when the [File] – [Exit] menu item is chosen or the application window is closed by the way your operation system provides. You can also quit the application by executing ‘exit’ or ‘quit’ command.</text>
    <sha1>5d5312361a8d1a81a43f8069a868602b0de3f6c6</sha1>
  </revision>
  <revision>
    <id>183</id>
    <parentid>182</parentid>
    <timestamp>2009-03-09T09:11:12Z</timestamp>
    <contributor>
      <username>JVuser</username>
      <id>2</id>
    </contributor>
    <comment>/* Operating molecules */</comment>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="12065" xml:space="preserve">== Starting up ==
It is assumed that Java Runtime Environment and JOGL have been appropriately installed. Once you extract the binary distribution file of jV3, the directory of the name, jV_(version), is generated (Ex. jV_3_6_2). The version is assumed to be 3_6_x hereafter. The application starts up by double-clicking the file ‘jv_3_6_x.jar’ in the jV_3_6_x directory or executing the following command from the command line interface.
 java –jar jv_3_6_x.jar
Figure 1 shows the start-up screen. The window has a 3-panel structure, and the upper-left panel with the black background is a 3D image display area. The status of files that have been loaded to the application is shown in the upper-right panel and the lower panel is a command-input and a message-output area.
[[File:Fig1.jpg|Figure 1 Start-up screen]]

== Displaying molecules ==
If you are working in the environment that is getting on the Internet and know the PDB ID of the molecule that you want to display, the simplest way is as follows. A dialog shown in Figure 2 is opened by selecting the [File] – [Open – Remote] – [PDB ID] menu item. Enter a PDB ID '12as', for example, to the text field and click the 'OK' button, then the PDBML file is read through the Internet and the molecule is displayed. The URL where the PDBML file is retrieved from is specified in the 'properties.txt' file in the jV_3_3_x directory. A molecule is displayed in a wire frame model with colored by atom type in the initial state.
[[File:Fig2.jpg|Dialog to open the molecule specified by PDB ID]]
Let us next attempt to load an arbitrary file on the Internet. Here we use 'http://ef-site.hgc.jp/eF-site/jV/1yec.pdb' as an example. The file is a conventional PDB file whose PDB ID is 1yec. In this case we choose the [File] – [Open – Remote] – [PDB] menu item. Then the open-remote dialog is appeared. Enter the above URL to the text field at the top of the dialog and click the 'OK' button and the molecule is read in and displayed. In jV3, each molecule is displayed according to the space coordination described in its file. Therefore, when loading and displaying more than one molecule together, they can be viewed with an appropriate separation in some cases; however, they may be displayed far separately or may be overlapped depending on the combination. In any case, when adding a new file, the position of the viewpoint is automatically controlled for the whole to be displayed.
The coordinate system is the right hand system with the x-y plane being on the screen (the x-axis is a horizontal line with positive values to the right and the y-axis is a vertical line with positive values up). Although, the above examples are about operations for remote files, a PDB file on your local hard disk can also be opened from the [File] – [Open – Local] – [PDB] menu item.

== Operating molecules ==
Interactive mouse operations are possible for 3D images. By left-dragging the mouse on the 3D-display panel, molecules are rotated around the x-axis or y-axis. By left-dragging the mouse while holding the Shift key or Alt key on the keyboard, molecules are translated along the z-axis. All mouse operations are as follows (as for the Macintosh environment, the Command key + left-drag substitutes for the right-drag).

{| border="1"
 ! Mouse operations !! Actions
 |-
 | Left-drag || The image is rotated around the x (for a vertical motion) and y (for a horizontal motion) axes.
 |-
 | Right-drag || The image is translated on the x-y plane.
 |-
 | [Alt or Shift] + left-drag || The image is translated along the z-axis.
 |-
 | [Alt or Shift] + right-drag || The image is rotated around the z-axis.
 |-
 | [Ctrl] + left-drag || The z-clipping plane is shifted when [Option]-[Slab] is checked.
 |-
 | Left-click || An atom of the molecule displayed on the screen is picked.
 |}

In the upper-right panel in the application window (see Figure 3), the file names that have been loaded to the application are listed, where sequential integers are automatically assigned to the individual file. Each integer is a file ID that can be used to specify the file in the command line interface. In addition, two checkboxes are attached to each file. If you change the status of a ‘display’ checkbox, the corresponding molecule is switched to be displayed or not to be displayed. If you change the status of a ‘select’ checkbox, the corresponding molecule is switched to be a target of the mouse operations or not. For example, set the both ‘display’ checkboxes on, and the both ‘select’ checkboxes off. In this case, either molecule does not move against mouse operations. 
Subsequently set the ‘select’ checkbox of file 1 on. In this case, mouse operations work for the molecule 1. Thus, each file is assigned either selected or not selected, and transform operations, such as rotation or translation, act only on selected files. On the other hand, every atom in a molecule is also assigned either selected or not selected, independently of whether the molecule itself is selected or not. Operations that modify display models or colors work for selected atoms. To see this, choose the [Display] – [Spacefill] menu item. Then the both molecules are displayed with the space fill model because all atoms are initially selected. In the same way, if you choose the [Colors] – [Monochrome] menu item, the both molecules are colored white. These operations are independent of the status of ‘select’ checkboxes mentioned above. 
Let us next try a more detailed operation. Type ‘select *@2’ in the command line area and press Enter key. This command means to select all atoms contained in the file 2 (the usage of the select command is summarized in the reference manual included in the binary distribution of jV3). Subsequently, choose the [Display] – [Cartoon] menu item. As a result, only the molecule 2 is displayed in the cartoon model. Furthermore select the [Colors] – [Structure] menu item, and each residue of the molecule 2 is colored according to its secondary structure type (see Figure 3). 
In order to reproduce the same view as that in Figure 3, first execute ‘reset’ command. It restores the position of the viewpoint and the transform of every file to the initial state. Note that the command line interface tries to complement a command word when the Tab key is pressed. If you enter ‘res’ to the command line and subsequently press the Tab key, the command ‘reset’ is automatically entered. Next set the both ‘select’ checkboxes on, and execute ‘translate z 100’ command. This command means to translate the molecules along the z-axis by 100 angstroms.
[[File:Fig3.jpg|An example of molecular images.]]

== Displaying polygons ==
In addition to molecules, arbitrary shapes described by polygons can be read in and displayed together, where the polygon file is an XML file, whose document type is described in the section 6. Here, we use ’http://ef-site.hgc.jp/eF-site/jV/1yec.surface.gz’ as an example. This polygon file represents a molecular surface of the molecule 2 (1yec) and the surface is colored according to the electrostatic potential and the hydrophobicity. It is assumed that the current image is the same as that in Figure 3. Then, open the open-remote dialog by choosing the [File] – [Open – Remote] – [Polygon] menu item, enter the above URL to the text field at the top of the dialog, and click the 'OK' button. As a result, the polygon is loaded, displayed and assigned file ID 3. 
Note that the polygon is displayed at the different position from the molecule 2 since the molecule 2 is translated. However, because the polygon and the molecule 2 are described by the same coordinates in their files, their images can be exactly superposed by executing ‘fit 3 2’ from the command line, where the ‘fit’ command performs the copy of the transform matrix. Finally, the image in Figure 4 appears.
[[File:Fig4.jpg|An example of polygon images.]]
You can control the transparency rate of polygons. Try ’set transparency 0.5’ from the command line, where 0.5 stands for 50% transparency. To restore the image, execute ‘reset transparency’ or ‘set transparency 0’. In the same sense as each atom of a molecule, each vertex of a polygon is assigned either selected or not selected. All vertices are selected in the initial state. Execute a command ’displayvertex off’ and all vertices become invisible. Next execute ’selectvertex within(10.0, 1&amp;*H@2)’, where this means to select vertices that exist within 10 angstroms from each atom that belongs to the first residue of the ‘H’ chain of the molecule 2. Subsequently execute ’displayvertex on’. As a result, only the selected vertices are appeared. The usage of the selectvertex command is summarized in the reference manual. 

== Working with xPSSS ==
Functional site information on a molecule stored at xPSSS (xml-based Protein Structure Search Service) is available in jV3. Before trying this, let us close the molecule 2 and the polygon 3 to make the situation simple. Select the [File] – [Close] – [2. 1yec.pdb] and [File] – [Close] – [3. 1yec.surface.gz] menu items sequentially. Then execute a ‘reset’ command and the transform of the molecule 1 and the position of the viewpoint are initialized. 
Next, confirm that the ‘select’ checkbox of the file 1 is checked, and try a ‘show xps3’ command. The functional site information of the molecule ‘12as’ is read from the xPSSS and ‘type’ and ‘subtype’ keywords for each functional site are listed. These keywords can be used to select a set of atoms. For example, if a keyword ‘CATRES’ exists (probably it does), the command ‘select xps3:CATRES’ selects the corresponding atoms. 
In addition, gene ontology information can be obtained from the xPSSS. The gene ontology information for the molecule 12as is displayed by the command ’show godata’. Similar operations can be applied to other external databases on the Internet provided that the external database supports the interface that jV3 requires. See the section 7 for details.

== Animation ==
The animation of molecules can be performed in jV3. The animation file takes the PDB format, where the MODEL line divides each frame. Let us open an animation file ’http://ef-site.hgc.jp/eF-site/jV/anim.pdb.gz’ as an example from the open-remote dialog shown by selecting the [File] – [Open – Remote] – [Animation] menu item. When an animation file is loaded to the application, the first frame is automatically displayed in the wire frame model. You can start the animation by using the animation-control dialog that is shown by choosing the [Options] – [Animation] menu item. The dialog provides operations such as start and stop of the animation, selection of the animation mode, and adjustment of the speed. Some sample figures of the dialog are shown in the [[GUI]]

== Saving your work ==
While in your work, you can create a script file that contains a set of commands that reproduces the current work by using the [File] – [Save] – [Script] menu item. The script file can be loaded by the [File] – [Open – Local] – [Script] menu item. On the other hand, the [File] – [Save] – [PDB] menu item enables to save a molecule to a PDB format file with the coordinates of the atoms being transformed according to the current image. Here, only one molecule must be selected and only selected atoms in the molecule are saved. The other two menu items in the [File] – [Save] menu, [PNG] and [JPEG], save the current screen image to an image file in the PNG and JPEG format, respectively. The created image file has the same size as that of the 3D-display panel in the application.

== Terminating the application ==
The application is terminated when the [File] – [Exit] menu item is chosen or the application window is closed by the way your operation system provides. You can also quit the application by executing ‘exit’ or ‘quit’ command.</text>
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    <id>184</id>
    <parentid>183</parentid>
    <timestamp>2009-03-09T09:13:22Z</timestamp>
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    <text bytes="12104" xml:space="preserve">{| style="float:right"
 |__TOC__
 |}
== Starting up ==
It is assumed that Java Runtime Environment and JOGL have been appropriately installed. Once you extract the binary distribution file of jV3, the directory of the name, jV_(version), is generated (Ex. jV_3_6_2). The version is assumed to be 3_6_x hereafter. The application starts up by double-clicking the file ‘jv_3_6_x.jar’ in the jV_3_6_x directory or executing the following command from the command line interface.
 java –jar jv_3_6_x.jar
Figure 1 shows the start-up screen. The window has a 3-panel structure, and the upper-left panel with the black background is a 3D image display area. The status of files that have been loaded to the application is shown in the upper-right panel and the lower panel is a command-input and a message-output area.
[[File:Fig1.jpg|Figure 1 Start-up screen]]

== Displaying molecules ==
If you are working in the environment that is getting on the Internet and know the PDB ID of the molecule that you want to display, the simplest way is as follows. A dialog shown in Figure 2 is opened by selecting the [File] – [Open – Remote] – [PDB ID] menu item. Enter a PDB ID '12as', for example, to the text field and click the 'OK' button, then the PDBML file is read through the Internet and the molecule is displayed. The URL where the PDBML file is retrieved from is specified in the 'properties.txt' file in the jV_3_3_x directory. A molecule is displayed in a wire frame model with colored by atom type in the initial state.
[[File:Fig2.jpg|Dialog to open the molecule specified by PDB ID]]
Let us next attempt to load an arbitrary file on the Internet. Here we use 'http://ef-site.hgc.jp/eF-site/jV/1yec.pdb' as an example. The file is a conventional PDB file whose PDB ID is 1yec. In this case we choose the [File] – [Open – Remote] – [PDB] menu item. Then the open-remote dialog is appeared. Enter the above URL to the text field at the top of the dialog and click the 'OK' button and the molecule is read in and displayed. In jV3, each molecule is displayed according to the space coordination described in its file. Therefore, when loading and displaying more than one molecule together, they can be viewed with an appropriate separation in some cases; however, they may be displayed far separately or may be overlapped depending on the combination. In any case, when adding a new file, the position of the viewpoint is automatically controlled for the whole to be displayed.
The coordinate system is the right hand system with the x-y plane being on the screen (the x-axis is a horizontal line with positive values to the right and the y-axis is a vertical line with positive values up). Although, the above examples are about operations for remote files, a PDB file on your local hard disk can also be opened from the [File] – [Open – Local] – [PDB] menu item.

== Operating molecules ==
Interactive mouse operations are possible for 3D images. By left-dragging the mouse on the 3D-display panel, molecules are rotated around the x-axis or y-axis. By left-dragging the mouse while holding the Shift key or Alt key on the keyboard, molecules are translated along the z-axis. All mouse operations are as follows (as for the Macintosh environment, the Command key + left-drag substitutes for the right-drag).

{| border="1"
 ! Mouse operations !! Actions
 |-
 | Left-drag || The image is rotated around the x (for a vertical motion) and y (for a horizontal motion) axes.
 |-
 | Right-drag || The image is translated on the x-y plane.
 |-
 | [Alt or Shift] + left-drag || The image is translated along the z-axis.
 |-
 | [Alt or Shift] + right-drag || The image is rotated around the z-axis.
 |-
 | [Ctrl] + left-drag || The z-clipping plane is shifted when [Option]-[Slab] is checked.
 |-
 | Left-click || An atom of the molecule displayed on the screen is picked.
 |}

In the upper-right panel in the application window (see Figure 3), the file names that have been loaded to the application are listed, where sequential integers are automatically assigned to the individual file. Each integer is a file ID that can be used to specify the file in the command line interface. In addition, two checkboxes are attached to each file. If you change the status of a ‘display’ checkbox, the corresponding molecule is switched to be displayed or not to be displayed. If you change the status of a ‘select’ checkbox, the corresponding molecule is switched to be a target of the mouse operations or not. For example, set the both ‘display’ checkboxes on, and the both ‘select’ checkboxes off. In this case, either molecule does not move against mouse operations. 
Subsequently set the ‘select’ checkbox of file 1 on. In this case, mouse operations work for the molecule 1. Thus, each file is assigned either selected or not selected, and transform operations, such as rotation or translation, act only on selected files. On the other hand, every atom in a molecule is also assigned either selected or not selected, independently of whether the molecule itself is selected or not. Operations that modify display models or colors work for selected atoms. To see this, choose the [Display] – [Spacefill] menu item. Then the both molecules are displayed with the space fill model because all atoms are initially selected. In the same way, if you choose the [Colors] – [Monochrome] menu item, the both molecules are colored white. These operations are independent of the status of ‘select’ checkboxes mentioned above. 
Let us next try a more detailed operation. Type ‘select *@2’ in the command line area and press Enter key. This command means to select all atoms contained in the file 2 (the usage of the select command is summarized in the reference manual included in the binary distribution of jV3). Subsequently, choose the [Display] – [Cartoon] menu item. As a result, only the molecule 2 is displayed in the cartoon model. Furthermore select the [Colors] – [Structure] menu item, and each residue of the molecule 2 is colored according to its secondary structure type (see Figure 3). 
In order to reproduce the same view as that in Figure 3, first execute ‘reset’ command. It restores the position of the viewpoint and the transform of every file to the initial state. Note that the command line interface tries to complement a command word when the Tab key is pressed. If you enter ‘res’ to the command line and subsequently press the Tab key, the command ‘reset’ is automatically entered. Next set the both ‘select’ checkboxes on, and execute ‘translate z 100’ command. This command means to translate the molecules along the z-axis by 100 angstroms.
[[File:Fig3.jpg|An example of molecular images.]]

== Displaying polygons ==
In addition to molecules, arbitrary shapes described by polygons can be read in and displayed together, where the polygon file is an XML file, whose document type is described in the section 6. Here, we use ’http://ef-site.hgc.jp/eF-site/jV/1yec.surface.gz’ as an example. This polygon file represents a molecular surface of the molecule 2 (1yec) and the surface is colored according to the electrostatic potential and the hydrophobicity. It is assumed that the current image is the same as that in Figure 3. Then, open the open-remote dialog by choosing the [File] – [Open – Remote] – [Polygon] menu item, enter the above URL to the text field at the top of the dialog, and click the 'OK' button. As a result, the polygon is loaded, displayed and assigned file ID 3. 
Note that the polygon is displayed at the different position from the molecule 2 since the molecule 2 is translated. However, because the polygon and the molecule 2 are described by the same coordinates in their files, their images can be exactly superposed by executing ‘fit 3 2’ from the command line, where the ‘fit’ command performs the copy of the transform matrix. Finally, the image in Figure 4 appears.
[[File:Fig4.jpg|An example of polygon images.]]
You can control the transparency rate of polygons. Try ’set transparency 0.5’ from the command line, where 0.5 stands for 50% transparency. To restore the image, execute ‘reset transparency’ or ‘set transparency 0’. In the same sense as each atom of a molecule, each vertex of a polygon is assigned either selected or not selected. All vertices are selected in the initial state. Execute a command ’displayvertex off’ and all vertices become invisible. Next execute ’selectvertex within(10.0, 1&amp;*H@2)’, where this means to select vertices that exist within 10 angstroms from each atom that belongs to the first residue of the ‘H’ chain of the molecule 2. Subsequently execute ’displayvertex on’. As a result, only the selected vertices are appeared. The usage of the selectvertex command is summarized in the reference manual. 

== Working with xPSSS ==
Functional site information on a molecule stored at xPSSS (xml-based Protein Structure Search Service) is available in jV3. Before trying this, let us close the molecule 2 and the polygon 3 to make the situation simple. Select the [File] – [Close] – [2. 1yec.pdb] and [File] – [Close] – [3. 1yec.surface.gz] menu items sequentially. Then execute a ‘reset’ command and the transform of the molecule 1 and the position of the viewpoint are initialized. 
Next, confirm that the ‘select’ checkbox of the file 1 is checked, and try a ‘show xps3’ command. The functional site information of the molecule ‘12as’ is read from the xPSSS and ‘type’ and ‘subtype’ keywords for each functional site are listed. These keywords can be used to select a set of atoms. For example, if a keyword ‘CATRES’ exists (probably it does), the command ‘select xps3:CATRES’ selects the corresponding atoms. 
In addition, gene ontology information can be obtained from the xPSSS. The gene ontology information for the molecule 12as is displayed by the command ’show godata’. Similar operations can be applied to other external databases on the Internet provided that the external database supports the interface that jV3 requires. See the section 7 for details.

== Animation ==
The animation of molecules can be performed in jV3. The animation file takes the PDB format, where the MODEL line divides each frame. Let us open an animation file ’http://ef-site.hgc.jp/eF-site/jV/anim.pdb.gz’ as an example from the open-remote dialog shown by selecting the [File] – [Open – Remote] – [Animation] menu item. When an animation file is loaded to the application, the first frame is automatically displayed in the wire frame model. You can start the animation by using the animation-control dialog that is shown by choosing the [Options] – [Animation] menu item. The dialog provides operations such as start and stop of the animation, selection of the animation mode, and adjustment of the speed. Some sample figures of the dialog are shown in the [[GUI#3]]

== Saving your work ==
While in your work, you can create a script file that contains a set of commands that reproduces the current work by using the [File] – [Save] – [Script] menu item. The script file can be loaded by the [File] – [Open – Local] – [Script] menu item. On the other hand, the [File] – [Save] – [PDB] menu item enables to save a molecule to a PDB format file with the coordinates of the atoms being transformed according to the current image. Here, only one molecule must be selected and only selected atoms in the molecule are saved. The other two menu items in the [File] – [Save] menu, [PNG] and [JPEG], save the current screen image to an image file in the PNG and JPEG format, respectively. The created image file has the same size as that of the 3D-display panel in the application.

== Terminating the application ==
The application is terminated when the [File] – [Exit] menu item is chosen or the application window is closed by the way your operation system provides. You can also quit the application by executing ‘exit’ or ‘quit’ command.</text>
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    <timestamp>2009-03-09T09:19:13Z</timestamp>
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    <text bytes="12114" xml:space="preserve">{| style="float:right"
 |__TOC__
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== Starting up ==
It is assumed that Java Runtime Environment and JOGL have been appropriately installed. Once you extract the binary distribution file of jV3, the directory of the name, jV_(version), is generated (Ex. jV_3_6_2). The version is assumed to be 3_6_x hereafter. The application starts up by double-clicking the file ‘jv_3_6_x.jar’ in the jV_3_6_x directory or executing the following command from the command line interface.
 java –jar jv_3_6_x.jar
Figure 1 shows the start-up screen. The window has a 3-panel structure, and the upper-left panel with the black background is a 3D image display area. The status of files that have been loaded to the application is shown in the upper-right panel and the lower panel is a command-input and a message-output area.
[[File:Fig1.jpg|Figure 1 Start-up screen|1000px]]

== Displaying molecules ==
If you are working in the environment that is getting on the Internet and know the PDB ID of the molecule that you want to display, the simplest way is as follows. A dialog shown in Figure 2 is opened by selecting the [File] – [Open – Remote] – [PDB ID] menu item. Enter a PDB ID '12as', for example, to the text field and click the 'OK' button, then the PDBML file is read through the Internet and the molecule is displayed. The URL where the PDBML file is retrieved from is specified in the 'properties.txt' file in the jV_3_3_x directory. A molecule is displayed in a wire frame model with colored by atom type in the initial state.

[[File:Fig2.jpg|Dialog to open the molecule specified by PDB ID]]

Let us next attempt to load an arbitrary file on the Internet. Here we use 'http://ef-site.hgc.jp/eF-site/jV/1yec.pdb' as an example. The file is a conventional PDB file whose PDB ID is 1yec. In this case we choose the [File] – [Open – Remote] – [PDB] menu item. Then the open-remote dialog is appeared. Enter the above URL to the text field at the top of the dialog and click the 'OK' button and the molecule is read in and displayed. In jV3, each molecule is displayed according to the space coordination described in its file. Therefore, when loading and displaying more than one molecule together, they can be viewed with an appropriate separation in some cases; however, they may be displayed far separately or may be overlapped depending on the combination. In any case, when adding a new file, the position of the viewpoint is automatically controlled for the whole to be displayed.
The coordinate system is the right hand system with the x-y plane being on the screen (the x-axis is a horizontal line with positive values to the right and the y-axis is a vertical line with positive values up). Although, the above examples are about operations for remote files, a PDB file on your local hard disk can also be opened from the [File] – [Open – Local] – [PDB] menu item.

== Operating molecules ==
Interactive mouse operations are possible for 3D images. By left-dragging the mouse on the 3D-display panel, molecules are rotated around the x-axis or y-axis. By left-dragging the mouse while holding the Shift key or Alt key on the keyboard, molecules are translated along the z-axis. All mouse operations are as follows (as for the Macintosh environment, the Command key + left-drag substitutes for the right-drag).

{| border="1"
 ! Mouse operations !! Actions
 |-
 | Left-drag || The image is rotated around the x (for a vertical motion) and y (for a horizontal motion) axes.
 |-
 | Right-drag || The image is translated on the x-y plane.
 |-
 | [Alt or Shift] + left-drag || The image is translated along the z-axis.
 |-
 | [Alt or Shift] + right-drag || The image is rotated around the z-axis.
 |-
 | [Ctrl] + left-drag || The z-clipping plane is shifted when [Option]-[Slab] is checked.
 |-
 | Left-click || An atom of the molecule displayed on the screen is picked.
 |}

In the upper-right panel in the application window (see Figure 3), the file names that have been loaded to the application are listed, where sequential integers are automatically assigned to the individual file. Each integer is a file ID that can be used to specify the file in the command line interface. In addition, two checkboxes are attached to each file. If you change the status of a ‘display’ checkbox, the corresponding molecule is switched to be displayed or not to be displayed. If you change the status of a ‘select’ checkbox, the corresponding molecule is switched to be a target of the mouse operations or not. For example, set the both ‘display’ checkboxes on, and the both ‘select’ checkboxes off. In this case, either molecule does not move against mouse operations. 
Subsequently set the ‘select’ checkbox of file 1 on. In this case, mouse operations work for the molecule 1. Thus, each file is assigned either selected or not selected, and transform operations, such as rotation or translation, act only on selected files. On the other hand, every atom in a molecule is also assigned either selected or not selected, independently of whether the molecule itself is selected or not. Operations that modify display models or colors work for selected atoms. To see this, choose the [Display] – [Spacefill] menu item. Then the both molecules are displayed with the space fill model because all atoms are initially selected. In the same way, if you choose the [Colors] – [Monochrome] menu item, the both molecules are colored white. These operations are independent of the status of ‘select’ checkboxes mentioned above. 
Let us next try a more detailed operation. Type ‘select *@2’ in the command line area and press Enter key. This command means to select all atoms contained in the file 2 (the usage of the select command is summarized in the reference manual included in the binary distribution of jV3). Subsequently, choose the [Display] – [Cartoon] menu item. As a result, only the molecule 2 is displayed in the cartoon model. Furthermore select the [Colors] – [Structure] menu item, and each residue of the molecule 2 is colored according to its secondary structure type (see Figure 3). 
In order to reproduce the same view as that in Figure 3, first execute ‘reset’ command. It restores the position of the viewpoint and the transform of every file to the initial state. Note that the command line interface tries to complement a command word when the Tab key is pressed. If you enter ‘res’ to the command line and subsequently press the Tab key, the command ‘reset’ is automatically entered. Next set the both ‘select’ checkboxes on, and execute ‘translate z 100’ command. This command means to translate the molecules along the z-axis by 100 angstroms.

[[File:Fig3.jpg|An example of molecular images.]]

== Displaying polygons ==
In addition to molecules, arbitrary shapes described by polygons can be read in and displayed together, where the polygon file is an XML file, whose document type is described in the section 6. Here, we use ’http://ef-site.hgc.jp/eF-site/jV/1yec.surface.gz’ as an example. This polygon file represents a molecular surface of the molecule 2 (1yec) and the surface is colored according to the electrostatic potential and the hydrophobicity. It is assumed that the current image is the same as that in Figure 3. Then, open the open-remote dialog by choosing the [File] – [Open – Remote] – [Polygon] menu item, enter the above URL to the text field at the top of the dialog, and click the 'OK' button. As a result, the polygon is loaded, displayed and assigned file ID 3. 
Note that the polygon is displayed at the different position from the molecule 2 since the molecule 2 is translated. However, because the polygon and the molecule 2 are described by the same coordinates in their files, their images can be exactly superposed by executing ‘fit 3 2’ from the command line, where the ‘fit’ command performs the copy of the transform matrix. Finally, the image in Figure 4 appears.
[[File:Fig4.jpg|An example of polygon images.]]
You can control the transparency rate of polygons. Try ’set transparency 0.5’ from the command line, where 0.5 stands for 50% transparency. To restore the image, execute ‘reset transparency’ or ‘set transparency 0’. In the same sense as each atom of a molecule, each vertex of a polygon is assigned either selected or not selected. All vertices are selected in the initial state. Execute a command ’displayvertex off’ and all vertices become invisible. Next execute ’selectvertex within(10.0, 1&amp;*H@2)’, where this means to select vertices that exist within 10 angstroms from each atom that belongs to the first residue of the ‘H’ chain of the molecule 2. Subsequently execute ’displayvertex on’. As a result, only the selected vertices are appeared. The usage of the selectvertex command is summarized in the reference manual. 

== Working with xPSSS ==
Functional site information on a molecule stored at xPSSS (xml-based Protein Structure Search Service) is available in jV3. Before trying this, let us close the molecule 2 and the polygon 3 to make the situation simple. Select the [File] – [Close] – [2. 1yec.pdb] and [File] – [Close] – [3. 1yec.surface.gz] menu items sequentially. Then execute a ‘reset’ command and the transform of the molecule 1 and the position of the viewpoint are initialized. 
Next, confirm that the ‘select’ checkbox of the file 1 is checked, and try a ‘show xps3’ command. The functional site information of the molecule ‘12as’ is read from the xPSSS and ‘type’ and ‘subtype’ keywords for each functional site are listed. These keywords can be used to select a set of atoms. For example, if a keyword ‘CATRES’ exists (probably it does), the command ‘select xps3:CATRES’ selects the corresponding atoms. 
In addition, gene ontology information can be obtained from the xPSSS. The gene ontology information for the molecule 12as is displayed by the command ’show godata’. Similar operations can be applied to other external databases on the Internet provided that the external database supports the interface that jV3 requires. See the section 7 for details.

== Animation ==
The animation of molecules can be performed in jV3. The animation file takes the PDB format, where the MODEL line divides each frame. Let us open an animation file ’http://ef-site.hgc.jp/eF-site/jV/anim.pdb.gz’ as an example from the open-remote dialog shown by selecting the [File] – [Open – Remote] – [Animation] menu item. When an animation file is loaded to the application, the first frame is automatically displayed in the wire frame model. You can start the animation by using the animation-control dialog that is shown by choosing the [Options] – [Animation] menu item. The dialog provides operations such as start and stop of the animation, selection of the animation mode, and adjustment of the speed. Some sample figures of the dialog are shown in the [[GUI#3]]

== Saving your work ==
While in your work, you can create a script file that contains a set of commands that reproduces the current work by using the [File] – [Save] – [Script] menu item. The script file can be loaded by the [File] – [Open – Local] – [Script] menu item. On the other hand, the [File] – [Save] – [PDB] menu item enables to save a molecule to a PDB format file with the coordinates of the atoms being transformed according to the current image. Here, only one molecule must be selected and only selected atoms in the molecule are saved. The other two menu items in the [File] – [Save] menu, [PNG] and [JPEG], save the current screen image to an image file in the PNG and JPEG format, respectively. The created image file has the same size as that of the 3D-display panel in the application.

== Terminating the application ==
The application is terminated when the [File] – [Exit] menu item is chosen or the application window is closed by the way your operation system provides. You can also quit the application by executing ‘exit’ or ‘quit’ command.</text>
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    <timestamp>2009-03-09T09:19:34Z</timestamp>
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 |__TOC__
 |}
== Starting up ==
It is assumed that Java Runtime Environment and JOGL have been appropriately installed. Once you extract the binary distribution file of jV3, the directory of the name, jV_(version), is generated (Ex. jV_3_6_2). The version is assumed to be 3_6_x hereafter. The application starts up by double-clicking the file ‘jv_3_6_x.jar’ in the jV_3_6_x directory or executing the following command from the command line interface.
 java –jar jv_3_6_x.jar
Figure 1 shows the start-up screen. The window has a 3-panel structure, and the upper-left panel with the black background is a 3D image display area. The status of files that have been loaded to the application is shown in the upper-right panel and the lower panel is a command-input and a message-output area.
[[File:Fig1.jpg|Figure 1 Start-up screen|900px]]

== Displaying molecules ==
If you are working in the environment that is getting on the Internet and know the PDB ID of the molecule that you want to display, the simplest way is as follows. A dialog shown in Figure 2 is opened by selecting the [File] – [Open – Remote] – [PDB ID] menu item. Enter a PDB ID '12as', for example, to the text field and click the 'OK' button, then the PDBML file is read through the Internet and the molecule is displayed. The URL where the PDBML file is retrieved from is specified in the 'properties.txt' file in the jV_3_3_x directory. A molecule is displayed in a wire frame model with colored by atom type in the initial state.

[[File:Fig2.jpg|Dialog to open the molecule specified by PDB ID]]

Let us next attempt to load an arbitrary file on the Internet. Here we use 'http://ef-site.hgc.jp/eF-site/jV/1yec.pdb' as an example. The file is a conventional PDB file whose PDB ID is 1yec. In this case we choose the [File] – [Open – Remote] – [PDB] menu item. Then the open-remote dialog is appeared. Enter the above URL to the text field at the top of the dialog and click the 'OK' button and the molecule is read in and displayed. In jV3, each molecule is displayed according to the space coordination described in its file. Therefore, when loading and displaying more than one molecule together, they can be viewed with an appropriate separation in some cases; however, they may be displayed far separately or may be overlapped depending on the combination. In any case, when adding a new file, the position of the viewpoint is automatically controlled for the whole to be displayed.
The coordinate system is the right hand system with the x-y plane being on the screen (the x-axis is a horizontal line with positive values to the right and the y-axis is a vertical line with positive values up). Although, the above examples are about operations for remote files, a PDB file on your local hard disk can also be opened from the [File] – [Open – Local] – [PDB] menu item.

== Operating molecules ==
Interactive mouse operations are possible for 3D images. By left-dragging the mouse on the 3D-display panel, molecules are rotated around the x-axis or y-axis. By left-dragging the mouse while holding the Shift key or Alt key on the keyboard, molecules are translated along the z-axis. All mouse operations are as follows (as for the Macintosh environment, the Command key + left-drag substitutes for the right-drag).

{| border="1"
 ! Mouse operations !! Actions
 |-
 | Left-drag || The image is rotated around the x (for a vertical motion) and y (for a horizontal motion) axes.
 |-
 | Right-drag || The image is translated on the x-y plane.
 |-
 | [Alt or Shift] + left-drag || The image is translated along the z-axis.
 |-
 | [Alt or Shift] + right-drag || The image is rotated around the z-axis.
 |-
 | [Ctrl] + left-drag || The z-clipping plane is shifted when [Option]-[Slab] is checked.
 |-
 | Left-click || An atom of the molecule displayed on the screen is picked.
 |}

In the upper-right panel in the application window (see Figure 3), the file names that have been loaded to the application are listed, where sequential integers are automatically assigned to the individual file. Each integer is a file ID that can be used to specify the file in the command line interface. In addition, two checkboxes are attached to each file. If you change the status of a ‘display’ checkbox, the corresponding molecule is switched to be displayed or not to be displayed. If you change the status of a ‘select’ checkbox, the corresponding molecule is switched to be a target of the mouse operations or not. For example, set the both ‘display’ checkboxes on, and the both ‘select’ checkboxes off. In this case, either molecule does not move against mouse operations. 
Subsequently set the ‘select’ checkbox of file 1 on. In this case, mouse operations work for the molecule 1. Thus, each file is assigned either selected or not selected, and transform operations, such as rotation or translation, act only on selected files. On the other hand, every atom in a molecule is also assigned either selected or not selected, independently of whether the molecule itself is selected or not. Operations that modify display models or colors work for selected atoms. To see this, choose the [Display] – [Spacefill] menu item. Then the both molecules are displayed with the space fill model because all atoms are initially selected. In the same way, if you choose the [Colors] – [Monochrome] menu item, the both molecules are colored white. These operations are independent of the status of ‘select’ checkboxes mentioned above. 
Let us next try a more detailed operation. Type ‘select *@2’ in the command line area and press Enter key. This command means to select all atoms contained in the file 2 (the usage of the select command is summarized in the reference manual included in the binary distribution of jV3). Subsequently, choose the [Display] – [Cartoon] menu item. As a result, only the molecule 2 is displayed in the cartoon model. Furthermore select the [Colors] – [Structure] menu item, and each residue of the molecule 2 is colored according to its secondary structure type (see Figure 3). 
In order to reproduce the same view as that in Figure 3, first execute ‘reset’ command. It restores the position of the viewpoint and the transform of every file to the initial state. Note that the command line interface tries to complement a command word when the Tab key is pressed. If you enter ‘res’ to the command line and subsequently press the Tab key, the command ‘reset’ is automatically entered. Next set the both ‘select’ checkboxes on, and execute ‘translate z 100’ command. This command means to translate the molecules along the z-axis by 100 angstroms.

[[File:Fig3.jpg|An example of molecular images.]]

== Displaying polygons ==
In addition to molecules, arbitrary shapes described by polygons can be read in and displayed together, where the polygon file is an XML file, whose document type is described in the section 6. Here, we use ’http://ef-site.hgc.jp/eF-site/jV/1yec.surface.gz’ as an example. This polygon file represents a molecular surface of the molecule 2 (1yec) and the surface is colored according to the electrostatic potential and the hydrophobicity. It is assumed that the current image is the same as that in Figure 3. Then, open the open-remote dialog by choosing the [File] – [Open – Remote] – [Polygon] menu item, enter the above URL to the text field at the top of the dialog, and click the 'OK' button. As a result, the polygon is loaded, displayed and assigned file ID 3. 
Note that the polygon is displayed at the different position from the molecule 2 since the molecule 2 is translated. However, because the polygon and the molecule 2 are described by the same coordinates in their files, their images can be exactly superposed by executing ‘fit 3 2’ from the command line, where the ‘fit’ command performs the copy of the transform matrix. Finally, the image in Figure 4 appears.
[[File:Fig4.jpg|An example of polygon images.]]
You can control the transparency rate of polygons. Try ’set transparency 0.5’ from the command line, where 0.5 stands for 50% transparency. To restore the image, execute ‘reset transparency’ or ‘set transparency 0’. In the same sense as each atom of a molecule, each vertex of a polygon is assigned either selected or not selected. All vertices are selected in the initial state. Execute a command ’displayvertex off’ and all vertices become invisible. Next execute ’selectvertex within(10.0, 1&amp;*H@2)’, where this means to select vertices that exist within 10 angstroms from each atom that belongs to the first residue of the ‘H’ chain of the molecule 2. Subsequently execute ’displayvertex on’. As a result, only the selected vertices are appeared. The usage of the selectvertex command is summarized in the reference manual. 

== Working with xPSSS ==
Functional site information on a molecule stored at xPSSS (xml-based Protein Structure Search Service) is available in jV3. Before trying this, let us close the molecule 2 and the polygon 3 to make the situation simple. Select the [File] – [Close] – [2. 1yec.pdb] and [File] – [Close] – [3. 1yec.surface.gz] menu items sequentially. Then execute a ‘reset’ command and the transform of the molecule 1 and the position of the viewpoint are initialized. 
Next, confirm that the ‘select’ checkbox of the file 1 is checked, and try a ‘show xps3’ command. The functional site information of the molecule ‘12as’ is read from the xPSSS and ‘type’ and ‘subtype’ keywords for each functional site are listed. These keywords can be used to select a set of atoms. For example, if a keyword ‘CATRES’ exists (probably it does), the command ‘select xps3:CATRES’ selects the corresponding atoms. 
In addition, gene ontology information can be obtained from the xPSSS. The gene ontology information for the molecule 12as is displayed by the command ’show godata’. Similar operations can be applied to other external databases on the Internet provided that the external database supports the interface that jV3 requires. See the section 7 for details.

== Animation ==
The animation of molecules can be performed in jV3. The animation file takes the PDB format, where the MODEL line divides each frame. Let us open an animation file ’http://ef-site.hgc.jp/eF-site/jV/anim.pdb.gz’ as an example from the open-remote dialog shown by selecting the [File] – [Open – Remote] – [Animation] menu item. When an animation file is loaded to the application, the first frame is automatically displayed in the wire frame model. You can start the animation by using the animation-control dialog that is shown by choosing the [Options] – [Animation] menu item. The dialog provides operations such as start and stop of the animation, selection of the animation mode, and adjustment of the speed. Some sample figures of the dialog are shown in the [[GUI#3]]

== Saving your work ==
While in your work, you can create a script file that contains a set of commands that reproduces the current work by using the [File] – [Save] – [Script] menu item. The script file can be loaded by the [File] – [Open – Local] – [Script] menu item. On the other hand, the [File] – [Save] – [PDB] menu item enables to save a molecule to a PDB format file with the coordinates of the atoms being transformed according to the current image. Here, only one molecule must be selected and only selected atoms in the molecule are saved. The other two menu items in the [File] – [Save] menu, [PNG] and [JPEG], save the current screen image to an image file in the PNG and JPEG format, respectively. The created image file has the same size as that of the 3D-display panel in the application.

== Terminating the application ==
The application is terminated when the [File] – [Exit] menu item is chosen or the application window is closed by the way your operation system provides. You can also quit the application by executing ‘exit’ or ‘quit’ command.</text>
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  <revision>
    <id>191</id>
    <parentid>190</parentid>
    <timestamp>2009-03-09T09:19:46Z</timestamp>
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== Starting up ==
It is assumed that Java Runtime Environment and JOGL have been appropriately installed. Once you extract the binary distribution file of jV3, the directory of the name, jV_(version), is generated (Ex. jV_3_6_2). The version is assumed to be 3_6_x hereafter. The application starts up by double-clicking the file ‘jv_3_6_x.jar’ in the jV_3_6_x directory or executing the following command from the command line interface.
 java –jar jv_3_6_x.jar
Figure 1 shows the start-up screen. The window has a 3-panel structure, and the upper-left panel with the black background is a 3D image display area. The status of files that have been loaded to the application is shown in the upper-right panel and the lower panel is a command-input and a message-output area.
[[File:Fig1.jpg|Figure 1 Start-up screen|600px]]

== Displaying molecules ==
If you are working in the environment that is getting on the Internet and know the PDB ID of the molecule that you want to display, the simplest way is as follows. A dialog shown in Figure 2 is opened by selecting the [File] – [Open – Remote] – [PDB ID] menu item. Enter a PDB ID '12as', for example, to the text field and click the 'OK' button, then the PDBML file is read through the Internet and the molecule is displayed. The URL where the PDBML file is retrieved from is specified in the 'properties.txt' file in the jV_3_3_x directory. A molecule is displayed in a wire frame model with colored by atom type in the initial state.

[[File:Fig2.jpg|Dialog to open the molecule specified by PDB ID]]

Let us next attempt to load an arbitrary file on the Internet. Here we use 'http://ef-site.hgc.jp/eF-site/jV/1yec.pdb' as an example. The file is a conventional PDB file whose PDB ID is 1yec. In this case we choose the [File] – [Open – Remote] – [PDB] menu item. Then the open-remote dialog is appeared. Enter the above URL to the text field at the top of the dialog and click the 'OK' button and the molecule is read in and displayed. In jV3, each molecule is displayed according to the space coordination described in its file. Therefore, when loading and displaying more than one molecule together, they can be viewed with an appropriate separation in some cases; however, they may be displayed far separately or may be overlapped depending on the combination. In any case, when adding a new file, the position of the viewpoint is automatically controlled for the whole to be displayed.
The coordinate system is the right hand system with the x-y plane being on the screen (the x-axis is a horizontal line with positive values to the right and the y-axis is a vertical line with positive values up). Although, the above examples are about operations for remote files, a PDB file on your local hard disk can also be opened from the [File] – [Open – Local] – [PDB] menu item.

== Operating molecules ==
Interactive mouse operations are possible for 3D images. By left-dragging the mouse on the 3D-display panel, molecules are rotated around the x-axis or y-axis. By left-dragging the mouse while holding the Shift key or Alt key on the keyboard, molecules are translated along the z-axis. All mouse operations are as follows (as for the Macintosh environment, the Command key + left-drag substitutes for the right-drag).

{| border="1"
 ! Mouse operations !! Actions
 |-
 | Left-drag || The image is rotated around the x (for a vertical motion) and y (for a horizontal motion) axes.
 |-
 | Right-drag || The image is translated on the x-y plane.
 |-
 | [Alt or Shift] + left-drag || The image is translated along the z-axis.
 |-
 | [Alt or Shift] + right-drag || The image is rotated around the z-axis.
 |-
 | [Ctrl] + left-drag || The z-clipping plane is shifted when [Option]-[Slab] is checked.
 |-
 | Left-click || An atom of the molecule displayed on the screen is picked.
 |}

In the upper-right panel in the application window (see Figure 3), the file names that have been loaded to the application are listed, where sequential integers are automatically assigned to the individual file. Each integer is a file ID that can be used to specify the file in the command line interface. In addition, two checkboxes are attached to each file. If you change the status of a ‘display’ checkbox, the corresponding molecule is switched to be displayed or not to be displayed. If you change the status of a ‘select’ checkbox, the corresponding molecule is switched to be a target of the mouse operations or not. For example, set the both ‘display’ checkboxes on, and the both ‘select’ checkboxes off. In this case, either molecule does not move against mouse operations. 
Subsequently set the ‘select’ checkbox of file 1 on. In this case, mouse operations work for the molecule 1. Thus, each file is assigned either selected or not selected, and transform operations, such as rotation or translation, act only on selected files. On the other hand, every atom in a molecule is also assigned either selected or not selected, independently of whether the molecule itself is selected or not. Operations that modify display models or colors work for selected atoms. To see this, choose the [Display] – [Spacefill] menu item. Then the both molecules are displayed with the space fill model because all atoms are initially selected. In the same way, if you choose the [Colors] – [Monochrome] menu item, the both molecules are colored white. These operations are independent of the status of ‘select’ checkboxes mentioned above. 
Let us next try a more detailed operation. Type ‘select *@2’ in the command line area and press Enter key. This command means to select all atoms contained in the file 2 (the usage of the select command is summarized in the reference manual included in the binary distribution of jV3). Subsequently, choose the [Display] – [Cartoon] menu item. As a result, only the molecule 2 is displayed in the cartoon model. Furthermore select the [Colors] – [Structure] menu item, and each residue of the molecule 2 is colored according to its secondary structure type (see Figure 3). 
In order to reproduce the same view as that in Figure 3, first execute ‘reset’ command. It restores the position of the viewpoint and the transform of every file to the initial state. Note that the command line interface tries to complement a command word when the Tab key is pressed. If you enter ‘res’ to the command line and subsequently press the Tab key, the command ‘reset’ is automatically entered. Next set the both ‘select’ checkboxes on, and execute ‘translate z 100’ command. This command means to translate the molecules along the z-axis by 100 angstroms.

[[File:Fig3.jpg|An example of molecular images.]]

== Displaying polygons ==
In addition to molecules, arbitrary shapes described by polygons can be read in and displayed together, where the polygon file is an XML file, whose document type is described in the section 6. Here, we use ’http://ef-site.hgc.jp/eF-site/jV/1yec.surface.gz’ as an example. This polygon file represents a molecular surface of the molecule 2 (1yec) and the surface is colored according to the electrostatic potential and the hydrophobicity. It is assumed that the current image is the same as that in Figure 3. Then, open the open-remote dialog by choosing the [File] – [Open – Remote] – [Polygon] menu item, enter the above URL to the text field at the top of the dialog, and click the 'OK' button. As a result, the polygon is loaded, displayed and assigned file ID 3. 
Note that the polygon is displayed at the different position from the molecule 2 since the molecule 2 is translated. However, because the polygon and the molecule 2 are described by the same coordinates in their files, their images can be exactly superposed by executing ‘fit 3 2’ from the command line, where the ‘fit’ command performs the copy of the transform matrix. Finally, the image in Figure 4 appears.
[[File:Fig4.jpg|An example of polygon images.]]
You can control the transparency rate of polygons. Try ’set transparency 0.5’ from the command line, where 0.5 stands for 50% transparency. To restore the image, execute ‘reset transparency’ or ‘set transparency 0’. In the same sense as each atom of a molecule, each vertex of a polygon is assigned either selected or not selected. All vertices are selected in the initial state. Execute a command ’displayvertex off’ and all vertices become invisible. Next execute ’selectvertex within(10.0, 1&amp;*H@2)’, where this means to select vertices that exist within 10 angstroms from each atom that belongs to the first residue of the ‘H’ chain of the molecule 2. Subsequently execute ’displayvertex on’. As a result, only the selected vertices are appeared. The usage of the selectvertex command is summarized in the reference manual. 

== Working with xPSSS ==
Functional site information on a molecule stored at xPSSS (xml-based Protein Structure Search Service) is available in jV3. Before trying this, let us close the molecule 2 and the polygon 3 to make the situation simple. Select the [File] – [Close] – [2. 1yec.pdb] and [File] – [Close] – [3. 1yec.surface.gz] menu items sequentially. Then execute a ‘reset’ command and the transform of the molecule 1 and the position of the viewpoint are initialized. 
Next, confirm that the ‘select’ checkbox of the file 1 is checked, and try a ‘show xps3’ command. The functional site information of the molecule ‘12as’ is read from the xPSSS and ‘type’ and ‘subtype’ keywords for each functional site are listed. These keywords can be used to select a set of atoms. For example, if a keyword ‘CATRES’ exists (probably it does), the command ‘select xps3:CATRES’ selects the corresponding atoms. 
In addition, gene ontology information can be obtained from the xPSSS. The gene ontology information for the molecule 12as is displayed by the command ’show godata’. Similar operations can be applied to other external databases on the Internet provided that the external database supports the interface that jV3 requires. See the section 7 for details.

== Animation ==
The animation of molecules can be performed in jV3. The animation file takes the PDB format, where the MODEL line divides each frame. Let us open an animation file ’http://ef-site.hgc.jp/eF-site/jV/anim.pdb.gz’ as an example from the open-remote dialog shown by selecting the [File] – [Open – Remote] – [Animation] menu item. When an animation file is loaded to the application, the first frame is automatically displayed in the wire frame model. You can start the animation by using the animation-control dialog that is shown by choosing the [Options] – [Animation] menu item. The dialog provides operations such as start and stop of the animation, selection of the animation mode, and adjustment of the speed. Some sample figures of the dialog are shown in the [[GUI#3]]

== Saving your work ==
While in your work, you can create a script file that contains a set of commands that reproduces the current work by using the [File] – [Save] – [Script] menu item. The script file can be loaded by the [File] – [Open – Local] – [Script] menu item. On the other hand, the [File] – [Save] – [PDB] menu item enables to save a molecule to a PDB format file with the coordinates of the atoms being transformed according to the current image. Here, only one molecule must be selected and only selected atoms in the molecule are saved. The other two menu items in the [File] – [Save] menu, [PNG] and [JPEG], save the current screen image to an image file in the PNG and JPEG format, respectively. The created image file has the same size as that of the 3D-display panel in the application.

== Terminating the application ==
The application is terminated when the [File] – [Exit] menu item is chosen or the application window is closed by the way your operation system provides. You can also quit the application by executing ‘exit’ or ‘quit’ command.</text>
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== Starting up ==
It is assumed that Java Runtime Environment and JOGL have been appropriately installed. Once you extract the binary distribution file of jV3, the directory of the name, jV_(version), is generated (Ex. jV_3_6_2). The version is assumed to be 3_6_x hereafter. The application starts up by double-clicking the file ‘jv_3_6_x.jar’ in the jV_3_6_x directory or executing the following command from the command line interface.
 java –jar jv_3_6_x.jar
Figure 1 shows the start-up screen. The window has a 3-panel structure, and the upper-left panel with the black background is a 3D image display area. The status of files that have been loaded to the application is shown in the upper-right panel and the lower panel is a command-input and a message-output area.
[[File:Fig1.jpg|Figure 1 Start-up screen|600px]]

== Displaying molecules ==
If you are working in the environment that is getting on the Internet and know the PDB ID of the molecule that you want to display, the simplest way is as follows. A dialog shown in Figure 2 is opened by selecting the [File] – [Open – Remote] – [PDB ID] menu item. Enter a PDB ID '12as', for example, to the text field and click the 'OK' button, then the PDBML file is read through the Internet and the molecule is displayed. The URL where the PDBML file is retrieved from is specified in the 'properties.txt' file in the jV_3_3_x directory. A molecule is displayed in a wire frame model with colored by atom type in the initial state.

[[File:Fig2.jpg|Dialog to open the molecule specified by PDB ID]]

Let us next attempt to load an arbitrary file on the Internet. Here we use 'http://ef-site.hgc.jp/eF-site/jV/1yec.pdb' as an example. The file is a conventional PDB file whose PDB ID is 1yec. In this case we choose the [File] – [Open – Remote] – [PDB] menu item. Then the open-remote dialog is appeared. Enter the above URL to the text field at the top of the dialog and click the 'OK' button and the molecule is read in and displayed. In jV3, each molecule is displayed according to the space coordination described in its file. Therefore, when loading and displaying more than one molecule together, they can be viewed with an appropriate separation in some cases; however, they may be displayed far separately or may be overlapped depending on the combination. In any case, when adding a new file, the position of the viewpoint is automatically controlled for the whole to be displayed.
The coordinate system is the right hand system with the x-y plane being on the screen (the x-axis is a horizontal line with positive values to the right and the y-axis is a vertical line with positive values up). Although, the above examples are about operations for remote files, a PDB file on your local hard disk can also be opened from the [File] – [Open – Local] – [PDB] menu item.

== Operating molecules ==
Interactive mouse operations are possible for 3D images. By left-dragging the mouse on the 3D-display panel, molecules are rotated around the x-axis or y-axis. By left-dragging the mouse while holding the Shift key or Alt key on the keyboard, molecules are translated along the z-axis. All mouse operations are as follows (as for the Macintosh environment, the Command key + left-drag substitutes for the right-drag).

{| border="1"
 ! Mouse operations !! Actions
 |-
 | Left-drag || The image is rotated around the x (for a vertical motion) and y (for a horizontal motion) axes.
 |-
 | Right-drag || The image is translated on the x-y plane.
 |-
 | [Alt or Shift] + left-drag || The image is translated along the z-axis.
 |-
 | [Alt or Shift] + right-drag || The image is rotated around the z-axis.
 |-
 | [Ctrl] + left-drag || The z-clipping plane is shifted when [Option]-[Slab] is checked.
 |-
 | Left-click || An atom of the molecule displayed on the screen is picked.
 |}

In the upper-right panel in the application window (see Figure 3), the file names that have been loaded to the application are listed, where sequential integers are automatically assigned to the individual file. Each integer is a file ID that can be used to specify the file in the command line interface. In addition, two checkboxes are attached to each file. If you change the status of a ‘display’ checkbox, the corresponding molecule is switched to be displayed or not to be displayed. If you change the status of a ‘select’ checkbox, the corresponding molecule is switched to be a target of the mouse operations or not. For example, set the both ‘display’ checkboxes on, and the both ‘select’ checkboxes off. In this case, either molecule does not move against mouse operations. 
Subsequently set the ‘select’ checkbox of file 1 on. In this case, mouse operations work for the molecule 1. Thus, each file is assigned either selected or not selected, and transform operations, such as rotation or translation, act only on selected files. On the other hand, every atom in a molecule is also assigned either selected or not selected, independently of whether the molecule itself is selected or not. Operations that modify display models or colors work for selected atoms. To see this, choose the [Display] – [Spacefill] menu item. Then the both molecules are displayed with the space fill model because all atoms are initially selected. In the same way, if you choose the [Colors] – [Monochrome] menu item, the both molecules are colored white. These operations are independent of the status of ‘select’ checkboxes mentioned above. 
Let us next try a more detailed operation. Type ‘select *@2’ in the command line area and press Enter key. This command means to select all atoms contained in the file 2 (the usage of the select command is summarized in the reference manual included in the binary distribution of jV3). Subsequently, choose the [Display] – [Cartoon] menu item. As a result, only the molecule 2 is displayed in the cartoon model. Furthermore select the [Colors] – [Structure] menu item, and each residue of the molecule 2 is colored according to its secondary structure type (see Figure 3). 
In order to reproduce the same view as that in Figure 3, first execute ‘reset’ command. It restores the position of the viewpoint and the transform of every file to the initial state. Note that the command line interface tries to complement a command word when the Tab key is pressed. If you enter ‘res’ to the command line and subsequently press the Tab key, the command ‘reset’ is automatically entered. Next set the both ‘select’ checkboxes on, and execute ‘translate z 100’ command. This command means to translate the molecules along the z-axis by 100 angstroms.

[[File:Fig3.jpg|An example of molecular images.|200px]]

== Displaying polygons ==
In addition to molecules, arbitrary shapes described by polygons can be read in and displayed together, where the polygon file is an XML file, whose document type is described in the section 6. Here, we use ’http://ef-site.hgc.jp/eF-site/jV/1yec.surface.gz’ as an example. This polygon file represents a molecular surface of the molecule 2 (1yec) and the surface is colored according to the electrostatic potential and the hydrophobicity. It is assumed that the current image is the same as that in Figure 3. Then, open the open-remote dialog by choosing the [File] – [Open – Remote] – [Polygon] menu item, enter the above URL to the text field at the top of the dialog, and click the 'OK' button. As a result, the polygon is loaded, displayed and assigned file ID 3. 
Note that the polygon is displayed at the different position from the molecule 2 since the molecule 2 is translated. However, because the polygon and the molecule 2 are described by the same coordinates in their files, their images can be exactly superposed by executing ‘fit 3 2’ from the command line, where the ‘fit’ command performs the copy of the transform matrix. Finally, the image in Figure 4 appears.
[[File:Fig4.jpg|An example of polygon images.|600px]]
You can control the transparency rate of polygons. Try ’set transparency 0.5’ from the command line, where 0.5 stands for 50% transparency. To restore the image, execute ‘reset transparency’ or ‘set transparency 0’. In the same sense as each atom of a molecule, each vertex of a polygon is assigned either selected or not selected. All vertices are selected in the initial state. Execute a command ’displayvertex off’ and all vertices become invisible. Next execute ’selectvertex within(10.0, 1&amp;*H@2)’, where this means to select vertices that exist within 10 angstroms from each atom that belongs to the first residue of the ‘H’ chain of the molecule 2. Subsequently execute ’displayvertex on’. As a result, only the selected vertices are appeared. The usage of the selectvertex command is summarized in the reference manual. 

== Working with xPSSS ==
Functional site information on a molecule stored at xPSSS (xml-based Protein Structure Search Service) is available in jV3. Before trying this, let us close the molecule 2 and the polygon 3 to make the situation simple. Select the [File] – [Close] – [2. 1yec.pdb] and [File] – [Close] – [3. 1yec.surface.gz] menu items sequentially. Then execute a ‘reset’ command and the transform of the molecule 1 and the position of the viewpoint are initialized. 
Next, confirm that the ‘select’ checkbox of the file 1 is checked, and try a ‘show xps3’ command. The functional site information of the molecule ‘12as’ is read from the xPSSS and ‘type’ and ‘subtype’ keywords for each functional site are listed. These keywords can be used to select a set of atoms. For example, if a keyword ‘CATRES’ exists (probably it does), the command ‘select xps3:CATRES’ selects the corresponding atoms. 
In addition, gene ontology information can be obtained from the xPSSS. The gene ontology information for the molecule 12as is displayed by the command ’show godata’. Similar operations can be applied to other external databases on the Internet provided that the external database supports the interface that jV3 requires. See the section 7 for details.

== Animation ==
The animation of molecules can be performed in jV3. The animation file takes the PDB format, where the MODEL line divides each frame. Let us open an animation file ’http://ef-site.hgc.jp/eF-site/jV/anim.pdb.gz’ as an example from the open-remote dialog shown by selecting the [File] – [Open – Remote] – [Animation] menu item. When an animation file is loaded to the application, the first frame is automatically displayed in the wire frame model. You can start the animation by using the animation-control dialog that is shown by choosing the [Options] – [Animation] menu item. The dialog provides operations such as start and stop of the animation, selection of the animation mode, and adjustment of the speed. Some sample figures of the dialog are shown in the [[GUI#3]]

== Saving your work ==
While in your work, you can create a script file that contains a set of commands that reproduces the current work by using the [File] – [Save] – [Script] menu item. The script file can be loaded by the [File] – [Open – Local] – [Script] menu item. On the other hand, the [File] – [Save] – [PDB] menu item enables to save a molecule to a PDB format file with the coordinates of the atoms being transformed according to the current image. Here, only one molecule must be selected and only selected atoms in the molecule are saved. The other two menu items in the [File] – [Save] menu, [PNG] and [JPEG], save the current screen image to an image file in the PNG and JPEG format, respectively. The created image file has the same size as that of the 3D-display panel in the application.

== Terminating the application ==
The application is terminated when the [File] – [Exit] menu item is chosen or the application window is closed by the way your operation system provides. You can also quit the application by executing ‘exit’ or ‘quit’ command.</text>
    <sha1>39668eaaf54b69a60a2b47f8a069e1dc38a760d8</sha1>
  </revision>
  <revision>
    <id>193</id>
    <parentid>192</parentid>
    <timestamp>2009-03-09T09:20:58Z</timestamp>
    <contributor>
      <username>JVuser</username>
      <id>2</id>
    </contributor>
    <comment>/* Operating molecules */</comment>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="12125" xml:space="preserve">{| style="float:right"
 |__TOC__
 |}
== Starting up ==
It is assumed that Java Runtime Environment and JOGL have been appropriately installed. Once you extract the binary distribution file of jV3, the directory of the name, jV_(version), is generated (Ex. jV_3_6_2). The version is assumed to be 3_6_x hereafter. The application starts up by double-clicking the file ‘jv_3_6_x.jar’ in the jV_3_6_x directory or executing the following command from the command line interface.
 java –jar jv_3_6_x.jar
Figure 1 shows the start-up screen. The window has a 3-panel structure, and the upper-left panel with the black background is a 3D image display area. The status of files that have been loaded to the application is shown in the upper-right panel and the lower panel is a command-input and a message-output area.
[[File:Fig1.jpg|Figure 1 Start-up screen|600px]]

== Displaying molecules ==
If you are working in the environment that is getting on the Internet and know the PDB ID of the molecule that you want to display, the simplest way is as follows. A dialog shown in Figure 2 is opened by selecting the [File] – [Open – Remote] – [PDB ID] menu item. Enter a PDB ID '12as', for example, to the text field and click the 'OK' button, then the PDBML file is read through the Internet and the molecule is displayed. The URL where the PDBML file is retrieved from is specified in the 'properties.txt' file in the jV_3_3_x directory. A molecule is displayed in a wire frame model with colored by atom type in the initial state.

[[File:Fig2.jpg|Dialog to open the molecule specified by PDB ID]]

Let us next attempt to load an arbitrary file on the Internet. Here we use 'http://ef-site.hgc.jp/eF-site/jV/1yec.pdb' as an example. The file is a conventional PDB file whose PDB ID is 1yec. In this case we choose the [File] – [Open – Remote] – [PDB] menu item. Then the open-remote dialog is appeared. Enter the above URL to the text field at the top of the dialog and click the 'OK' button and the molecule is read in and displayed. In jV3, each molecule is displayed according to the space coordination described in its file. Therefore, when loading and displaying more than one molecule together, they can be viewed with an appropriate separation in some cases; however, they may be displayed far separately or may be overlapped depending on the combination. In any case, when adding a new file, the position of the viewpoint is automatically controlled for the whole to be displayed.
The coordinate system is the right hand system with the x-y plane being on the screen (the x-axis is a horizontal line with positive values to the right and the y-axis is a vertical line with positive values up). Although, the above examples are about operations for remote files, a PDB file on your local hard disk can also be opened from the [File] – [Open – Local] – [PDB] menu item.

== Operating molecules ==
Interactive mouse operations are possible for 3D images. By left-dragging the mouse on the 3D-display panel, molecules are rotated around the x-axis or y-axis. By left-dragging the mouse while holding the Shift key or Alt key on the keyboard, molecules are translated along the z-axis. All mouse operations are as follows (as for the Macintosh environment, the Command key + left-drag substitutes for the right-drag).

{| border="1"
 ! Mouse operations !! Actions
 |-
 | Left-drag || The image is rotated around the x (for a vertical motion) and y (for a horizontal motion) axes.
 |-
 | Right-drag || The image is translated on the x-y plane.
 |-
 | [Alt or Shift] + left-drag || The image is translated along the z-axis.
 |-
 | [Alt or Shift] + right-drag || The image is rotated around the z-axis.
 |-
 | [Ctrl] + left-drag || The z-clipping plane is shifted when [Option]-[Slab] is checked.
 |-
 | Left-click || An atom of the molecule displayed on the screen is picked.
 |}

In the upper-right panel in the application window (see Figure 3), the file names that have been loaded to the application are listed, where sequential integers are automatically assigned to the individual file. Each integer is a file ID that can be used to specify the file in the command line interface. In addition, two checkboxes are attached to each file. If you change the status of a ‘display’ checkbox, the corresponding molecule is switched to be displayed or not to be displayed. If you change the status of a ‘select’ checkbox, the corresponding molecule is switched to be a target of the mouse operations or not. For example, set the both ‘display’ checkboxes on, and the both ‘select’ checkboxes off. In this case, either molecule does not move against mouse operations. 
Subsequently set the ‘select’ checkbox of file 1 on. In this case, mouse operations work for the molecule 1. Thus, each file is assigned either selected or not selected, and transform operations, such as rotation or translation, act only on selected files. On the other hand, every atom in a molecule is also assigned either selected or not selected, independently of whether the molecule itself is selected or not. Operations that modify display models or colors work for selected atoms. To see this, choose the [Display] – [Spacefill] menu item. Then the both molecules are displayed with the space fill model because all atoms are initially selected. In the same way, if you choose the [Colors] – [Monochrome] menu item, the both molecules are colored white. These operations are independent of the status of ‘select’ checkboxes mentioned above. 
Let us next try a more detailed operation. Type ‘select *@2’ in the command line area and press Enter key. This command means to select all atoms contained in the file 2 (the usage of the select command is summarized in the reference manual included in the binary distribution of jV3). Subsequently, choose the [Display] – [Cartoon] menu item. As a result, only the molecule 2 is displayed in the cartoon model. Furthermore select the [Colors] – [Structure] menu item, and each residue of the molecule 2 is colored according to its secondary structure type (see Figure 3). 
In order to reproduce the same view as that in Figure 3, first execute ‘reset’ command. It restores the position of the viewpoint and the transform of every file to the initial state. Note that the command line interface tries to complement a command word when the Tab key is pressed. If you enter ‘res’ to the command line and subsequently press the Tab key, the command ‘reset’ is automatically entered. Next set the both ‘select’ checkboxes on, and execute ‘translate z 100’ command. This command means to translate the molecules along the z-axis by 100 angstroms.

[[File:Fig3.jpg|An example of molecular images.|600px]]

== Displaying polygons ==
In addition to molecules, arbitrary shapes described by polygons can be read in and displayed together, where the polygon file is an XML file, whose document type is described in the section 6. Here, we use ’http://ef-site.hgc.jp/eF-site/jV/1yec.surface.gz’ as an example. This polygon file represents a molecular surface of the molecule 2 (1yec) and the surface is colored according to the electrostatic potential and the hydrophobicity. It is assumed that the current image is the same as that in Figure 3. Then, open the open-remote dialog by choosing the [File] – [Open – Remote] – [Polygon] menu item, enter the above URL to the text field at the top of the dialog, and click the 'OK' button. As a result, the polygon is loaded, displayed and assigned file ID 3. 
Note that the polygon is displayed at the different position from the molecule 2 since the molecule 2 is translated. However, because the polygon and the molecule 2 are described by the same coordinates in their files, their images can be exactly superposed by executing ‘fit 3 2’ from the command line, where the ‘fit’ command performs the copy of the transform matrix. Finally, the image in Figure 4 appears.
[[File:Fig4.jpg|An example of polygon images.|600px]]
You can control the transparency rate of polygons. Try ’set transparency 0.5’ from the command line, where 0.5 stands for 50% transparency. To restore the image, execute ‘reset transparency’ or ‘set transparency 0’. In the same sense as each atom of a molecule, each vertex of a polygon is assigned either selected or not selected. All vertices are selected in the initial state. Execute a command ’displayvertex off’ and all vertices become invisible. Next execute ’selectvertex within(10.0, 1&amp;*H@2)’, where this means to select vertices that exist within 10 angstroms from each atom that belongs to the first residue of the ‘H’ chain of the molecule 2. Subsequently execute ’displayvertex on’. As a result, only the selected vertices are appeared. The usage of the selectvertex command is summarized in the reference manual. 

== Working with xPSSS ==
Functional site information on a molecule stored at xPSSS (xml-based Protein Structure Search Service) is available in jV3. Before trying this, let us close the molecule 2 and the polygon 3 to make the situation simple. Select the [File] – [Close] – [2. 1yec.pdb] and [File] – [Close] – [3. 1yec.surface.gz] menu items sequentially. Then execute a ‘reset’ command and the transform of the molecule 1 and the position of the viewpoint are initialized. 
Next, confirm that the ‘select’ checkbox of the file 1 is checked, and try a ‘show xps3’ command. The functional site information of the molecule ‘12as’ is read from the xPSSS and ‘type’ and ‘subtype’ keywords for each functional site are listed. These keywords can be used to select a set of atoms. For example, if a keyword ‘CATRES’ exists (probably it does), the command ‘select xps3:CATRES’ selects the corresponding atoms. 
In addition, gene ontology information can be obtained from the xPSSS. The gene ontology information for the molecule 12as is displayed by the command ’show godata’. Similar operations can be applied to other external databases on the Internet provided that the external database supports the interface that jV3 requires. See the section 7 for details.

== Animation ==
The animation of molecules can be performed in jV3. The animation file takes the PDB format, where the MODEL line divides each frame. Let us open an animation file ’http://ef-site.hgc.jp/eF-site/jV/anim.pdb.gz’ as an example from the open-remote dialog shown by selecting the [File] – [Open – Remote] – [Animation] menu item. When an animation file is loaded to the application, the first frame is automatically displayed in the wire frame model. You can start the animation by using the animation-control dialog that is shown by choosing the [Options] – [Animation] menu item. The dialog provides operations such as start and stop of the animation, selection of the animation mode, and adjustment of the speed. Some sample figures of the dialog are shown in the [[GUI#3]]

== Saving your work ==
While in your work, you can create a script file that contains a set of commands that reproduces the current work by using the [File] – [Save] – [Script] menu item. The script file can be loaded by the [File] – [Open – Local] – [Script] menu item. On the other hand, the [File] – [Save] – [PDB] menu item enables to save a molecule to a PDB format file with the coordinates of the atoms being transformed according to the current image. Here, only one molecule must be selected and only selected atoms in the molecule are saved. The other two menu items in the [File] – [Save] menu, [PNG] and [JPEG], save the current screen image to an image file in the PNG and JPEG format, respectively. The created image file has the same size as that of the 3D-display panel in the application.

== Terminating the application ==
The application is terminated when the [File] – [Exit] menu item is chosen or the application window is closed by the way your operation system provides. You can also quit the application by executing ‘exit’ or ‘quit’ command.</text>
    <sha1>247e2dd72f4926048aefd52cfc5c51373001994e</sha1>
  </revision>
  <revision>
    <id>194</id>
    <parentid>193</parentid>
    <timestamp>2009-03-09T09:21:30Z</timestamp>
    <contributor>
      <username>JVuser</username>
      <id>2</id>
    </contributor>
    <comment>/* Displaying molecules */</comment>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="12131" xml:space="preserve">{| style="float:right"
 |__TOC__
 |}
== Starting up ==
It is assumed that Java Runtime Environment and JOGL have been appropriately installed. Once you extract the binary distribution file of jV3, the directory of the name, jV_(version), is generated (Ex. jV_3_6_2). The version is assumed to be 3_6_x hereafter. The application starts up by double-clicking the file ‘jv_3_6_x.jar’ in the jV_3_6_x directory or executing the following command from the command line interface.
 java –jar jv_3_6_x.jar
Figure 1 shows the start-up screen. The window has a 3-panel structure, and the upper-left panel with the black background is a 3D image display area. The status of files that have been loaded to the application is shown in the upper-right panel and the lower panel is a command-input and a message-output area.
[[File:Fig1.jpg|Figure 1 Start-up screen|600px]]

== Displaying molecules ==
If you are working in the environment that is getting on the Internet and know the PDB ID of the molecule that you want to display, the simplest way is as follows. A dialog shown in Figure 2 is opened by selecting the [File] – [Open – Remote] – [PDB ID] menu item. Enter a PDB ID '12as', for example, to the text field and click the 'OK' button, then the PDBML file is read through the Internet and the molecule is displayed. The URL where the PDBML file is retrieved from is specified in the 'properties.txt' file in the jV_3_3_x directory. A molecule is displayed in a wire frame model with colored by atom type in the initial state.

[[File:Fig2.jpg|Dialog to open the molecule specified by PDB ID|200px]]

Let us next attempt to load an arbitrary file on the Internet. Here we use 'http://ef-site.hgc.jp/eF-site/jV/1yec.pdb' as an example. The file is a conventional PDB file whose PDB ID is 1yec. In this case we choose the [File] – [Open – Remote] – [PDB] menu item. Then the open-remote dialog is appeared. Enter the above URL to the text field at the top of the dialog and click the 'OK' button and the molecule is read in and displayed. In jV3, each molecule is displayed according to the space coordination described in its file. Therefore, when loading and displaying more than one molecule together, they can be viewed with an appropriate separation in some cases; however, they may be displayed far separately or may be overlapped depending on the combination. In any case, when adding a new file, the position of the viewpoint is automatically controlled for the whole to be displayed.
The coordinate system is the right hand system with the x-y plane being on the screen (the x-axis is a horizontal line with positive values to the right and the y-axis is a vertical line with positive values up). Although, the above examples are about operations for remote files, a PDB file on your local hard disk can also be opened from the [File] – [Open – Local] – [PDB] menu item.

== Operating molecules ==
Interactive mouse operations are possible for 3D images. By left-dragging the mouse on the 3D-display panel, molecules are rotated around the x-axis or y-axis. By left-dragging the mouse while holding the Shift key or Alt key on the keyboard, molecules are translated along the z-axis. All mouse operations are as follows (as for the Macintosh environment, the Command key + left-drag substitutes for the right-drag).

{| border="1"
 ! Mouse operations !! Actions
 |-
 | Left-drag || The image is rotated around the x (for a vertical motion) and y (for a horizontal motion) axes.
 |-
 | Right-drag || The image is translated on the x-y plane.
 |-
 | [Alt or Shift] + left-drag || The image is translated along the z-axis.
 |-
 | [Alt or Shift] + right-drag || The image is rotated around the z-axis.
 |-
 | [Ctrl] + left-drag || The z-clipping plane is shifted when [Option]-[Slab] is checked.
 |-
 | Left-click || An atom of the molecule displayed on the screen is picked.
 |}

In the upper-right panel in the application window (see Figure 3), the file names that have been loaded to the application are listed, where sequential integers are automatically assigned to the individual file. Each integer is a file ID that can be used to specify the file in the command line interface. In addition, two checkboxes are attached to each file. If you change the status of a ‘display’ checkbox, the corresponding molecule is switched to be displayed or not to be displayed. If you change the status of a ‘select’ checkbox, the corresponding molecule is switched to be a target of the mouse operations or not. For example, set the both ‘display’ checkboxes on, and the both ‘select’ checkboxes off. In this case, either molecule does not move against mouse operations. 
Subsequently set the ‘select’ checkbox of file 1 on. In this case, mouse operations work for the molecule 1. Thus, each file is assigned either selected or not selected, and transform operations, such as rotation or translation, act only on selected files. On the other hand, every atom in a molecule is also assigned either selected or not selected, independently of whether the molecule itself is selected or not. Operations that modify display models or colors work for selected atoms. To see this, choose the [Display] – [Spacefill] menu item. Then the both molecules are displayed with the space fill model because all atoms are initially selected. In the same way, if you choose the [Colors] – [Monochrome] menu item, the both molecules are colored white. These operations are independent of the status of ‘select’ checkboxes mentioned above. 
Let us next try a more detailed operation. Type ‘select *@2’ in the command line area and press Enter key. This command means to select all atoms contained in the file 2 (the usage of the select command is summarized in the reference manual included in the binary distribution of jV3). Subsequently, choose the [Display] – [Cartoon] menu item. As a result, only the molecule 2 is displayed in the cartoon model. Furthermore select the [Colors] – [Structure] menu item, and each residue of the molecule 2 is colored according to its secondary structure type (see Figure 3). 
In order to reproduce the same view as that in Figure 3, first execute ‘reset’ command. It restores the position of the viewpoint and the transform of every file to the initial state. Note that the command line interface tries to complement a command word when the Tab key is pressed. If you enter ‘res’ to the command line and subsequently press the Tab key, the command ‘reset’ is automatically entered. Next set the both ‘select’ checkboxes on, and execute ‘translate z 100’ command. This command means to translate the molecules along the z-axis by 100 angstroms.

[[File:Fig3.jpg|An example of molecular images.|600px]]

== Displaying polygons ==
In addition to molecules, arbitrary shapes described by polygons can be read in and displayed together, where the polygon file is an XML file, whose document type is described in the section 6. Here, we use ’http://ef-site.hgc.jp/eF-site/jV/1yec.surface.gz’ as an example. This polygon file represents a molecular surface of the molecule 2 (1yec) and the surface is colored according to the electrostatic potential and the hydrophobicity. It is assumed that the current image is the same as that in Figure 3. Then, open the open-remote dialog by choosing the [File] – [Open – Remote] – [Polygon] menu item, enter the above URL to the text field at the top of the dialog, and click the 'OK' button. As a result, the polygon is loaded, displayed and assigned file ID 3. 
Note that the polygon is displayed at the different position from the molecule 2 since the molecule 2 is translated. However, because the polygon and the molecule 2 are described by the same coordinates in their files, their images can be exactly superposed by executing ‘fit 3 2’ from the command line, where the ‘fit’ command performs the copy of the transform matrix. Finally, the image in Figure 4 appears.
[[File:Fig4.jpg|An example of polygon images.|600px]]
You can control the transparency rate of polygons. Try ’set transparency 0.5’ from the command line, where 0.5 stands for 50% transparency. To restore the image, execute ‘reset transparency’ or ‘set transparency 0’. In the same sense as each atom of a molecule, each vertex of a polygon is assigned either selected or not selected. All vertices are selected in the initial state. Execute a command ’displayvertex off’ and all vertices become invisible. Next execute ’selectvertex within(10.0, 1&amp;*H@2)’, where this means to select vertices that exist within 10 angstroms from each atom that belongs to the first residue of the ‘H’ chain of the molecule 2. Subsequently execute ’displayvertex on’. As a result, only the selected vertices are appeared. The usage of the selectvertex command is summarized in the reference manual. 

== Working with xPSSS ==
Functional site information on a molecule stored at xPSSS (xml-based Protein Structure Search Service) is available in jV3. Before trying this, let us close the molecule 2 and the polygon 3 to make the situation simple. Select the [File] – [Close] – [2. 1yec.pdb] and [File] – [Close] – [3. 1yec.surface.gz] menu items sequentially. Then execute a ‘reset’ command and the transform of the molecule 1 and the position of the viewpoint are initialized. 
Next, confirm that the ‘select’ checkbox of the file 1 is checked, and try a ‘show xps3’ command. The functional site information of the molecule ‘12as’ is read from the xPSSS and ‘type’ and ‘subtype’ keywords for each functional site are listed. These keywords can be used to select a set of atoms. For example, if a keyword ‘CATRES’ exists (probably it does), the command ‘select xps3:CATRES’ selects the corresponding atoms. 
In addition, gene ontology information can be obtained from the xPSSS. The gene ontology information for the molecule 12as is displayed by the command ’show godata’. Similar operations can be applied to other external databases on the Internet provided that the external database supports the interface that jV3 requires. See the section 7 for details.

== Animation ==
The animation of molecules can be performed in jV3. The animation file takes the PDB format, where the MODEL line divides each frame. Let us open an animation file ’http://ef-site.hgc.jp/eF-site/jV/anim.pdb.gz’ as an example from the open-remote dialog shown by selecting the [File] – [Open – Remote] – [Animation] menu item. When an animation file is loaded to the application, the first frame is automatically displayed in the wire frame model. You can start the animation by using the animation-control dialog that is shown by choosing the [Options] – [Animation] menu item. The dialog provides operations such as start and stop of the animation, selection of the animation mode, and adjustment of the speed. Some sample figures of the dialog are shown in the [[GUI#3]]

== Saving your work ==
While in your work, you can create a script file that contains a set of commands that reproduces the current work by using the [File] – [Save] – [Script] menu item. The script file can be loaded by the [File] – [Open – Local] – [Script] menu item. On the other hand, the [File] – [Save] – [PDB] menu item enables to save a molecule to a PDB format file with the coordinates of the atoms being transformed according to the current image. Here, only one molecule must be selected and only selected atoms in the molecule are saved. The other two menu items in the [File] – [Save] menu, [PNG] and [JPEG], save the current screen image to an image file in the PNG and JPEG format, respectively. The created image file has the same size as that of the 3D-display panel in the application.

== Terminating the application ==
The application is terminated when the [File] – [Exit] menu item is chosen or the application window is closed by the way your operation system provides. You can also quit the application by executing ‘exit’ or ‘quit’ command.</text>
    <sha1>d93d3fa061b7926d0a236d930bd47435cd84f369</sha1>
  </revision>
  <revision>
    <id>195</id>
    <parentid>194</parentid>
    <timestamp>2009-03-09T09:21:46Z</timestamp>
    <contributor>
      <username>JVuser</username>
      <id>2</id>
    </contributor>
    <comment>/* Displaying polygons */</comment>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="12132" xml:space="preserve">{| style="float:right"
 |__TOC__
 |}
== Starting up ==
It is assumed that Java Runtime Environment and JOGL have been appropriately installed. Once you extract the binary distribution file of jV3, the directory of the name, jV_(version), is generated (Ex. jV_3_6_2). The version is assumed to be 3_6_x hereafter. The application starts up by double-clicking the file ‘jv_3_6_x.jar’ in the jV_3_6_x directory or executing the following command from the command line interface.
 java –jar jv_3_6_x.jar
Figure 1 shows the start-up screen. The window has a 3-panel structure, and the upper-left panel with the black background is a 3D image display area. The status of files that have been loaded to the application is shown in the upper-right panel and the lower panel is a command-input and a message-output area.
[[File:Fig1.jpg|Figure 1 Start-up screen|600px]]

== Displaying molecules ==
If you are working in the environment that is getting on the Internet and know the PDB ID of the molecule that you want to display, the simplest way is as follows. A dialog shown in Figure 2 is opened by selecting the [File] – [Open – Remote] – [PDB ID] menu item. Enter a PDB ID '12as', for example, to the text field and click the 'OK' button, then the PDBML file is read through the Internet and the molecule is displayed. The URL where the PDBML file is retrieved from is specified in the 'properties.txt' file in the jV_3_3_x directory. A molecule is displayed in a wire frame model with colored by atom type in the initial state.

[[File:Fig2.jpg|Dialog to open the molecule specified by PDB ID|200px]]

Let us next attempt to load an arbitrary file on the Internet. Here we use 'http://ef-site.hgc.jp/eF-site/jV/1yec.pdb' as an example. The file is a conventional PDB file whose PDB ID is 1yec. In this case we choose the [File] – [Open – Remote] – [PDB] menu item. Then the open-remote dialog is appeared. Enter the above URL to the text field at the top of the dialog and click the 'OK' button and the molecule is read in and displayed. In jV3, each molecule is displayed according to the space coordination described in its file. Therefore, when loading and displaying more than one molecule together, they can be viewed with an appropriate separation in some cases; however, they may be displayed far separately or may be overlapped depending on the combination. In any case, when adding a new file, the position of the viewpoint is automatically controlled for the whole to be displayed.
The coordinate system is the right hand system with the x-y plane being on the screen (the x-axis is a horizontal line with positive values to the right and the y-axis is a vertical line with positive values up). Although, the above examples are about operations for remote files, a PDB file on your local hard disk can also be opened from the [File] – [Open – Local] – [PDB] menu item.

== Operating molecules ==
Interactive mouse operations are possible for 3D images. By left-dragging the mouse on the 3D-display panel, molecules are rotated around the x-axis or y-axis. By left-dragging the mouse while holding the Shift key or Alt key on the keyboard, molecules are translated along the z-axis. All mouse operations are as follows (as for the Macintosh environment, the Command key + left-drag substitutes for the right-drag).

{| border="1"
 ! Mouse operations !! Actions
 |-
 | Left-drag || The image is rotated around the x (for a vertical motion) and y (for a horizontal motion) axes.
 |-
 | Right-drag || The image is translated on the x-y plane.
 |-
 | [Alt or Shift] + left-drag || The image is translated along the z-axis.
 |-
 | [Alt or Shift] + right-drag || The image is rotated around the z-axis.
 |-
 | [Ctrl] + left-drag || The z-clipping plane is shifted when [Option]-[Slab] is checked.
 |-
 | Left-click || An atom of the molecule displayed on the screen is picked.
 |}

In the upper-right panel in the application window (see Figure 3), the file names that have been loaded to the application are listed, where sequential integers are automatically assigned to the individual file. Each integer is a file ID that can be used to specify the file in the command line interface. In addition, two checkboxes are attached to each file. If you change the status of a ‘display’ checkbox, the corresponding molecule is switched to be displayed or not to be displayed. If you change the status of a ‘select’ checkbox, the corresponding molecule is switched to be a target of the mouse operations or not. For example, set the both ‘display’ checkboxes on, and the both ‘select’ checkboxes off. In this case, either molecule does not move against mouse operations. 
Subsequently set the ‘select’ checkbox of file 1 on. In this case, mouse operations work for the molecule 1. Thus, each file is assigned either selected or not selected, and transform operations, such as rotation or translation, act only on selected files. On the other hand, every atom in a molecule is also assigned either selected or not selected, independently of whether the molecule itself is selected or not. Operations that modify display models or colors work for selected atoms. To see this, choose the [Display] – [Spacefill] menu item. Then the both molecules are displayed with the space fill model because all atoms are initially selected. In the same way, if you choose the [Colors] – [Monochrome] menu item, the both molecules are colored white. These operations are independent of the status of ‘select’ checkboxes mentioned above. 
Let us next try a more detailed operation. Type ‘select *@2’ in the command line area and press Enter key. This command means to select all atoms contained in the file 2 (the usage of the select command is summarized in the reference manual included in the binary distribution of jV3). Subsequently, choose the [Display] – [Cartoon] menu item. As a result, only the molecule 2 is displayed in the cartoon model. Furthermore select the [Colors] – [Structure] menu item, and each residue of the molecule 2 is colored according to its secondary structure type (see Figure 3). 
In order to reproduce the same view as that in Figure 3, first execute ‘reset’ command. It restores the position of the viewpoint and the transform of every file to the initial state. Note that the command line interface tries to complement a command word when the Tab key is pressed. If you enter ‘res’ to the command line and subsequently press the Tab key, the command ‘reset’ is automatically entered. Next set the both ‘select’ checkboxes on, and execute ‘translate z 100’ command. This command means to translate the molecules along the z-axis by 100 angstroms.

[[File:Fig3.jpg|An example of molecular images.|600px]]

== Displaying polygons ==
In addition to molecules, arbitrary shapes described by polygons can be read in and displayed together, where the polygon file is an XML file, whose document type is described in the section 6. Here, we use ’http://ef-site.hgc.jp/eF-site/jV/1yec.surface.gz’ as an example. This polygon file represents a molecular surface of the molecule 2 (1yec) and the surface is colored according to the electrostatic potential and the hydrophobicity. It is assumed that the current image is the same as that in Figure 3. Then, open the open-remote dialog by choosing the [File] – [Open – Remote] – [Polygon] menu item, enter the above URL to the text field at the top of the dialog, and click the 'OK' button. As a result, the polygon is loaded, displayed and assigned file ID 3. 
Note that the polygon is displayed at the different position from the molecule 2 since the molecule 2 is translated. However, because the polygon and the molecule 2 are described by the same coordinates in their files, their images can be exactly superposed by executing ‘fit 3 2’ from the command line, where the ‘fit’ command performs the copy of the transform matrix. Finally, the image in Figure 4 appears.

[[File:Fig4.jpg|An example of polygon images.|600px]]

You can control the transparency rate of polygons. Try ’set transparency 0.5’ from the command line, where 0.5 stands for 50% transparency. To restore the image, execute ‘reset transparency’ or ‘set transparency 0’. In the same sense as each atom of a molecule, each vertex of a polygon is assigned either selected or not selected. All vertices are selected in the initial state. Execute a command ’displayvertex off’ and all vertices become invisible. Next execute ’selectvertex within(10.0, 1&amp;*H@2)’, where this means to select vertices that exist within 10 angstroms from each atom that belongs to the first residue of the ‘H’ chain of the molecule 2. Subsequently execute ’displayvertex on’. As a result, only the selected vertices are appeared. The usage of the selectvertex command is summarized in the reference manual.

== Working with xPSSS ==
Functional site information on a molecule stored at xPSSS (xml-based Protein Structure Search Service) is available in jV3. Before trying this, let us close the molecule 2 and the polygon 3 to make the situation simple. Select the [File] – [Close] – [2. 1yec.pdb] and [File] – [Close] – [3. 1yec.surface.gz] menu items sequentially. Then execute a ‘reset’ command and the transform of the molecule 1 and the position of the viewpoint are initialized. 
Next, confirm that the ‘select’ checkbox of the file 1 is checked, and try a ‘show xps3’ command. The functional site information of the molecule ‘12as’ is read from the xPSSS and ‘type’ and ‘subtype’ keywords for each functional site are listed. These keywords can be used to select a set of atoms. For example, if a keyword ‘CATRES’ exists (probably it does), the command ‘select xps3:CATRES’ selects the corresponding atoms. 
In addition, gene ontology information can be obtained from the xPSSS. The gene ontology information for the molecule 12as is displayed by the command ’show godata’. Similar operations can be applied to other external databases on the Internet provided that the external database supports the interface that jV3 requires. See the section 7 for details.

== Animation ==
The animation of molecules can be performed in jV3. The animation file takes the PDB format, where the MODEL line divides each frame. Let us open an animation file ’http://ef-site.hgc.jp/eF-site/jV/anim.pdb.gz’ as an example from the open-remote dialog shown by selecting the [File] – [Open – Remote] – [Animation] menu item. When an animation file is loaded to the application, the first frame is automatically displayed in the wire frame model. You can start the animation by using the animation-control dialog that is shown by choosing the [Options] – [Animation] menu item. The dialog provides operations such as start and stop of the animation, selection of the animation mode, and adjustment of the speed. Some sample figures of the dialog are shown in the [[GUI#3]]

== Saving your work ==
While in your work, you can create a script file that contains a set of commands that reproduces the current work by using the [File] – [Save] – [Script] menu item. The script file can be loaded by the [File] – [Open – Local] – [Script] menu item. On the other hand, the [File] – [Save] – [PDB] menu item enables to save a molecule to a PDB format file with the coordinates of the atoms being transformed according to the current image. Here, only one molecule must be selected and only selected atoms in the molecule are saved. The other two menu items in the [File] – [Save] menu, [PNG] and [JPEG], save the current screen image to an image file in the PNG and JPEG format, respectively. The created image file has the same size as that of the 3D-display panel in the application.

== Terminating the application ==
The application is terminated when the [File] – [Exit] menu item is chosen or the application window is closed by the way your operation system provides. You can also quit the application by executing ‘exit’ or ‘quit’ command.</text>
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  </revision>
  <revision>
    <id>196</id>
    <parentid>195</parentid>
    <timestamp>2009-03-09T09:23:09Z</timestamp>
    <contributor>
      <username>JVuser</username>
      <id>2</id>
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    <text bytes="12160" xml:space="preserve">{| style="float:right"
 |__TOC__
 |}
== Starting up ==
It is assumed that Java Runtime Environment and JOGL have been appropriately installed. Once you extract the binary distribution file of jV3, the directory of the name, jV_(version), is generated (Ex. jV_3_6_2). The version is assumed to be 3_6_x hereafter. The application starts up by double-clicking the file ‘jv_3_6_x.jar’ in the jV_3_6_x directory or executing the following command from the command line interface.
 java –jar jv_3_6_x.jar
Figure 1 shows the start-up screen. The window has a 3-panel structure, and the upper-left panel with the black background is a 3D image display area. The status of files that have been loaded to the application is shown in the upper-right panel and the lower panel is a command-input and a message-output area.
[[File:Fig1.jpg|Figure 1 Start-up screen|center|600px]]

== Displaying molecules ==
If you are working in the environment that is getting on the Internet and know the PDB ID of the molecule that you want to display, the simplest way is as follows. A dialog shown in Figure 2 is opened by selecting the [File] – [Open – Remote] – [PDB ID] menu item. Enter a PDB ID '12as', for example, to the text field and click the 'OK' button, then the PDBML file is read through the Internet and the molecule is displayed. The URL where the PDBML file is retrieved from is specified in the 'properties.txt' file in the jV_3_3_x directory. A molecule is displayed in a wire frame model with colored by atom type in the initial state.

[[File:Fig2.jpg|Dialog to open the molecule specified by PDB ID|center|200px]]

Let us next attempt to load an arbitrary file on the Internet. Here we use 'http://ef-site.hgc.jp/eF-site/jV/1yec.pdb' as an example. The file is a conventional PDB file whose PDB ID is 1yec. In this case we choose the [File] – [Open – Remote] – [PDB] menu item. Then the open-remote dialog is appeared. Enter the above URL to the text field at the top of the dialog and click the 'OK' button and the molecule is read in and displayed. In jV3, each molecule is displayed according to the space coordination described in its file. Therefore, when loading and displaying more than one molecule together, they can be viewed with an appropriate separation in some cases; however, they may be displayed far separately or may be overlapped depending on the combination. In any case, when adding a new file, the position of the viewpoint is automatically controlled for the whole to be displayed.
The coordinate system is the right hand system with the x-y plane being on the screen (the x-axis is a horizontal line with positive values to the right and the y-axis is a vertical line with positive values up). Although, the above examples are about operations for remote files, a PDB file on your local hard disk can also be opened from the [File] – [Open – Local] – [PDB] menu item.

== Operating molecules ==
Interactive mouse operations are possible for 3D images. By left-dragging the mouse on the 3D-display panel, molecules are rotated around the x-axis or y-axis. By left-dragging the mouse while holding the Shift key or Alt key on the keyboard, molecules are translated along the z-axis. All mouse operations are as follows (as for the Macintosh environment, the Command key + left-drag substitutes for the right-drag).

{| border="1"
 ! Mouse operations !! Actions
 |-
 | Left-drag || The image is rotated around the x (for a vertical motion) and y (for a horizontal motion) axes.
 |-
 | Right-drag || The image is translated on the x-y plane.
 |-
 | [Alt or Shift] + left-drag || The image is translated along the z-axis.
 |-
 | [Alt or Shift] + right-drag || The image is rotated around the z-axis.
 |-
 | [Ctrl] + left-drag || The z-clipping plane is shifted when [Option]-[Slab] is checked.
 |-
 | Left-click || An atom of the molecule displayed on the screen is picked.
 |}

In the upper-right panel in the application window (see Figure 3), the file names that have been loaded to the application are listed, where sequential integers are automatically assigned to the individual file. Each integer is a file ID that can be used to specify the file in the command line interface. In addition, two checkboxes are attached to each file. If you change the status of a ‘display’ checkbox, the corresponding molecule is switched to be displayed or not to be displayed. If you change the status of a ‘select’ checkbox, the corresponding molecule is switched to be a target of the mouse operations or not. For example, set the both ‘display’ checkboxes on, and the both ‘select’ checkboxes off. In this case, either molecule does not move against mouse operations. 
Subsequently set the ‘select’ checkbox of file 1 on. In this case, mouse operations work for the molecule 1. Thus, each file is assigned either selected or not selected, and transform operations, such as rotation or translation, act only on selected files. On the other hand, every atom in a molecule is also assigned either selected or not selected, independently of whether the molecule itself is selected or not. Operations that modify display models or colors work for selected atoms. To see this, choose the [Display] – [Spacefill] menu item. Then the both molecules are displayed with the space fill model because all atoms are initially selected. In the same way, if you choose the [Colors] – [Monochrome] menu item, the both molecules are colored white. These operations are independent of the status of ‘select’ checkboxes mentioned above. 
Let us next try a more detailed operation. Type ‘select *@2’ in the command line area and press Enter key. This command means to select all atoms contained in the file 2 (the usage of the select command is summarized in the reference manual included in the binary distribution of jV3). Subsequently, choose the [Display] – [Cartoon] menu item. As a result, only the molecule 2 is displayed in the cartoon model. Furthermore select the [Colors] – [Structure] menu item, and each residue of the molecule 2 is colored according to its secondary structure type (see Figure 3). 
In order to reproduce the same view as that in Figure 3, first execute ‘reset’ command. It restores the position of the viewpoint and the transform of every file to the initial state. Note that the command line interface tries to complement a command word when the Tab key is pressed. If you enter ‘res’ to the command line and subsequently press the Tab key, the command ‘reset’ is automatically entered. Next set the both ‘select’ checkboxes on, and execute ‘translate z 100’ command. This command means to translate the molecules along the z-axis by 100 angstroms.

[[File:Fig3.jpg|An example of molecular images.|center|600px]]

== Displaying polygons ==
In addition to molecules, arbitrary shapes described by polygons can be read in and displayed together, where the polygon file is an XML file, whose document type is described in the section 6. Here, we use ’http://ef-site.hgc.jp/eF-site/jV/1yec.surface.gz’ as an example. This polygon file represents a molecular surface of the molecule 2 (1yec) and the surface is colored according to the electrostatic potential and the hydrophobicity. It is assumed that the current image is the same as that in Figure 3. Then, open the open-remote dialog by choosing the [File] – [Open – Remote] – [Polygon] menu item, enter the above URL to the text field at the top of the dialog, and click the 'OK' button. As a result, the polygon is loaded, displayed and assigned file ID 3. 
Note that the polygon is displayed at the different position from the molecule 2 since the molecule 2 is translated. However, because the polygon and the molecule 2 are described by the same coordinates in their files, their images can be exactly superposed by executing ‘fit 3 2’ from the command line, where the ‘fit’ command performs the copy of the transform matrix. Finally, the image in Figure 4 appears.

[[File:Fig4.jpg|An example of polygon images.|center|600px]]

You can control the transparency rate of polygons. Try ’set transparency 0.5’ from the command line, where 0.5 stands for 50% transparency. To restore the image, execute ‘reset transparency’ or ‘set transparency 0’. In the same sense as each atom of a molecule, each vertex of a polygon is assigned either selected or not selected. All vertices are selected in the initial state. Execute a command ’displayvertex off’ and all vertices become invisible. Next execute ’selectvertex within(10.0, 1&amp;*H@2)’, where this means to select vertices that exist within 10 angstroms from each atom that belongs to the first residue of the ‘H’ chain of the molecule 2. Subsequently execute ’displayvertex on’. As a result, only the selected vertices are appeared. The usage of the selectvertex command is summarized in the reference manual.

== Working with xPSSS ==
Functional site information on a molecule stored at xPSSS (xml-based Protein Structure Search Service) is available in jV3. Before trying this, let us close the molecule 2 and the polygon 3 to make the situation simple. Select the [File] – [Close] – [2. 1yec.pdb] and [File] – [Close] – [3. 1yec.surface.gz] menu items sequentially. Then execute a ‘reset’ command and the transform of the molecule 1 and the position of the viewpoint are initialized. 
Next, confirm that the ‘select’ checkbox of the file 1 is checked, and try a ‘show xps3’ command. The functional site information of the molecule ‘12as’ is read from the xPSSS and ‘type’ and ‘subtype’ keywords for each functional site are listed. These keywords can be used to select a set of atoms. For example, if a keyword ‘CATRES’ exists (probably it does), the command ‘select xps3:CATRES’ selects the corresponding atoms. 
In addition, gene ontology information can be obtained from the xPSSS. The gene ontology information for the molecule 12as is displayed by the command ’show godata’. Similar operations can be applied to other external databases on the Internet provided that the external database supports the interface that jV3 requires. See the section 7 for details.

== Animation ==
The animation of molecules can be performed in jV3. The animation file takes the PDB format, where the MODEL line divides each frame. Let us open an animation file ’http://ef-site.hgc.jp/eF-site/jV/anim.pdb.gz’ as an example from the open-remote dialog shown by selecting the [File] – [Open – Remote] – [Animation] menu item. When an animation file is loaded to the application, the first frame is automatically displayed in the wire frame model. You can start the animation by using the animation-control dialog that is shown by choosing the [Options] – [Animation] menu item. The dialog provides operations such as start and stop of the animation, selection of the animation mode, and adjustment of the speed. Some sample figures of the dialog are shown in the [[GUI#3]]

== Saving your work ==
While in your work, you can create a script file that contains a set of commands that reproduces the current work by using the [File] – [Save] – [Script] menu item. The script file can be loaded by the [File] – [Open – Local] – [Script] menu item. On the other hand, the [File] – [Save] – [PDB] menu item enables to save a molecule to a PDB format file with the coordinates of the atoms being transformed according to the current image. Here, only one molecule must be selected and only selected atoms in the molecule are saved. The other two menu items in the [File] – [Save] menu, [PNG] and [JPEG], save the current screen image to an image file in the PNG and JPEG format, respectively. The created image file has the same size as that of the 3D-display panel in the application.

== Terminating the application ==
The application is terminated when the [File] – [Exit] menu item is chosen or the application window is closed by the way your operation system provides. You can also quit the application by executing ‘exit’ or ‘quit’ command.</text>
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    <parentid>196</parentid>
    <timestamp>2009-03-09T09:24:23Z</timestamp>
    <contributor>
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    <comment>/* Working with xPSSS */</comment>
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    <text bytes="12196" xml:space="preserve">{| style="float:right"
 |__TOC__
 |}
== Starting up ==
It is assumed that Java Runtime Environment and JOGL have been appropriately installed. Once you extract the binary distribution file of jV3, the directory of the name, jV_(version), is generated (Ex. jV_3_6_2). The version is assumed to be 3_6_x hereafter. The application starts up by double-clicking the file ‘jv_3_6_x.jar’ in the jV_3_6_x directory or executing the following command from the command line interface.
 java –jar jv_3_6_x.jar
Figure 1 shows the start-up screen. The window has a 3-panel structure, and the upper-left panel with the black background is a 3D image display area. The status of files that have been loaded to the application is shown in the upper-right panel and the lower panel is a command-input and a message-output area.
[[File:Fig1.jpg|Figure 1 Start-up screen|center|600px]]

== Displaying molecules ==
If you are working in the environment that is getting on the Internet and know the PDB ID of the molecule that you want to display, the simplest way is as follows. A dialog shown in Figure 2 is opened by selecting the [File] – [Open – Remote] – [PDB ID] menu item. Enter a PDB ID '12as', for example, to the text field and click the 'OK' button, then the PDBML file is read through the Internet and the molecule is displayed. The URL where the PDBML file is retrieved from is specified in the 'properties.txt' file in the jV_3_3_x directory. A molecule is displayed in a wire frame model with colored by atom type in the initial state.

[[File:Fig2.jpg|Dialog to open the molecule specified by PDB ID|center|200px]]

Let us next attempt to load an arbitrary file on the Internet. Here we use 'http://ef-site.hgc.jp/eF-site/jV/1yec.pdb' as an example. The file is a conventional PDB file whose PDB ID is 1yec. In this case we choose the [File] – [Open – Remote] – [PDB] menu item. Then the open-remote dialog is appeared. Enter the above URL to the text field at the top of the dialog and click the 'OK' button and the molecule is read in and displayed. In jV3, each molecule is displayed according to the space coordination described in its file. Therefore, when loading and displaying more than one molecule together, they can be viewed with an appropriate separation in some cases; however, they may be displayed far separately or may be overlapped depending on the combination. In any case, when adding a new file, the position of the viewpoint is automatically controlled for the whole to be displayed.
The coordinate system is the right hand system with the x-y plane being on the screen (the x-axis is a horizontal line with positive values to the right and the y-axis is a vertical line with positive values up). Although, the above examples are about operations for remote files, a PDB file on your local hard disk can also be opened from the [File] – [Open – Local] – [PDB] menu item.

== Operating molecules ==
Interactive mouse operations are possible for 3D images. By left-dragging the mouse on the 3D-display panel, molecules are rotated around the x-axis or y-axis. By left-dragging the mouse while holding the Shift key or Alt key on the keyboard, molecules are translated along the z-axis. All mouse operations are as follows (as for the Macintosh environment, the Command key + left-drag substitutes for the right-drag).

{| border="1"
 ! Mouse operations !! Actions
 |-
 | Left-drag || The image is rotated around the x (for a vertical motion) and y (for a horizontal motion) axes.
 |-
 | Right-drag || The image is translated on the x-y plane.
 |-
 | [Alt or Shift] + left-drag || The image is translated along the z-axis.
 |-
 | [Alt or Shift] + right-drag || The image is rotated around the z-axis.
 |-
 | [Ctrl] + left-drag || The z-clipping plane is shifted when [Option]-[Slab] is checked.
 |-
 | Left-click || An atom of the molecule displayed on the screen is picked.
 |}

In the upper-right panel in the application window (see Figure 3), the file names that have been loaded to the application are listed, where sequential integers are automatically assigned to the individual file. Each integer is a file ID that can be used to specify the file in the command line interface. In addition, two checkboxes are attached to each file. If you change the status of a ‘display’ checkbox, the corresponding molecule is switched to be displayed or not to be displayed. If you change the status of a ‘select’ checkbox, the corresponding molecule is switched to be a target of the mouse operations or not. For example, set the both ‘display’ checkboxes on, and the both ‘select’ checkboxes off. In this case, either molecule does not move against mouse operations. 
Subsequently set the ‘select’ checkbox of file 1 on. In this case, mouse operations work for the molecule 1. Thus, each file is assigned either selected or not selected, and transform operations, such as rotation or translation, act only on selected files. On the other hand, every atom in a molecule is also assigned either selected or not selected, independently of whether the molecule itself is selected or not. Operations that modify display models or colors work for selected atoms. To see this, choose the [Display] – [Spacefill] menu item. Then the both molecules are displayed with the space fill model because all atoms are initially selected. In the same way, if you choose the [Colors] – [Monochrome] menu item, the both molecules are colored white. These operations are independent of the status of ‘select’ checkboxes mentioned above. 
Let us next try a more detailed operation. Type ‘select *@2’ in the command line area and press Enter key. This command means to select all atoms contained in the file 2 (the usage of the select command is summarized in the reference manual included in the binary distribution of jV3). Subsequently, choose the [Display] – [Cartoon] menu item. As a result, only the molecule 2 is displayed in the cartoon model. Furthermore select the [Colors] – [Structure] menu item, and each residue of the molecule 2 is colored according to its secondary structure type (see Figure 3). 
In order to reproduce the same view as that in Figure 3, first execute ‘reset’ command. It restores the position of the viewpoint and the transform of every file to the initial state. Note that the command line interface tries to complement a command word when the Tab key is pressed. If you enter ‘res’ to the command line and subsequently press the Tab key, the command ‘reset’ is automatically entered. Next set the both ‘select’ checkboxes on, and execute ‘translate z 100’ command. This command means to translate the molecules along the z-axis by 100 angstroms.

[[File:Fig3.jpg|An example of molecular images.|center|600px]]

== Displaying polygons ==
In addition to molecules, arbitrary shapes described by polygons can be read in and displayed together, where the polygon file is an XML file, whose document type is described in the section 6. Here, we use ’http://ef-site.hgc.jp/eF-site/jV/1yec.surface.gz’ as an example. This polygon file represents a molecular surface of the molecule 2 (1yec) and the surface is colored according to the electrostatic potential and the hydrophobicity. It is assumed that the current image is the same as that in Figure 3. Then, open the open-remote dialog by choosing the [File] – [Open – Remote] – [Polygon] menu item, enter the above URL to the text field at the top of the dialog, and click the 'OK' button. As a result, the polygon is loaded, displayed and assigned file ID 3. 
Note that the polygon is displayed at the different position from the molecule 2 since the molecule 2 is translated. However, because the polygon and the molecule 2 are described by the same coordinates in their files, their images can be exactly superposed by executing ‘fit 3 2’ from the command line, where the ‘fit’ command performs the copy of the transform matrix. Finally, the image in Figure 4 appears.

[[File:Fig4.jpg|An example of polygon images.|center|600px]]

You can control the transparency rate of polygons. Try ’set transparency 0.5’ from the command line, where 0.5 stands for 50% transparency. To restore the image, execute ‘reset transparency’ or ‘set transparency 0’. In the same sense as each atom of a molecule, each vertex of a polygon is assigned either selected or not selected. All vertices are selected in the initial state. Execute a command ’displayvertex off’ and all vertices become invisible. Next execute ’selectvertex within(10.0, 1&amp;*H@2)’, where this means to select vertices that exist within 10 angstroms from each atom that belongs to the first residue of the ‘H’ chain of the molecule 2. Subsequently execute ’displayvertex on’. As a result, only the selected vertices are appeared. The usage of the selectvertex command is summarized in the reference manual.

== Working with xPSSS ==
Functional site information on a molecule stored at xPSSS (xml-based Protein Structure Search Service) is available in jV3. Before trying this, let us close the molecule 2 and the polygon 3 to make the situation simple. Select the [File] – [Close] – [2. 1yec.pdb] and [File] – [Close] – [3. 1yec.surface.gz] menu items sequentially. Then execute a ‘reset’ command and the transform of the molecule 1 and the position of the viewpoint are initialized. 
Next, confirm that the ‘select’ checkbox of the file 1 is checked, and try a ‘show xps3’ command. The functional site information of the molecule ‘12as’ is read from the xPSSS and ‘type’ and ‘subtype’ keywords for each functional site are listed. These keywords can be used to select a set of atoms. For example, if a keyword ‘CATRES’ exists (probably it does), the command ‘select xps3:CATRES’ selects the corresponding atoms. 
In addition, gene ontology information can be obtained from the xPSSS. The gene ontology information for the molecule 12as is displayed by the command ’show godata’. Similar operations can be applied to other external databases on the Internet provided that the external database supports the interface that jV3 requires. See the [[Functional site information for molecules]] for details.

== Animation ==
The animation of molecules can be performed in jV3. The animation file takes the PDB format, where the MODEL line divides each frame. Let us open an animation file ’http://ef-site.hgc.jp/eF-site/jV/anim.pdb.gz’ as an example from the open-remote dialog shown by selecting the [File] – [Open – Remote] – [Animation] menu item. When an animation file is loaded to the application, the first frame is automatically displayed in the wire frame model. You can start the animation by using the animation-control dialog that is shown by choosing the [Options] – [Animation] menu item. The dialog provides operations such as start and stop of the animation, selection of the animation mode, and adjustment of the speed. Some sample figures of the dialog are shown in the [[GUI#3]]

== Saving your work ==
While in your work, you can create a script file that contains a set of commands that reproduces the current work by using the [File] – [Save] – [Script] menu item. The script file can be loaded by the [File] – [Open – Local] – [Script] menu item. On the other hand, the [File] – [Save] – [PDB] menu item enables to save a molecule to a PDB format file with the coordinates of the atoms being transformed according to the current image. Here, only one molecule must be selected and only selected atoms in the molecule are saved. The other two menu items in the [File] – [Save] menu, [PNG] and [JPEG], save the current screen image to an image file in the PNG and JPEG format, respectively. The created image file has the same size as that of the 3D-display panel in the application.

== Terminating the application ==
The application is terminated when the [File] – [Exit] menu item is chosen or the application window is closed by the way your operation system provides. You can also quit the application by executing ‘exit’ or ‘quit’ command.</text>
    <sha1>ffa00ae6f0aff7e0abbdcfbff461b863eafa189f</sha1>
  </revision>
  <revision>
    <id>198</id>
    <parentid>197</parentid>
    <timestamp>2009-03-09T09:26:30Z</timestamp>
    <contributor>
      <username>JVuser</username>
      <id>2</id>
    </contributor>
    <comment>/* Displaying polygons */</comment>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="12196" xml:space="preserve">{| style="float:right"
 |__TOC__
 |}
== Starting up ==
It is assumed that Java Runtime Environment and JOGL have been appropriately installed. Once you extract the binary distribution file of jV3, the directory of the name, jV_(version), is generated (Ex. jV_3_6_2). The version is assumed to be 3_6_x hereafter. The application starts up by double-clicking the file ‘jv_3_6_x.jar’ in the jV_3_6_x directory or executing the following command from the command line interface.
 java –jar jv_3_6_x.jar
Figure 1 shows the start-up screen. The window has a 3-panel structure, and the upper-left panel with the black background is a 3D image display area. The status of files that have been loaded to the application is shown in the upper-right panel and the lower panel is a command-input and a message-output area.
[[File:Fig1.jpg|Figure 1 Start-up screen|center|600px]]

== Displaying molecules ==
If you are working in the environment that is getting on the Internet and know the PDB ID of the molecule that you want to display, the simplest way is as follows. A dialog shown in Figure 2 is opened by selecting the [File] – [Open – Remote] – [PDB ID] menu item. Enter a PDB ID '12as', for example, to the text field and click the 'OK' button, then the PDBML file is read through the Internet and the molecule is displayed. The URL where the PDBML file is retrieved from is specified in the 'properties.txt' file in the jV_3_3_x directory. A molecule is displayed in a wire frame model with colored by atom type in the initial state.

[[File:Fig2.jpg|Dialog to open the molecule specified by PDB ID|center|200px]]

Let us next attempt to load an arbitrary file on the Internet. Here we use 'http://ef-site.hgc.jp/eF-site/jV/1yec.pdb' as an example. The file is a conventional PDB file whose PDB ID is 1yec. In this case we choose the [File] – [Open – Remote] – [PDB] menu item. Then the open-remote dialog is appeared. Enter the above URL to the text field at the top of the dialog and click the 'OK' button and the molecule is read in and displayed. In jV3, each molecule is displayed according to the space coordination described in its file. Therefore, when loading and displaying more than one molecule together, they can be viewed with an appropriate separation in some cases; however, they may be displayed far separately or may be overlapped depending on the combination. In any case, when adding a new file, the position of the viewpoint is automatically controlled for the whole to be displayed.
The coordinate system is the right hand system with the x-y plane being on the screen (the x-axis is a horizontal line with positive values to the right and the y-axis is a vertical line with positive values up). Although, the above examples are about operations for remote files, a PDB file on your local hard disk can also be opened from the [File] – [Open – Local] – [PDB] menu item.

== Operating molecules ==
Interactive mouse operations are possible for 3D images. By left-dragging the mouse on the 3D-display panel, molecules are rotated around the x-axis or y-axis. By left-dragging the mouse while holding the Shift key or Alt key on the keyboard, molecules are translated along the z-axis. All mouse operations are as follows (as for the Macintosh environment, the Command key + left-drag substitutes for the right-drag).

{| border="1"
 ! Mouse operations !! Actions
 |-
 | Left-drag || The image is rotated around the x (for a vertical motion) and y (for a horizontal motion) axes.
 |-
 | Right-drag || The image is translated on the x-y plane.
 |-
 | [Alt or Shift] + left-drag || The image is translated along the z-axis.
 |-
 | [Alt or Shift] + right-drag || The image is rotated around the z-axis.
 |-
 | [Ctrl] + left-drag || The z-clipping plane is shifted when [Option]-[Slab] is checked.
 |-
 | Left-click || An atom of the molecule displayed on the screen is picked.
 |}

In the upper-right panel in the application window (see Figure 3), the file names that have been loaded to the application are listed, where sequential integers are automatically assigned to the individual file. Each integer is a file ID that can be used to specify the file in the command line interface. In addition, two checkboxes are attached to each file. If you change the status of a ‘display’ checkbox, the corresponding molecule is switched to be displayed or not to be displayed. If you change the status of a ‘select’ checkbox, the corresponding molecule is switched to be a target of the mouse operations or not. For example, set the both ‘display’ checkboxes on, and the both ‘select’ checkboxes off. In this case, either molecule does not move against mouse operations. 
Subsequently set the ‘select’ checkbox of file 1 on. In this case, mouse operations work for the molecule 1. Thus, each file is assigned either selected or not selected, and transform operations, such as rotation or translation, act only on selected files. On the other hand, every atom in a molecule is also assigned either selected or not selected, independently of whether the molecule itself is selected or not. Operations that modify display models or colors work for selected atoms. To see this, choose the [Display] – [Spacefill] menu item. Then the both molecules are displayed with the space fill model because all atoms are initially selected. In the same way, if you choose the [Colors] – [Monochrome] menu item, the both molecules are colored white. These operations are independent of the status of ‘select’ checkboxes mentioned above. 
Let us next try a more detailed operation. Type ‘select *@2’ in the command line area and press Enter key. This command means to select all atoms contained in the file 2 (the usage of the select command is summarized in the reference manual included in the binary distribution of jV3). Subsequently, choose the [Display] – [Cartoon] menu item. As a result, only the molecule 2 is displayed in the cartoon model. Furthermore select the [Colors] – [Structure] menu item, and each residue of the molecule 2 is colored according to its secondary structure type (see Figure 3). 
In order to reproduce the same view as that in Figure 3, first execute ‘reset’ command. It restores the position of the viewpoint and the transform of every file to the initial state. Note that the command line interface tries to complement a command word when the Tab key is pressed. If you enter ‘res’ to the command line and subsequently press the Tab key, the command ‘reset’ is automatically entered. Next set the both ‘select’ checkboxes on, and execute ‘translate z 100’ command. This command means to translate the molecules along the z-axis by 100 angstroms.

[[File:Fig3.jpg|An example of molecular images.|center|600px]]

== Displaying polygons ==
In addition to molecules, arbitrary shapes described by polygons can be read in and displayed together, where the polygon file is an XML file, whose document type is described in the section 6. Here, we use ’http://ef-site.hgc.jp/eF-site/jV/1yec.surface.gz’ as an example. This polygon file represents a molecular surface of the molecule 2 (1yec) and the surface is colored according to the electrostatic potential and the hydrophobicity. It is assumed that the current image is the same as that in Figure 3. Then, open the open-remote dialog by choosing the [File] – [Open – Remote] – [Polygon] menu item, enter the above URL to the text field at the top of the dialog, and click the 'OK' button. As a result, the polygon is loaded, displayed and assigned file ID 3. 
Note that the polygon is displayed at the different position from the molecule 2 since the molecule 2 is translated. However, because the polygon and the molecule 2 are described by the same coordinates in their files, their images can be exactly superposed by executing ‘fit 3 2’ from the command line, where the ‘fit’ command performs the copy of the transform matrix. Finally, the image in Figure 4 appears.

[[File:Fig4.jpg|An example of polygon images.|center|600px]]

You can control the transparency rate of polygons. Try ’set transparency 0.5’ from the command line, where 0.5 stands for 50% transparency. To restore the image, execute ‘reset transparency’ or ‘set transparency 0’. In the same sense as each atom of a molecule, each vertex of a polygon is assigned either selected or not selected. All vertices are selected in the initial state. Execute a command ’displayvertex off’ and all vertices become invisible. Next execute ’selectvertex within(10.0, 1&amp;*H@2)’, where this means to select vertices that exist within 10 angstroms from each atom that belongs to the first residue of the ‘H’ chain of the molecule 2. Subsequently execute ’displayvertex on’. As a result, only the selected vertices are appeared. The usage of the selectvertex command is summarized in the [[Command List]].

== Working with xPSSS ==
Functional site information on a molecule stored at xPSSS (xml-based Protein Structure Search Service) is available in jV3. Before trying this, let us close the molecule 2 and the polygon 3 to make the situation simple. Select the [File] – [Close] – [2. 1yec.pdb] and [File] – [Close] – [3. 1yec.surface.gz] menu items sequentially. Then execute a ‘reset’ command and the transform of the molecule 1 and the position of the viewpoint are initialized. 
Next, confirm that the ‘select’ checkbox of the file 1 is checked, and try a ‘show xps3’ command. The functional site information of the molecule ‘12as’ is read from the xPSSS and ‘type’ and ‘subtype’ keywords for each functional site are listed. These keywords can be used to select a set of atoms. For example, if a keyword ‘CATRES’ exists (probably it does), the command ‘select xps3:CATRES’ selects the corresponding atoms. 
In addition, gene ontology information can be obtained from the xPSSS. The gene ontology information for the molecule 12as is displayed by the command ’show godata’. Similar operations can be applied to other external databases on the Internet provided that the external database supports the interface that jV3 requires. See the [[Functional site information for molecules]] for details.

== Animation ==
The animation of molecules can be performed in jV3. The animation file takes the PDB format, where the MODEL line divides each frame. Let us open an animation file ’http://ef-site.hgc.jp/eF-site/jV/anim.pdb.gz’ as an example from the open-remote dialog shown by selecting the [File] – [Open – Remote] – [Animation] menu item. When an animation file is loaded to the application, the first frame is automatically displayed in the wire frame model. You can start the animation by using the animation-control dialog that is shown by choosing the [Options] – [Animation] menu item. The dialog provides operations such as start and stop of the animation, selection of the animation mode, and adjustment of the speed. Some sample figures of the dialog are shown in the [[GUI#3]]

== Saving your work ==
While in your work, you can create a script file that contains a set of commands that reproduces the current work by using the [File] – [Save] – [Script] menu item. The script file can be loaded by the [File] – [Open – Local] – [Script] menu item. On the other hand, the [File] – [Save] – [PDB] menu item enables to save a molecule to a PDB format file with the coordinates of the atoms being transformed according to the current image. Here, only one molecule must be selected and only selected atoms in the molecule are saved. The other two menu items in the [File] – [Save] menu, [PNG] and [JPEG], save the current screen image to an image file in the PNG and JPEG format, respectively. The created image file has the same size as that of the 3D-display panel in the application.

== Terminating the application ==
The application is terminated when the [File] – [Exit] menu item is chosen or the application window is closed by the way your operation system provides. You can also quit the application by executing ‘exit’ or ‘quit’ command.</text>
    <sha1>e95ca44a14b6ea8f29271f53aa002e02e8db3c4c</sha1>
  </revision>
  <revision>
    <id>199</id>
    <parentid>198</parentid>
    <timestamp>2009-03-09T09:28:23Z</timestamp>
    <contributor>
      <username>JVuser</username>
      <id>2</id>
    </contributor>
    <comment>/* Starting up */</comment>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="12202" xml:space="preserve">{| style="float:right"
 |__TOC__
 |}
== Starting up ==
It is assumed that Java Runtime Environment and JOGL have been appropriately installed. Once you extract the binary distribution file of jV3, the directory of the name, jV_(version), is generated (Ex. jV_3_6_2). The version is assumed to be 3_6_x hereafter. The application starts up by double-clicking the file ‘jv_3_6_x.jar’ in the jV_3_6_x directory or executing the following command from the command line interface.
 java –jar jv_3_6_x.jar
Figure 1 shows the start-up screen. The window has a 3-panel structure, and the upper-left panel with the black background is a 3D image display area. The status of files that have been loaded to the application is shown in the upper-right panel and the lower panel is a command-input and a message-output area.
[[File:Fig1.jpg|thumb|Figure 1 Start-up screen|center|600px]]

== Displaying molecules ==
If you are working in the environment that is getting on the Internet and know the PDB ID of the molecule that you want to display, the simplest way is as follows. A dialog shown in Figure 2 is opened by selecting the [File] – [Open – Remote] – [PDB ID] menu item. Enter a PDB ID '12as', for example, to the text field and click the 'OK' button, then the PDBML file is read through the Internet and the molecule is displayed. The URL where the PDBML file is retrieved from is specified in the 'properties.txt' file in the jV_3_3_x directory. A molecule is displayed in a wire frame model with colored by atom type in the initial state.

[[File:Fig2.jpg|Dialog to open the molecule specified by PDB ID|center|200px]]

Let us next attempt to load an arbitrary file on the Internet. Here we use 'http://ef-site.hgc.jp/eF-site/jV/1yec.pdb' as an example. The file is a conventional PDB file whose PDB ID is 1yec. In this case we choose the [File] – [Open – Remote] – [PDB] menu item. Then the open-remote dialog is appeared. Enter the above URL to the text field at the top of the dialog and click the 'OK' button and the molecule is read in and displayed. In jV3, each molecule is displayed according to the space coordination described in its file. Therefore, when loading and displaying more than one molecule together, they can be viewed with an appropriate separation in some cases; however, they may be displayed far separately or may be overlapped depending on the combination. In any case, when adding a new file, the position of the viewpoint is automatically controlled for the whole to be displayed.
The coordinate system is the right hand system with the x-y plane being on the screen (the x-axis is a horizontal line with positive values to the right and the y-axis is a vertical line with positive values up). Although, the above examples are about operations for remote files, a PDB file on your local hard disk can also be opened from the [File] – [Open – Local] – [PDB] menu item.

== Operating molecules ==
Interactive mouse operations are possible for 3D images. By left-dragging the mouse on the 3D-display panel, molecules are rotated around the x-axis or y-axis. By left-dragging the mouse while holding the Shift key or Alt key on the keyboard, molecules are translated along the z-axis. All mouse operations are as follows (as for the Macintosh environment, the Command key + left-drag substitutes for the right-drag).

{| border="1"
 ! Mouse operations !! Actions
 |-
 | Left-drag || The image is rotated around the x (for a vertical motion) and y (for a horizontal motion) axes.
 |-
 | Right-drag || The image is translated on the x-y plane.
 |-
 | [Alt or Shift] + left-drag || The image is translated along the z-axis.
 |-
 | [Alt or Shift] + right-drag || The image is rotated around the z-axis.
 |-
 | [Ctrl] + left-drag || The z-clipping plane is shifted when [Option]-[Slab] is checked.
 |-
 | Left-click || An atom of the molecule displayed on the screen is picked.
 |}

In the upper-right panel in the application window (see Figure 3), the file names that have been loaded to the application are listed, where sequential integers are automatically assigned to the individual file. Each integer is a file ID that can be used to specify the file in the command line interface. In addition, two checkboxes are attached to each file. If you change the status of a ‘display’ checkbox, the corresponding molecule is switched to be displayed or not to be displayed. If you change the status of a ‘select’ checkbox, the corresponding molecule is switched to be a target of the mouse operations or not. For example, set the both ‘display’ checkboxes on, and the both ‘select’ checkboxes off. In this case, either molecule does not move against mouse operations. 
Subsequently set the ‘select’ checkbox of file 1 on. In this case, mouse operations work for the molecule 1. Thus, each file is assigned either selected or not selected, and transform operations, such as rotation or translation, act only on selected files. On the other hand, every atom in a molecule is also assigned either selected or not selected, independently of whether the molecule itself is selected or not. Operations that modify display models or colors work for selected atoms. To see this, choose the [Display] – [Spacefill] menu item. Then the both molecules are displayed with the space fill model because all atoms are initially selected. In the same way, if you choose the [Colors] – [Monochrome] menu item, the both molecules are colored white. These operations are independent of the status of ‘select’ checkboxes mentioned above. 
Let us next try a more detailed operation. Type ‘select *@2’ in the command line area and press Enter key. This command means to select all atoms contained in the file 2 (the usage of the select command is summarized in the reference manual included in the binary distribution of jV3). Subsequently, choose the [Display] – [Cartoon] menu item. As a result, only the molecule 2 is displayed in the cartoon model. Furthermore select the [Colors] – [Structure] menu item, and each residue of the molecule 2 is colored according to its secondary structure type (see Figure 3). 
In order to reproduce the same view as that in Figure 3, first execute ‘reset’ command. It restores the position of the viewpoint and the transform of every file to the initial state. Note that the command line interface tries to complement a command word when the Tab key is pressed. If you enter ‘res’ to the command line and subsequently press the Tab key, the command ‘reset’ is automatically entered. Next set the both ‘select’ checkboxes on, and execute ‘translate z 100’ command. This command means to translate the molecules along the z-axis by 100 angstroms.

[[File:Fig3.jpg|An example of molecular images.|center|600px]]

== Displaying polygons ==
In addition to molecules, arbitrary shapes described by polygons can be read in and displayed together, where the polygon file is an XML file, whose document type is described in the section 6. Here, we use ’http://ef-site.hgc.jp/eF-site/jV/1yec.surface.gz’ as an example. This polygon file represents a molecular surface of the molecule 2 (1yec) and the surface is colored according to the electrostatic potential and the hydrophobicity. It is assumed that the current image is the same as that in Figure 3. Then, open the open-remote dialog by choosing the [File] – [Open – Remote] – [Polygon] menu item, enter the above URL to the text field at the top of the dialog, and click the 'OK' button. As a result, the polygon is loaded, displayed and assigned file ID 3. 
Note that the polygon is displayed at the different position from the molecule 2 since the molecule 2 is translated. However, because the polygon and the molecule 2 are described by the same coordinates in their files, their images can be exactly superposed by executing ‘fit 3 2’ from the command line, where the ‘fit’ command performs the copy of the transform matrix. Finally, the image in Figure 4 appears.

[[File:Fig4.jpg|An example of polygon images.|center|600px]]

You can control the transparency rate of polygons. Try ’set transparency 0.5’ from the command line, where 0.5 stands for 50% transparency. To restore the image, execute ‘reset transparency’ or ‘set transparency 0’. In the same sense as each atom of a molecule, each vertex of a polygon is assigned either selected or not selected. All vertices are selected in the initial state. Execute a command ’displayvertex off’ and all vertices become invisible. Next execute ’selectvertex within(10.0, 1&amp;*H@2)’, where this means to select vertices that exist within 10 angstroms from each atom that belongs to the first residue of the ‘H’ chain of the molecule 2. Subsequently execute ’displayvertex on’. As a result, only the selected vertices are appeared. The usage of the selectvertex command is summarized in the [[Command List]].

== Working with xPSSS ==
Functional site information on a molecule stored at xPSSS (xml-based Protein Structure Search Service) is available in jV3. Before trying this, let us close the molecule 2 and the polygon 3 to make the situation simple. Select the [File] – [Close] – [2. 1yec.pdb] and [File] – [Close] – [3. 1yec.surface.gz] menu items sequentially. Then execute a ‘reset’ command and the transform of the molecule 1 and the position of the viewpoint are initialized. 
Next, confirm that the ‘select’ checkbox of the file 1 is checked, and try a ‘show xps3’ command. The functional site information of the molecule ‘12as’ is read from the xPSSS and ‘type’ and ‘subtype’ keywords for each functional site are listed. These keywords can be used to select a set of atoms. For example, if a keyword ‘CATRES’ exists (probably it does), the command ‘select xps3:CATRES’ selects the corresponding atoms. 
In addition, gene ontology information can be obtained from the xPSSS. The gene ontology information for the molecule 12as is displayed by the command ’show godata’. Similar operations can be applied to other external databases on the Internet provided that the external database supports the interface that jV3 requires. See the [[Functional site information for molecules]] for details.

== Animation ==
The animation of molecules can be performed in jV3. The animation file takes the PDB format, where the MODEL line divides each frame. Let us open an animation file ’http://ef-site.hgc.jp/eF-site/jV/anim.pdb.gz’ as an example from the open-remote dialog shown by selecting the [File] – [Open – Remote] – [Animation] menu item. When an animation file is loaded to the application, the first frame is automatically displayed in the wire frame model. You can start the animation by using the animation-control dialog that is shown by choosing the [Options] – [Animation] menu item. The dialog provides operations such as start and stop of the animation, selection of the animation mode, and adjustment of the speed. Some sample figures of the dialog are shown in the [[GUI#3]]

== Saving your work ==
While in your work, you can create a script file that contains a set of commands that reproduces the current work by using the [File] – [Save] – [Script] menu item. The script file can be loaded by the [File] – [Open – Local] – [Script] menu item. On the other hand, the [File] – [Save] – [PDB] menu item enables to save a molecule to a PDB format file with the coordinates of the atoms being transformed according to the current image. Here, only one molecule must be selected and only selected atoms in the molecule are saved. The other two menu items in the [File] – [Save] menu, [PNG] and [JPEG], save the current screen image to an image file in the PNG and JPEG format, respectively. The created image file has the same size as that of the 3D-display panel in the application.

== Terminating the application ==
The application is terminated when the [File] – [Exit] menu item is chosen or the application window is closed by the way your operation system provides. You can also quit the application by executing ‘exit’ or ‘quit’ command.</text>
    <sha1>deffb79101d0923d05cba51996f4ecd71f489ba1</sha1>
  </revision>
  <revision>
    <id>200</id>
    <parentid>199</parentid>
    <timestamp>2009-03-09T09:30:05Z</timestamp>
    <contributor>
      <username>JVuser</username>
      <id>2</id>
    </contributor>
    <comment>/* Displaying molecules */</comment>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="12218" xml:space="preserve">{| style="float:right"
 |__TOC__
 |}
== Starting up ==
It is assumed that Java Runtime Environment and JOGL have been appropriately installed. Once you extract the binary distribution file of jV3, the directory of the name, jV_(version), is generated (Ex. jV_3_6_2). The version is assumed to be 3_6_x hereafter. The application starts up by double-clicking the file ‘jv_3_6_x.jar’ in the jV_3_6_x directory or executing the following command from the command line interface.
 java –jar jv_3_6_x.jar
Figure 1 shows the start-up screen. The window has a 3-panel structure, and the upper-left panel with the black background is a 3D image display area. The status of files that have been loaded to the application is shown in the upper-right panel and the lower panel is a command-input and a message-output area.
[[File:Fig1.jpg|thumb|Figure 1 Start-up screen|center|600px]]

== Displaying molecules ==
If you are working in the environment that is getting on the Internet and know the PDB ID of the molecule that you want to display, the simplest way is as follows. A dialog shown in Figure 2 is opened by selecting the [File] – [Open – Remote] – [PDB ID] menu item. Enter a PDB ID '12as', for example, to the text field and click the 'OK' button, then the PDBML file is read through the Internet and the molecule is displayed. The URL where the PDBML file is retrieved from is specified in the 'properties.txt' file in the jV_3_3_x directory. A molecule is displayed in a wire frame model with colored by atom type in the initial state.

[[File:Fig2.jpg|thumb|Figure 2: Dialog to open the molecule specified by PDB ID|center|200px]]

Let us next attempt to load an arbitrary file on the Internet. Here we use 'http://ef-site.hgc.jp/eF-site/jV/1yec.pdb' as an example. The file is a conventional PDB file whose PDB ID is 1yec. In this case we choose the [File] – [Open – Remote] – [PDB] menu item. Then the open-remote dialog is appeared. Enter the above URL to the text field at the top of the dialog and click the 'OK' button and the molecule is read in and displayed. In jV3, each molecule is displayed according to the space coordination described in its file. Therefore, when loading and displaying more than one molecule together, they can be viewed with an appropriate separation in some cases; however, they may be displayed far separately or may be overlapped depending on the combination. In any case, when adding a new file, the position of the viewpoint is automatically controlled for the whole to be displayed.
The coordinate system is the right hand system with the x-y plane being on the screen (the x-axis is a horizontal line with positive values to the right and the y-axis is a vertical line with positive values up). Although, the above examples are about operations for remote files, a PDB file on your local hard disk can also be opened from the [File] – [Open – Local] – [PDB] menu item.

== Operating molecules ==
Interactive mouse operations are possible for 3D images. By left-dragging the mouse on the 3D-display panel, molecules are rotated around the x-axis or y-axis. By left-dragging the mouse while holding the Shift key or Alt key on the keyboard, molecules are translated along the z-axis. All mouse operations are as follows (as for the Macintosh environment, the Command key + left-drag substitutes for the right-drag).

{| border="1"
 ! Mouse operations !! Actions
 |-
 | Left-drag || The image is rotated around the x (for a vertical motion) and y (for a horizontal motion) axes.
 |-
 | Right-drag || The image is translated on the x-y plane.
 |-
 | [Alt or Shift] + left-drag || The image is translated along the z-axis.
 |-
 | [Alt or Shift] + right-drag || The image is rotated around the z-axis.
 |-
 | [Ctrl] + left-drag || The z-clipping plane is shifted when [Option]-[Slab] is checked.
 |-
 | Left-click || An atom of the molecule displayed on the screen is picked.
 |}

In the upper-right panel in the application window (see Figure 3), the file names that have been loaded to the application are listed, where sequential integers are automatically assigned to the individual file. Each integer is a file ID that can be used to specify the file in the command line interface. In addition, two checkboxes are attached to each file. If you change the status of a ‘display’ checkbox, the corresponding molecule is switched to be displayed or not to be displayed. If you change the status of a ‘select’ checkbox, the corresponding molecule is switched to be a target of the mouse operations or not. For example, set the both ‘display’ checkboxes on, and the both ‘select’ checkboxes off. In this case, either molecule does not move against mouse operations. 
Subsequently set the ‘select’ checkbox of file 1 on. In this case, mouse operations work for the molecule 1. Thus, each file is assigned either selected or not selected, and transform operations, such as rotation or translation, act only on selected files. On the other hand, every atom in a molecule is also assigned either selected or not selected, independently of whether the molecule itself is selected or not. Operations that modify display models or colors work for selected atoms. To see this, choose the [Display] – [Spacefill] menu item. Then the both molecules are displayed with the space fill model because all atoms are initially selected. In the same way, if you choose the [Colors] – [Monochrome] menu item, the both molecules are colored white. These operations are independent of the status of ‘select’ checkboxes mentioned above. 
Let us next try a more detailed operation. Type ‘select *@2’ in the command line area and press Enter key. This command means to select all atoms contained in the file 2 (the usage of the select command is summarized in the reference manual included in the binary distribution of jV3). Subsequently, choose the [Display] – [Cartoon] menu item. As a result, only the molecule 2 is displayed in the cartoon model. Furthermore select the [Colors] – [Structure] menu item, and each residue of the molecule 2 is colored according to its secondary structure type (see Figure 3). 
In order to reproduce the same view as that in Figure 3, first execute ‘reset’ command. It restores the position of the viewpoint and the transform of every file to the initial state. Note that the command line interface tries to complement a command word when the Tab key is pressed. If you enter ‘res’ to the command line and subsequently press the Tab key, the command ‘reset’ is automatically entered. Next set the both ‘select’ checkboxes on, and execute ‘translate z 100’ command. This command means to translate the molecules along the z-axis by 100 angstroms.

[[File:Fig3.jpg|An example of molecular images.|center|600px]]

== Displaying polygons ==
In addition to molecules, arbitrary shapes described by polygons can be read in and displayed together, where the polygon file is an XML file, whose document type is described in the section 6. Here, we use ’http://ef-site.hgc.jp/eF-site/jV/1yec.surface.gz’ as an example. This polygon file represents a molecular surface of the molecule 2 (1yec) and the surface is colored according to the electrostatic potential and the hydrophobicity. It is assumed that the current image is the same as that in Figure 3. Then, open the open-remote dialog by choosing the [File] – [Open – Remote] – [Polygon] menu item, enter the above URL to the text field at the top of the dialog, and click the 'OK' button. As a result, the polygon is loaded, displayed and assigned file ID 3. 
Note that the polygon is displayed at the different position from the molecule 2 since the molecule 2 is translated. However, because the polygon and the molecule 2 are described by the same coordinates in their files, their images can be exactly superposed by executing ‘fit 3 2’ from the command line, where the ‘fit’ command performs the copy of the transform matrix. Finally, the image in Figure 4 appears.

[[File:Fig4.jpg|An example of polygon images.|center|600px]]

You can control the transparency rate of polygons. Try ’set transparency 0.5’ from the command line, where 0.5 stands for 50% transparency. To restore the image, execute ‘reset transparency’ or ‘set transparency 0’. In the same sense as each atom of a molecule, each vertex of a polygon is assigned either selected or not selected. All vertices are selected in the initial state. Execute a command ’displayvertex off’ and all vertices become invisible. Next execute ’selectvertex within(10.0, 1&amp;*H@2)’, where this means to select vertices that exist within 10 angstroms from each atom that belongs to the first residue of the ‘H’ chain of the molecule 2. Subsequently execute ’displayvertex on’. As a result, only the selected vertices are appeared. The usage of the selectvertex command is summarized in the [[Command List]].

== Working with xPSSS ==
Functional site information on a molecule stored at xPSSS (xml-based Protein Structure Search Service) is available in jV3. Before trying this, let us close the molecule 2 and the polygon 3 to make the situation simple. Select the [File] – [Close] – [2. 1yec.pdb] and [File] – [Close] – [3. 1yec.surface.gz] menu items sequentially. Then execute a ‘reset’ command and the transform of the molecule 1 and the position of the viewpoint are initialized. 
Next, confirm that the ‘select’ checkbox of the file 1 is checked, and try a ‘show xps3’ command. The functional site information of the molecule ‘12as’ is read from the xPSSS and ‘type’ and ‘subtype’ keywords for each functional site are listed. These keywords can be used to select a set of atoms. For example, if a keyword ‘CATRES’ exists (probably it does), the command ‘select xps3:CATRES’ selects the corresponding atoms. 
In addition, gene ontology information can be obtained from the xPSSS. The gene ontology information for the molecule 12as is displayed by the command ’show godata’. Similar operations can be applied to other external databases on the Internet provided that the external database supports the interface that jV3 requires. See the [[Functional site information for molecules]] for details.

== Animation ==
The animation of molecules can be performed in jV3. The animation file takes the PDB format, where the MODEL line divides each frame. Let us open an animation file ’http://ef-site.hgc.jp/eF-site/jV/anim.pdb.gz’ as an example from the open-remote dialog shown by selecting the [File] – [Open – Remote] – [Animation] menu item. When an animation file is loaded to the application, the first frame is automatically displayed in the wire frame model. You can start the animation by using the animation-control dialog that is shown by choosing the [Options] – [Animation] menu item. The dialog provides operations such as start and stop of the animation, selection of the animation mode, and adjustment of the speed. Some sample figures of the dialog are shown in the [[GUI#3]]

== Saving your work ==
While in your work, you can create a script file that contains a set of commands that reproduces the current work by using the [File] – [Save] – [Script] menu item. The script file can be loaded by the [File] – [Open – Local] – [Script] menu item. On the other hand, the [File] – [Save] – [PDB] menu item enables to save a molecule to a PDB format file with the coordinates of the atoms being transformed according to the current image. Here, only one molecule must be selected and only selected atoms in the molecule are saved. The other two menu items in the [File] – [Save] menu, [PNG] and [JPEG], save the current screen image to an image file in the PNG and JPEG format, respectively. The created image file has the same size as that of the 3D-display panel in the application.

== Terminating the application ==
The application is terminated when the [File] – [Exit] menu item is chosen or the application window is closed by the way your operation system provides. You can also quit the application by executing ‘exit’ or ‘quit’ command.</text>
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 |__TOC__
 |}
== Starting up ==
It is assumed that Java Runtime Environment and JOGL have been appropriately installed. Once you extract the binary distribution file of jV3, the directory of the name, jV_(version), is generated (Ex. jV_3_6_2). The version is assumed to be 3_6_x hereafter. The application starts up by double-clicking the file ‘jv_3_6_x.jar’ in the jV_3_6_x directory or executing the following command from the command line interface.
 java –jar jv_3_6_x.jar
Figure 1 shows the start-up screen. The window has a 3-panel structure, and the upper-left panel with the black background is a 3D image display area. The status of files that have been loaded to the application is shown in the upper-right panel and the lower panel is a command-input and a message-output area.
[[File:Fig1.jpg|thumb|Figure 1: Start-up screen|center|600px]]

== Displaying molecules ==
If you are working in the environment that is getting on the Internet and know the PDB ID of the molecule that you want to display, the simplest way is as follows. A dialog shown in Figure 2 is opened by selecting the [File] – [Open – Remote] – [PDB ID] menu item. Enter a PDB ID '12as', for example, to the text field and click the 'OK' button, then the PDBML file is read through the Internet and the molecule is displayed. The URL where the PDBML file is retrieved from is specified in the 'properties.txt' file in the jV_3_3_x directory. A molecule is displayed in a wire frame model with colored by atom type in the initial state.

[[File:Fig2.jpg|thumb|Figure 2: Dialog to open the molecule specified by PDB ID|center|200px]]

Let us next attempt to load an arbitrary file on the Internet. Here we use 'http://ef-site.hgc.jp/eF-site/jV/1yec.pdb' as an example. The file is a conventional PDB file whose PDB ID is 1yec. In this case we choose the [File] – [Open – Remote] – [PDB] menu item. Then the open-remote dialog is appeared. Enter the above URL to the text field at the top of the dialog and click the 'OK' button and the molecule is read in and displayed. In jV3, each molecule is displayed according to the space coordination described in its file. Therefore, when loading and displaying more than one molecule together, they can be viewed with an appropriate separation in some cases; however, they may be displayed far separately or may be overlapped depending on the combination. In any case, when adding a new file, the position of the viewpoint is automatically controlled for the whole to be displayed.
The coordinate system is the right hand system with the x-y plane being on the screen (the x-axis is a horizontal line with positive values to the right and the y-axis is a vertical line with positive values up). Although, the above examples are about operations for remote files, a PDB file on your local hard disk can also be opened from the [File] – [Open – Local] – [PDB] menu item.

== Operating molecules ==
Interactive mouse operations are possible for 3D images. By left-dragging the mouse on the 3D-display panel, molecules are rotated around the x-axis or y-axis. By left-dragging the mouse while holding the Shift key or Alt key on the keyboard, molecules are translated along the z-axis. All mouse operations are as follows (as for the Macintosh environment, the Command key + left-drag substitutes for the right-drag).

{| border="1"
 ! Mouse operations !! Actions
 |-
 | Left-drag || The image is rotated around the x (for a vertical motion) and y (for a horizontal motion) axes.
 |-
 | Right-drag || The image is translated on the x-y plane.
 |-
 | [Alt or Shift] + left-drag || The image is translated along the z-axis.
 |-
 | [Alt or Shift] + right-drag || The image is rotated around the z-axis.
 |-
 | [Ctrl] + left-drag || The z-clipping plane is shifted when [Option]-[Slab] is checked.
 |-
 | Left-click || An atom of the molecule displayed on the screen is picked.
 |}

In the upper-right panel in the application window (see Figure 3), the file names that have been loaded to the application are listed, where sequential integers are automatically assigned to the individual file. Each integer is a file ID that can be used to specify the file in the command line interface. In addition, two checkboxes are attached to each file. If you change the status of a ‘display’ checkbox, the corresponding molecule is switched to be displayed or not to be displayed. If you change the status of a ‘select’ checkbox, the corresponding molecule is switched to be a target of the mouse operations or not. For example, set the both ‘display’ checkboxes on, and the both ‘select’ checkboxes off. In this case, either molecule does not move against mouse operations. 
Subsequently set the ‘select’ checkbox of file 1 on. In this case, mouse operations work for the molecule 1. Thus, each file is assigned either selected or not selected, and transform operations, such as rotation or translation, act only on selected files. On the other hand, every atom in a molecule is also assigned either selected or not selected, independently of whether the molecule itself is selected or not. Operations that modify display models or colors work for selected atoms. To see this, choose the [Display] – [Spacefill] menu item. Then the both molecules are displayed with the space fill model because all atoms are initially selected. In the same way, if you choose the [Colors] – [Monochrome] menu item, the both molecules are colored white. These operations are independent of the status of ‘select’ checkboxes mentioned above. 
Let us next try a more detailed operation. Type ‘select *@2’ in the command line area and press Enter key. This command means to select all atoms contained in the file 2 (the usage of the select command is summarized in the reference manual included in the binary distribution of jV3). Subsequently, choose the [Display] – [Cartoon] menu item. As a result, only the molecule 2 is displayed in the cartoon model. Furthermore select the [Colors] – [Structure] menu item, and each residue of the molecule 2 is colored according to its secondary structure type (see Figure 3). 
In order to reproduce the same view as that in Figure 3, first execute ‘reset’ command. It restores the position of the viewpoint and the transform of every file to the initial state. Note that the command line interface tries to complement a command word when the Tab key is pressed. If you enter ‘res’ to the command line and subsequently press the Tab key, the command ‘reset’ is automatically entered. Next set the both ‘select’ checkboxes on, and execute ‘translate z 100’ command. This command means to translate the molecules along the z-axis by 100 angstroms.

[[File:Fig3.jpg|An example of molecular images.|center|600px]]

== Displaying polygons ==
In addition to molecules, arbitrary shapes described by polygons can be read in and displayed together, where the polygon file is an XML file, whose document type is described in the section 6. Here, we use ’http://ef-site.hgc.jp/eF-site/jV/1yec.surface.gz’ as an example. This polygon file represents a molecular surface of the molecule 2 (1yec) and the surface is colored according to the electrostatic potential and the hydrophobicity. It is assumed that the current image is the same as that in Figure 3. Then, open the open-remote dialog by choosing the [File] – [Open – Remote] – [Polygon] menu item, enter the above URL to the text field at the top of the dialog, and click the 'OK' button. As a result, the polygon is loaded, displayed and assigned file ID 3. 
Note that the polygon is displayed at the different position from the molecule 2 since the molecule 2 is translated. However, because the polygon and the molecule 2 are described by the same coordinates in their files, their images can be exactly superposed by executing ‘fit 3 2’ from the command line, where the ‘fit’ command performs the copy of the transform matrix. Finally, the image in Figure 4 appears.

[[File:Fig4.jpg|An example of polygon images.|center|600px]]

You can control the transparency rate of polygons. Try ’set transparency 0.5’ from the command line, where 0.5 stands for 50% transparency. To restore the image, execute ‘reset transparency’ or ‘set transparency 0’. In the same sense as each atom of a molecule, each vertex of a polygon is assigned either selected or not selected. All vertices are selected in the initial state. Execute a command ’displayvertex off’ and all vertices become invisible. Next execute ’selectvertex within(10.0, 1&amp;*H@2)’, where this means to select vertices that exist within 10 angstroms from each atom that belongs to the first residue of the ‘H’ chain of the molecule 2. Subsequently execute ’displayvertex on’. As a result, only the selected vertices are appeared. The usage of the selectvertex command is summarized in the [[Command List]].

== Working with xPSSS ==
Functional site information on a molecule stored at xPSSS (xml-based Protein Structure Search Service) is available in jV3. Before trying this, let us close the molecule 2 and the polygon 3 to make the situation simple. Select the [File] – [Close] – [2. 1yec.pdb] and [File] – [Close] – [3. 1yec.surface.gz] menu items sequentially. Then execute a ‘reset’ command and the transform of the molecule 1 and the position of the viewpoint are initialized. 
Next, confirm that the ‘select’ checkbox of the file 1 is checked, and try a ‘show xps3’ command. The functional site information of the molecule ‘12as’ is read from the xPSSS and ‘type’ and ‘subtype’ keywords for each functional site are listed. These keywords can be used to select a set of atoms. For example, if a keyword ‘CATRES’ exists (probably it does), the command ‘select xps3:CATRES’ selects the corresponding atoms. 
In addition, gene ontology information can be obtained from the xPSSS. The gene ontology information for the molecule 12as is displayed by the command ’show godata’. Similar operations can be applied to other external databases on the Internet provided that the external database supports the interface that jV3 requires. See the [[Functional site information for molecules]] for details.

== Animation ==
The animation of molecules can be performed in jV3. The animation file takes the PDB format, where the MODEL line divides each frame. Let us open an animation file ’http://ef-site.hgc.jp/eF-site/jV/anim.pdb.gz’ as an example from the open-remote dialog shown by selecting the [File] – [Open – Remote] – [Animation] menu item. When an animation file is loaded to the application, the first frame is automatically displayed in the wire frame model. You can start the animation by using the animation-control dialog that is shown by choosing the [Options] – [Animation] menu item. The dialog provides operations such as start and stop of the animation, selection of the animation mode, and adjustment of the speed. Some sample figures of the dialog are shown in the [[GUI#3]]

== Saving your work ==
While in your work, you can create a script file that contains a set of commands that reproduces the current work by using the [File] – [Save] – [Script] menu item. The script file can be loaded by the [File] – [Open – Local] – [Script] menu item. On the other hand, the [File] – [Save] – [PDB] menu item enables to save a molecule to a PDB format file with the coordinates of the atoms being transformed according to the current image. Here, only one molecule must be selected and only selected atoms in the molecule are saved. The other two menu items in the [File] – [Save] menu, [PNG] and [JPEG], save the current screen image to an image file in the PNG and JPEG format, respectively. The created image file has the same size as that of the 3D-display panel in the application.

== Terminating the application ==
The application is terminated when the [File] – [Exit] menu item is chosen or the application window is closed by the way your operation system provides. You can also quit the application by executing ‘exit’ or ‘quit’ command.</text>
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    <text bytes="12235" xml:space="preserve">{| style="float:right"
 |__TOC__
 |}
== Starting up ==
It is assumed that Java Runtime Environment and JOGL have been appropriately installed. Once you extract the binary distribution file of jV3, the directory of the name, jV_(version), is generated (Ex. jV_3_6_2). The version is assumed to be 3_6_x hereafter. The application starts up by double-clicking the file ‘jv_3_6_x.jar’ in the jV_3_6_x directory or executing the following command from the command line interface.
 java –jar jv_3_6_x.jar
Figure 1 shows the start-up screen. The window has a 3-panel structure, and the upper-left panel with the black background is a 3D image display area. The status of files that have been loaded to the application is shown in the upper-right panel and the lower panel is a command-input and a message-output area.
[[File:Fig1.jpg|thumb|Figure 1: Start-up screen|center|600px]]

== Displaying molecules ==
If you are working in the environment that is getting on the Internet and know the PDB ID of the molecule that you want to display, the simplest way is as follows. A dialog shown in Figure 2 is opened by selecting the [File] – [Open – Remote] – [PDB ID] menu item. Enter a PDB ID '12as', for example, to the text field and click the 'OK' button, then the PDBML file is read through the Internet and the molecule is displayed. The URL where the PDBML file is retrieved from is specified in the 'properties.txt' file in the jV_3_3_x directory. A molecule is displayed in a wire frame model with colored by atom type in the initial state.

[[File:Fig2.jpg|thumb|Figure 2: Dialog to open the molecule specified by PDB ID|center|200px]]

Let us next attempt to load an arbitrary file on the Internet. Here we use 'http://ef-site.hgc.jp/eF-site/jV/1yec.pdb' as an example. The file is a conventional PDB file whose PDB ID is 1yec. In this case we choose the [File] – [Open – Remote] – [PDB] menu item. Then the open-remote dialog is appeared. Enter the above URL to the text field at the top of the dialog and click the 'OK' button and the molecule is read in and displayed. In jV3, each molecule is displayed according to the space coordination described in its file. Therefore, when loading and displaying more than one molecule together, they can be viewed with an appropriate separation in some cases; however, they may be displayed far separately or may be overlapped depending on the combination. In any case, when adding a new file, the position of the viewpoint is automatically controlled for the whole to be displayed.
The coordinate system is the right hand system with the x-y plane being on the screen (the x-axis is a horizontal line with positive values to the right and the y-axis is a vertical line with positive values up). Although, the above examples are about operations for remote files, a PDB file on your local hard disk can also be opened from the [File] – [Open – Local] – [PDB] menu item.

== Operating molecules ==
Interactive mouse operations are possible for 3D images. By left-dragging the mouse on the 3D-display panel, molecules are rotated around the x-axis or y-axis. By left-dragging the mouse while holding the Shift key or Alt key on the keyboard, molecules are translated along the z-axis. All mouse operations are as follows (as for the Macintosh environment, the Command key + left-drag substitutes for the right-drag).

{| border="1"
 ! Mouse operations !! Actions
 |-
 | Left-drag || The image is rotated around the x (for a vertical motion) and y (for a horizontal motion) axes.
 |-
 | Right-drag || The image is translated on the x-y plane.
 |-
 | [Alt or Shift] + left-drag || The image is translated along the z-axis.
 |-
 | [Alt or Shift] + right-drag || The image is rotated around the z-axis.
 |-
 | [Ctrl] + left-drag || The z-clipping plane is shifted when [Option]-[Slab] is checked.
 |-
 | Left-click || An atom of the molecule displayed on the screen is picked.
 |}

In the upper-right panel in the application window (see Figure 3), the file names that have been loaded to the application are listed, where sequential integers are automatically assigned to the individual file. Each integer is a file ID that can be used to specify the file in the command line interface. In addition, two checkboxes are attached to each file. If you change the status of a ‘display’ checkbox, the corresponding molecule is switched to be displayed or not to be displayed. If you change the status of a ‘select’ checkbox, the corresponding molecule is switched to be a target of the mouse operations or not. For example, set the both ‘display’ checkboxes on, and the both ‘select’ checkboxes off. In this case, either molecule does not move against mouse operations. 
Subsequently set the ‘select’ checkbox of file 1 on. In this case, mouse operations work for the molecule 1. Thus, each file is assigned either selected or not selected, and transform operations, such as rotation or translation, act only on selected files. On the other hand, every atom in a molecule is also assigned either selected or not selected, independently of whether the molecule itself is selected or not. Operations that modify display models or colors work for selected atoms. To see this, choose the [Display] – [Spacefill] menu item. Then the both molecules are displayed with the space fill model because all atoms are initially selected. In the same way, if you choose the [Colors] – [Monochrome] menu item, the both molecules are colored white. These operations are independent of the status of ‘select’ checkboxes mentioned above. 
Let us next try a more detailed operation. Type ‘select *@2’ in the command line area and press Enter key. This command means to select all atoms contained in the file 2 (the usage of the select command is summarized in the reference manual included in the binary distribution of jV3). Subsequently, choose the [Display] – [Cartoon] menu item. As a result, only the molecule 2 is displayed in the cartoon model. Furthermore select the [Colors] – [Structure] menu item, and each residue of the molecule 2 is colored according to its secondary structure type (see Figure 3). 
In order to reproduce the same view as that in Figure 3, first execute ‘reset’ command. It restores the position of the viewpoint and the transform of every file to the initial state. Note that the command line interface tries to complement a command word when the Tab key is pressed. If you enter ‘res’ to the command line and subsequently press the Tab key, the command ‘reset’ is automatically entered. Next set the both ‘select’ checkboxes on, and execute ‘translate z 100’ command. This command means to translate the molecules along the z-axis by 100 angstroms.

[[File:Fig3.jpg|thumb|Figure 3: An example of molecular images.|center|600px]]

== Displaying polygons ==
In addition to molecules, arbitrary shapes described by polygons can be read in and displayed together, where the polygon file is an XML file, whose document type is described in the section 6. Here, we use ’http://ef-site.hgc.jp/eF-site/jV/1yec.surface.gz’ as an example. This polygon file represents a molecular surface of the molecule 2 (1yec) and the surface is colored according to the electrostatic potential and the hydrophobicity. It is assumed that the current image is the same as that in Figure 3. Then, open the open-remote dialog by choosing the [File] – [Open – Remote] – [Polygon] menu item, enter the above URL to the text field at the top of the dialog, and click the 'OK' button. As a result, the polygon is loaded, displayed and assigned file ID 3. 
Note that the polygon is displayed at the different position from the molecule 2 since the molecule 2 is translated. However, because the polygon and the molecule 2 are described by the same coordinates in their files, their images can be exactly superposed by executing ‘fit 3 2’ from the command line, where the ‘fit’ command performs the copy of the transform matrix. Finally, the image in Figure 4 appears.

[[File:Fig4.jpg|An example of polygon images.|center|600px]]

You can control the transparency rate of polygons. Try ’set transparency 0.5’ from the command line, where 0.5 stands for 50% transparency. To restore the image, execute ‘reset transparency’ or ‘set transparency 0’. In the same sense as each atom of a molecule, each vertex of a polygon is assigned either selected or not selected. All vertices are selected in the initial state. Execute a command ’displayvertex off’ and all vertices become invisible. Next execute ’selectvertex within(10.0, 1&amp;*H@2)’, where this means to select vertices that exist within 10 angstroms from each atom that belongs to the first residue of the ‘H’ chain of the molecule 2. Subsequently execute ’displayvertex on’. As a result, only the selected vertices are appeared. The usage of the selectvertex command is summarized in the [[Command List]].

== Working with xPSSS ==
Functional site information on a molecule stored at xPSSS (xml-based Protein Structure Search Service) is available in jV3. Before trying this, let us close the molecule 2 and the polygon 3 to make the situation simple. Select the [File] – [Close] – [2. 1yec.pdb] and [File] – [Close] – [3. 1yec.surface.gz] menu items sequentially. Then execute a ‘reset’ command and the transform of the molecule 1 and the position of the viewpoint are initialized. 
Next, confirm that the ‘select’ checkbox of the file 1 is checked, and try a ‘show xps3’ command. The functional site information of the molecule ‘12as’ is read from the xPSSS and ‘type’ and ‘subtype’ keywords for each functional site are listed. These keywords can be used to select a set of atoms. For example, if a keyword ‘CATRES’ exists (probably it does), the command ‘select xps3:CATRES’ selects the corresponding atoms. 
In addition, gene ontology information can be obtained from the xPSSS. The gene ontology information for the molecule 12as is displayed by the command ’show godata’. Similar operations can be applied to other external databases on the Internet provided that the external database supports the interface that jV3 requires. See the [[Functional site information for molecules]] for details.

== Animation ==
The animation of molecules can be performed in jV3. The animation file takes the PDB format, where the MODEL line divides each frame. Let us open an animation file ’http://ef-site.hgc.jp/eF-site/jV/anim.pdb.gz’ as an example from the open-remote dialog shown by selecting the [File] – [Open – Remote] – [Animation] menu item. When an animation file is loaded to the application, the first frame is automatically displayed in the wire frame model. You can start the animation by using the animation-control dialog that is shown by choosing the [Options] – [Animation] menu item. The dialog provides operations such as start and stop of the animation, selection of the animation mode, and adjustment of the speed. Some sample figures of the dialog are shown in the [[GUI#3]]

== Saving your work ==
While in your work, you can create a script file that contains a set of commands that reproduces the current work by using the [File] – [Save] – [Script] menu item. The script file can be loaded by the [File] – [Open – Local] – [Script] menu item. On the other hand, the [File] – [Save] – [PDB] menu item enables to save a molecule to a PDB format file with the coordinates of the atoms being transformed according to the current image. Here, only one molecule must be selected and only selected atoms in the molecule are saved. The other two menu items in the [File] – [Save] menu, [PNG] and [JPEG], save the current screen image to an image file in the PNG and JPEG format, respectively. The created image file has the same size as that of the 3D-display panel in the application.

== Terminating the application ==
The application is terminated when the [File] – [Exit] menu item is chosen or the application window is closed by the way your operation system provides. You can also quit the application by executing ‘exit’ or ‘quit’ command.</text>
    <sha1>8bc28aa5262c32bb6e2d6fa27fcf57b51526ff31</sha1>
  </revision>
  <revision>
    <id>203</id>
    <parentid>202</parentid>
    <timestamp>2009-03-09T09:31:08Z</timestamp>
    <contributor>
      <username>JVuser</username>
      <id>2</id>
    </contributor>
    <comment>/* Displaying polygons */</comment>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="12250" xml:space="preserve">{| style="float:right"
 |__TOC__
 |}
== Starting up ==
It is assumed that Java Runtime Environment and JOGL have been appropriately installed. Once you extract the binary distribution file of jV3, the directory of the name, jV_(version), is generated (Ex. jV_3_6_2). The version is assumed to be 3_6_x hereafter. The application starts up by double-clicking the file ‘jv_3_6_x.jar’ in the jV_3_6_x directory or executing the following command from the command line interface.
 java –jar jv_3_6_x.jar
Figure 1 shows the start-up screen. The window has a 3-panel structure, and the upper-left panel with the black background is a 3D image display area. The status of files that have been loaded to the application is shown in the upper-right panel and the lower panel is a command-input and a message-output area.
[[File:Fig1.jpg|thumb|Figure 1: Start-up screen|center|600px]]

== Displaying molecules ==
If you are working in the environment that is getting on the Internet and know the PDB ID of the molecule that you want to display, the simplest way is as follows. A dialog shown in Figure 2 is opened by selecting the [File] – [Open – Remote] – [PDB ID] menu item. Enter a PDB ID '12as', for example, to the text field and click the 'OK' button, then the PDBML file is read through the Internet and the molecule is displayed. The URL where the PDBML file is retrieved from is specified in the 'properties.txt' file in the jV_3_3_x directory. A molecule is displayed in a wire frame model with colored by atom type in the initial state.

[[File:Fig2.jpg|thumb|Figure 2: Dialog to open the molecule specified by PDB ID|center|200px]]

Let us next attempt to load an arbitrary file on the Internet. Here we use 'http://ef-site.hgc.jp/eF-site/jV/1yec.pdb' as an example. The file is a conventional PDB file whose PDB ID is 1yec. In this case we choose the [File] – [Open – Remote] – [PDB] menu item. Then the open-remote dialog is appeared. Enter the above URL to the text field at the top of the dialog and click the 'OK' button and the molecule is read in and displayed. In jV3, each molecule is displayed according to the space coordination described in its file. Therefore, when loading and displaying more than one molecule together, they can be viewed with an appropriate separation in some cases; however, they may be displayed far separately or may be overlapped depending on the combination. In any case, when adding a new file, the position of the viewpoint is automatically controlled for the whole to be displayed.
The coordinate system is the right hand system with the x-y plane being on the screen (the x-axis is a horizontal line with positive values to the right and the y-axis is a vertical line with positive values up). Although, the above examples are about operations for remote files, a PDB file on your local hard disk can also be opened from the [File] – [Open – Local] – [PDB] menu item.

== Operating molecules ==
Interactive mouse operations are possible for 3D images. By left-dragging the mouse on the 3D-display panel, molecules are rotated around the x-axis or y-axis. By left-dragging the mouse while holding the Shift key or Alt key on the keyboard, molecules are translated along the z-axis. All mouse operations are as follows (as for the Macintosh environment, the Command key + left-drag substitutes for the right-drag).

{| border="1"
 ! Mouse operations !! Actions
 |-
 | Left-drag || The image is rotated around the x (for a vertical motion) and y (for a horizontal motion) axes.
 |-
 | Right-drag || The image is translated on the x-y plane.
 |-
 | [Alt or Shift] + left-drag || The image is translated along the z-axis.
 |-
 | [Alt or Shift] + right-drag || The image is rotated around the z-axis.
 |-
 | [Ctrl] + left-drag || The z-clipping plane is shifted when [Option]-[Slab] is checked.
 |-
 | Left-click || An atom of the molecule displayed on the screen is picked.
 |}

In the upper-right panel in the application window (see Figure 3), the file names that have been loaded to the application are listed, where sequential integers are automatically assigned to the individual file. Each integer is a file ID that can be used to specify the file in the command line interface. In addition, two checkboxes are attached to each file. If you change the status of a ‘display’ checkbox, the corresponding molecule is switched to be displayed or not to be displayed. If you change the status of a ‘select’ checkbox, the corresponding molecule is switched to be a target of the mouse operations or not. For example, set the both ‘display’ checkboxes on, and the both ‘select’ checkboxes off. In this case, either molecule does not move against mouse operations. 
Subsequently set the ‘select’ checkbox of file 1 on. In this case, mouse operations work for the molecule 1. Thus, each file is assigned either selected or not selected, and transform operations, such as rotation or translation, act only on selected files. On the other hand, every atom in a molecule is also assigned either selected or not selected, independently of whether the molecule itself is selected or not. Operations that modify display models or colors work for selected atoms. To see this, choose the [Display] – [Spacefill] menu item. Then the both molecules are displayed with the space fill model because all atoms are initially selected. In the same way, if you choose the [Colors] – [Monochrome] menu item, the both molecules are colored white. These operations are independent of the status of ‘select’ checkboxes mentioned above. 
Let us next try a more detailed operation. Type ‘select *@2’ in the command line area and press Enter key. This command means to select all atoms contained in the file 2 (the usage of the select command is summarized in the reference manual included in the binary distribution of jV3). Subsequently, choose the [Display] – [Cartoon] menu item. As a result, only the molecule 2 is displayed in the cartoon model. Furthermore select the [Colors] – [Structure] menu item, and each residue of the molecule 2 is colored according to its secondary structure type (see Figure 3). 
In order to reproduce the same view as that in Figure 3, first execute ‘reset’ command. It restores the position of the viewpoint and the transform of every file to the initial state. Note that the command line interface tries to complement a command word when the Tab key is pressed. If you enter ‘res’ to the command line and subsequently press the Tab key, the command ‘reset’ is automatically entered. Next set the both ‘select’ checkboxes on, and execute ‘translate z 100’ command. This command means to translate the molecules along the z-axis by 100 angstroms.

[[File:Fig3.jpg|thumb|Figure 3: An example of molecular images.|center|600px]]

== Displaying polygons ==
In addition to molecules, arbitrary shapes described by polygons can be read in and displayed together, where the polygon file is an XML file, whose document type is described in the section 6. Here, we use ’http://ef-site.hgc.jp/eF-site/jV/1yec.surface.gz’ as an example. This polygon file represents a molecular surface of the molecule 2 (1yec) and the surface is colored according to the electrostatic potential and the hydrophobicity. It is assumed that the current image is the same as that in Figure 3. Then, open the open-remote dialog by choosing the [File] – [Open – Remote] – [Polygon] menu item, enter the above URL to the text field at the top of the dialog, and click the 'OK' button. As a result, the polygon is loaded, displayed and assigned file ID 3. 
Note that the polygon is displayed at the different position from the molecule 2 since the molecule 2 is translated. However, because the polygon and the molecule 2 are described by the same coordinates in their files, their images can be exactly superposed by executing ‘fit 3 2’ from the command line, where the ‘fit’ command performs the copy of the transform matrix. Finally, the image in Figure 4 appears.

[[File:Fig4.jpg|thumb|Figure4: An example of polygon images.|center|600px]]

You can control the transparency rate of polygons. Try ’set transparency 0.5’ from the command line, where 0.5 stands for 50% transparency. To restore the image, execute ‘reset transparency’ or ‘set transparency 0’. In the same sense as each atom of a molecule, each vertex of a polygon is assigned either selected or not selected. All vertices are selected in the initial state. Execute a command ’displayvertex off’ and all vertices become invisible. Next execute ’selectvertex within(10.0, 1&amp;*H@2)’, where this means to select vertices that exist within 10 angstroms from each atom that belongs to the first residue of the ‘H’ chain of the molecule 2. Subsequently execute ’displayvertex on’. As a result, only the selected vertices are appeared. The usage of the selectvertex command is summarized in the [[Command List]].

== Working with xPSSS ==
Functional site information on a molecule stored at xPSSS (xml-based Protein Structure Search Service) is available in jV3. Before trying this, let us close the molecule 2 and the polygon 3 to make the situation simple. Select the [File] – [Close] – [2. 1yec.pdb] and [File] – [Close] – [3. 1yec.surface.gz] menu items sequentially. Then execute a ‘reset’ command and the transform of the molecule 1 and the position of the viewpoint are initialized. 
Next, confirm that the ‘select’ checkbox of the file 1 is checked, and try a ‘show xps3’ command. The functional site information of the molecule ‘12as’ is read from the xPSSS and ‘type’ and ‘subtype’ keywords for each functional site are listed. These keywords can be used to select a set of atoms. For example, if a keyword ‘CATRES’ exists (probably it does), the command ‘select xps3:CATRES’ selects the corresponding atoms. 
In addition, gene ontology information can be obtained from the xPSSS. The gene ontology information for the molecule 12as is displayed by the command ’show godata’. Similar operations can be applied to other external databases on the Internet provided that the external database supports the interface that jV3 requires. See the [[Functional site information for molecules]] for details.

== Animation ==
The animation of molecules can be performed in jV3. The animation file takes the PDB format, where the MODEL line divides each frame. Let us open an animation file ’http://ef-site.hgc.jp/eF-site/jV/anim.pdb.gz’ as an example from the open-remote dialog shown by selecting the [File] – [Open – Remote] – [Animation] menu item. When an animation file is loaded to the application, the first frame is automatically displayed in the wire frame model. You can start the animation by using the animation-control dialog that is shown by choosing the [Options] – [Animation] menu item. The dialog provides operations such as start and stop of the animation, selection of the animation mode, and adjustment of the speed. Some sample figures of the dialog are shown in the [[GUI#3]]

== Saving your work ==
While in your work, you can create a script file that contains a set of commands that reproduces the current work by using the [File] – [Save] – [Script] menu item. The script file can be loaded by the [File] – [Open – Local] – [Script] menu item. On the other hand, the [File] – [Save] – [PDB] menu item enables to save a molecule to a PDB format file with the coordinates of the atoms being transformed according to the current image. Here, only one molecule must be selected and only selected atoms in the molecule are saved. The other two menu items in the [File] – [Save] menu, [PNG] and [JPEG], save the current screen image to an image file in the PNG and JPEG format, respectively. The created image file has the same size as that of the 3D-display panel in the application.

== Terminating the application ==
The application is terminated when the [File] – [Exit] menu item is chosen or the application window is closed by the way your operation system provides. You can also quit the application by executing ‘exit’ or ‘quit’ command.</text>
    <sha1>11c4872c6c8ceccb7a34702f54c57c23fef3bd5c</sha1>
  </revision>
  <revision>
    <id>204</id>
    <parentid>203</parentid>
    <timestamp>2009-03-09T09:32:44Z</timestamp>
    <contributor>
      <username>JVuser</username>
      <id>2</id>
    </contributor>
    <comment>/* Displaying molecules */</comment>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="12251" xml:space="preserve">{| style="float:right"
 |__TOC__
 |}
== Starting up ==
It is assumed that Java Runtime Environment and JOGL have been appropriately installed. Once you extract the binary distribution file of jV3, the directory of the name, jV_(version), is generated (Ex. jV_3_6_2). The version is assumed to be 3_6_x hereafter. The application starts up by double-clicking the file ‘jv_3_6_x.jar’ in the jV_3_6_x directory or executing the following command from the command line interface.
 java –jar jv_3_6_x.jar
Figure 1 shows the start-up screen. The window has a 3-panel structure, and the upper-left panel with the black background is a 3D image display area. The status of files that have been loaded to the application is shown in the upper-right panel and the lower panel is a command-input and a message-output area.
[[File:Fig1.jpg|thumb|Figure 1: Start-up screen|center|600px]]

== Displaying molecules ==
If you are working in the environment that is getting on the Internet and know the PDB ID of the molecule that you want to display, the simplest way is as follows. A dialog shown in Figure 2 is opened by selecting the [File] – [Open – Remote] – [PDB ID] menu item. Enter a PDB ID '12as', for example, to the text field and click the 'OK' button, then the PDBML file is read through the Internet and the molecule is displayed. The URL where the PDBML file is retrieved from is specified in the 'properties.txt' file in the jV_3_3_x directory. A molecule is displayed in a wire frame model with colored by atom type in the initial state.

[[File:Fig2.jpg|thumb|Figure 2: Dialog to open the molecule specified by PDB ID|center|200px]]

Let us next attempt to load an arbitrary file on the Internet. Here we use 'http://ef-site.hgc.jp/eF-site/jV/1yec.pdb' as an example. The file is a conventional PDB file whose PDB ID is 1yec. In this case we choose the [File] – [Open – Remote] – [PDB] menu item. Then the open-remote dialog is appeared. Enter the above URL to the text field at the top of the dialog and click the 'OK' button and the molecule is read in and displayed. In jV3, each molecule is displayed according to the space coordination described in its file. Therefore, when loading and displaying more than one molecule together, they can be viewed with an appropriate separation in some cases; however, they may be displayed far separately or may be overlapped depending on the combination. In any case, when adding a new file, the position of the viewpoint is automatically controlled for the whole to be displayed.

The coordinate system is the right hand system with the x-y plane being on the screen (the x-axis is a horizontal line with positive values to the right and the y-axis is a vertical line with positive values up). Although, the above examples are about operations for remote files, a PDB file on your local hard disk can also be opened from the [File] – [Open – Local] – [PDB] menu item.

== Operating molecules ==
Interactive mouse operations are possible for 3D images. By left-dragging the mouse on the 3D-display panel, molecules are rotated around the x-axis or y-axis. By left-dragging the mouse while holding the Shift key or Alt key on the keyboard, molecules are translated along the z-axis. All mouse operations are as follows (as for the Macintosh environment, the Command key + left-drag substitutes for the right-drag).

{| border="1"
 ! Mouse operations !! Actions
 |-
 | Left-drag || The image is rotated around the x (for a vertical motion) and y (for a horizontal motion) axes.
 |-
 | Right-drag || The image is translated on the x-y plane.
 |-
 | [Alt or Shift] + left-drag || The image is translated along the z-axis.
 |-
 | [Alt or Shift] + right-drag || The image is rotated around the z-axis.
 |-
 | [Ctrl] + left-drag || The z-clipping plane is shifted when [Option]-[Slab] is checked.
 |-
 | Left-click || An atom of the molecule displayed on the screen is picked.
 |}

In the upper-right panel in the application window (see Figure 3), the file names that have been loaded to the application are listed, where sequential integers are automatically assigned to the individual file. Each integer is a file ID that can be used to specify the file in the command line interface. In addition, two checkboxes are attached to each file. If you change the status of a ‘display’ checkbox, the corresponding molecule is switched to be displayed or not to be displayed. If you change the status of a ‘select’ checkbox, the corresponding molecule is switched to be a target of the mouse operations or not. For example, set the both ‘display’ checkboxes on, and the both ‘select’ checkboxes off. In this case, either molecule does not move against mouse operations. 
Subsequently set the ‘select’ checkbox of file 1 on. In this case, mouse operations work for the molecule 1. Thus, each file is assigned either selected or not selected, and transform operations, such as rotation or translation, act only on selected files. On the other hand, every atom in a molecule is also assigned either selected or not selected, independently of whether the molecule itself is selected or not. Operations that modify display models or colors work for selected atoms. To see this, choose the [Display] – [Spacefill] menu item. Then the both molecules are displayed with the space fill model because all atoms are initially selected. In the same way, if you choose the [Colors] – [Monochrome] menu item, the both molecules are colored white. These operations are independent of the status of ‘select’ checkboxes mentioned above. 
Let us next try a more detailed operation. Type ‘select *@2’ in the command line area and press Enter key. This command means to select all atoms contained in the file 2 (the usage of the select command is summarized in the reference manual included in the binary distribution of jV3). Subsequently, choose the [Display] – [Cartoon] menu item. As a result, only the molecule 2 is displayed in the cartoon model. Furthermore select the [Colors] – [Structure] menu item, and each residue of the molecule 2 is colored according to its secondary structure type (see Figure 3). 
In order to reproduce the same view as that in Figure 3, first execute ‘reset’ command. It restores the position of the viewpoint and the transform of every file to the initial state. Note that the command line interface tries to complement a command word when the Tab key is pressed. If you enter ‘res’ to the command line and subsequently press the Tab key, the command ‘reset’ is automatically entered. Next set the both ‘select’ checkboxes on, and execute ‘translate z 100’ command. This command means to translate the molecules along the z-axis by 100 angstroms.

[[File:Fig3.jpg|thumb|Figure 3: An example of molecular images.|center|600px]]

== Displaying polygons ==
In addition to molecules, arbitrary shapes described by polygons can be read in and displayed together, where the polygon file is an XML file, whose document type is described in the section 6. Here, we use ’http://ef-site.hgc.jp/eF-site/jV/1yec.surface.gz’ as an example. This polygon file represents a molecular surface of the molecule 2 (1yec) and the surface is colored according to the electrostatic potential and the hydrophobicity. It is assumed that the current image is the same as that in Figure 3. Then, open the open-remote dialog by choosing the [File] – [Open – Remote] – [Polygon] menu item, enter the above URL to the text field at the top of the dialog, and click the 'OK' button. As a result, the polygon is loaded, displayed and assigned file ID 3. 
Note that the polygon is displayed at the different position from the molecule 2 since the molecule 2 is translated. However, because the polygon and the molecule 2 are described by the same coordinates in their files, their images can be exactly superposed by executing ‘fit 3 2’ from the command line, where the ‘fit’ command performs the copy of the transform matrix. Finally, the image in Figure 4 appears.

[[File:Fig4.jpg|thumb|Figure4: An example of polygon images.|center|600px]]

You can control the transparency rate of polygons. Try ’set transparency 0.5’ from the command line, where 0.5 stands for 50% transparency. To restore the image, execute ‘reset transparency’ or ‘set transparency 0’. In the same sense as each atom of a molecule, each vertex of a polygon is assigned either selected or not selected. All vertices are selected in the initial state. Execute a command ’displayvertex off’ and all vertices become invisible. Next execute ’selectvertex within(10.0, 1&amp;*H@2)’, where this means to select vertices that exist within 10 angstroms from each atom that belongs to the first residue of the ‘H’ chain of the molecule 2. Subsequently execute ’displayvertex on’. As a result, only the selected vertices are appeared. The usage of the selectvertex command is summarized in the [[Command List]].

== Working with xPSSS ==
Functional site information on a molecule stored at xPSSS (xml-based Protein Structure Search Service) is available in jV3. Before trying this, let us close the molecule 2 and the polygon 3 to make the situation simple. Select the [File] – [Close] – [2. 1yec.pdb] and [File] – [Close] – [3. 1yec.surface.gz] menu items sequentially. Then execute a ‘reset’ command and the transform of the molecule 1 and the position of the viewpoint are initialized. 
Next, confirm that the ‘select’ checkbox of the file 1 is checked, and try a ‘show xps3’ command. The functional site information of the molecule ‘12as’ is read from the xPSSS and ‘type’ and ‘subtype’ keywords for each functional site are listed. These keywords can be used to select a set of atoms. For example, if a keyword ‘CATRES’ exists (probably it does), the command ‘select xps3:CATRES’ selects the corresponding atoms. 
In addition, gene ontology information can be obtained from the xPSSS. The gene ontology information for the molecule 12as is displayed by the command ’show godata’. Similar operations can be applied to other external databases on the Internet provided that the external database supports the interface that jV3 requires. See the [[Functional site information for molecules]] for details.

== Animation ==
The animation of molecules can be performed in jV3. The animation file takes the PDB format, where the MODEL line divides each frame. Let us open an animation file ’http://ef-site.hgc.jp/eF-site/jV/anim.pdb.gz’ as an example from the open-remote dialog shown by selecting the [File] – [Open – Remote] – [Animation] menu item. When an animation file is loaded to the application, the first frame is automatically displayed in the wire frame model. You can start the animation by using the animation-control dialog that is shown by choosing the [Options] – [Animation] menu item. The dialog provides operations such as start and stop of the animation, selection of the animation mode, and adjustment of the speed. Some sample figures of the dialog are shown in the [[GUI#3]]

== Saving your work ==
While in your work, you can create a script file that contains a set of commands that reproduces the current work by using the [File] – [Save] – [Script] menu item. The script file can be loaded by the [File] – [Open – Local] – [Script] menu item. On the other hand, the [File] – [Save] – [PDB] menu item enables to save a molecule to a PDB format file with the coordinates of the atoms being transformed according to the current image. Here, only one molecule must be selected and only selected atoms in the molecule are saved. The other two menu items in the [File] – [Save] menu, [PNG] and [JPEG], save the current screen image to an image file in the PNG and JPEG format, respectively. The created image file has the same size as that of the 3D-display panel in the application.

== Terminating the application ==
The application is terminated when the [File] – [Exit] menu item is chosen or the application window is closed by the way your operation system provides. You can also quit the application by executing ‘exit’ or ‘quit’ command.</text>
    <sha1>c3893d58841268779a67e50cae06428570734557</sha1>
  </revision>
  <revision>
    <id>205</id>
    <parentid>204</parentid>
    <timestamp>2009-03-09T09:33:31Z</timestamp>
    <contributor>
      <username>JVuser</username>
      <id>2</id>
    </contributor>
    <comment>/* Operating molecules */</comment>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="12254" xml:space="preserve">{| style="float:right"
 |__TOC__
 |}
== Starting up ==
It is assumed that Java Runtime Environment and JOGL have been appropriately installed. Once you extract the binary distribution file of jV3, the directory of the name, jV_(version), is generated (Ex. jV_3_6_2). The version is assumed to be 3_6_x hereafter. The application starts up by double-clicking the file ‘jv_3_6_x.jar’ in the jV_3_6_x directory or executing the following command from the command line interface.
 java –jar jv_3_6_x.jar
Figure 1 shows the start-up screen. The window has a 3-panel structure, and the upper-left panel with the black background is a 3D image display area. The status of files that have been loaded to the application is shown in the upper-right panel and the lower panel is a command-input and a message-output area.
[[File:Fig1.jpg|thumb|Figure 1: Start-up screen|center|600px]]

== Displaying molecules ==
If you are working in the environment that is getting on the Internet and know the PDB ID of the molecule that you want to display, the simplest way is as follows. A dialog shown in Figure 2 is opened by selecting the [File] – [Open – Remote] – [PDB ID] menu item. Enter a PDB ID '12as', for example, to the text field and click the 'OK' button, then the PDBML file is read through the Internet and the molecule is displayed. The URL where the PDBML file is retrieved from is specified in the 'properties.txt' file in the jV_3_3_x directory. A molecule is displayed in a wire frame model with colored by atom type in the initial state.

[[File:Fig2.jpg|thumb|Figure 2: Dialog to open the molecule specified by PDB ID|center|200px]]

Let us next attempt to load an arbitrary file on the Internet. Here we use 'http://ef-site.hgc.jp/eF-site/jV/1yec.pdb' as an example. The file is a conventional PDB file whose PDB ID is 1yec. In this case we choose the [File] – [Open – Remote] – [PDB] menu item. Then the open-remote dialog is appeared. Enter the above URL to the text field at the top of the dialog and click the 'OK' button and the molecule is read in and displayed. In jV3, each molecule is displayed according to the space coordination described in its file. Therefore, when loading and displaying more than one molecule together, they can be viewed with an appropriate separation in some cases; however, they may be displayed far separately or may be overlapped depending on the combination. In any case, when adding a new file, the position of the viewpoint is automatically controlled for the whole to be displayed.

The coordinate system is the right hand system with the x-y plane being on the screen (the x-axis is a horizontal line with positive values to the right and the y-axis is a vertical line with positive values up). Although, the above examples are about operations for remote files, a PDB file on your local hard disk can also be opened from the [File] – [Open – Local] – [PDB] menu item.

== Operating molecules ==
Interactive mouse operations are possible for 3D images. By left-dragging the mouse on the 3D-display panel, molecules are rotated around the x-axis or y-axis. By left-dragging the mouse while holding the Shift key or Alt key on the keyboard, molecules are translated along the z-axis. All mouse operations are as follows (as for the Macintosh environment, the Command key + left-drag substitutes for the right-drag).

{| border="1"
 ! Mouse operations !! Actions
 |-
 | Left-drag || The image is rotated around the x (for a vertical motion) and y (for a horizontal motion) axes.
 |-
 | Right-drag || The image is translated on the x-y plane.
 |-
 | [Alt or Shift] + left-drag || The image is translated along the z-axis.
 |-
 | [Alt or Shift] + right-drag || The image is rotated around the z-axis.
 |-
 | [Ctrl] + left-drag || The z-clipping plane is shifted when [Option]-[Slab] is checked.
 |-
 | Left-click || An atom of the molecule displayed on the screen is picked.
 |}

In the upper-right panel in the application window (see Figure 3), the file names that have been loaded to the application are listed, where sequential integers are automatically assigned to the individual file. Each integer is a file ID that can be used to specify the file in the command line interface. In addition, two checkboxes are attached to each file. If you change the status of a ‘display’ checkbox, the corresponding molecule is switched to be displayed or not to be displayed. If you change the status of a ‘select’ checkbox, the corresponding molecule is switched to be a target of the mouse operations or not. For example, set the both ‘display’ checkboxes on, and the both ‘select’ checkboxes off. In this case, either molecule does not move against mouse operations. 

Subsequently set the ‘select’ checkbox of file 1 on. In this case, mouse operations work for the molecule 1. Thus, each file is assigned either selected or not selected, and transform operations, such as rotation or translation, act only on selected files. On the other hand, every atom in a molecule is also assigned either selected or not selected, independently of whether the molecule itself is selected or not. Operations that modify display models or colors work for selected atoms. To see this, choose the [Display] – [Spacefill] menu item. Then the both molecules are displayed with the space fill model because all atoms are initially selected. In the same way, if you choose the [Colors] – [Monochrome] menu item, the both molecules are colored white. These operations are independent of the status of ‘select’ checkboxes mentioned above. 

Let us next try a more detailed operation. Type ‘select *@2’ in the command line area and press Enter key. This command means to select all atoms contained in the file 2 (the usage of the select command is summarized in the reference manual included in the binary distribution of jV3). Subsequently, choose the [Display] – [Cartoon] menu item. As a result, only the molecule 2 is displayed in the cartoon model. Furthermore select the [Colors] – [Structure] menu item, and each residue of the molecule 2 is colored according to its secondary structure type (see Figure 3). 

In order to reproduce the same view as that in Figure 3, first execute ‘reset’ command. It restores the position of the viewpoint and the transform of every file to the initial state. Note that the command line interface tries to complement a command word when the Tab key is pressed. If you enter ‘res’ to the command line and subsequently press the Tab key, the command ‘reset’ is automatically entered. Next set the both ‘select’ checkboxes on, and execute ‘translate z 100’ command. This command means to translate the molecules along the z-axis by 100 angstroms.

[[File:Fig3.jpg|thumb|Figure 3: An example of molecular images.|center|600px]]

== Displaying polygons ==
In addition to molecules, arbitrary shapes described by polygons can be read in and displayed together, where the polygon file is an XML file, whose document type is described in the section 6. Here, we use ’http://ef-site.hgc.jp/eF-site/jV/1yec.surface.gz’ as an example. This polygon file represents a molecular surface of the molecule 2 (1yec) and the surface is colored according to the electrostatic potential and the hydrophobicity. It is assumed that the current image is the same as that in Figure 3. Then, open the open-remote dialog by choosing the [File] – [Open – Remote] – [Polygon] menu item, enter the above URL to the text field at the top of the dialog, and click the 'OK' button. As a result, the polygon is loaded, displayed and assigned file ID 3. 
Note that the polygon is displayed at the different position from the molecule 2 since the molecule 2 is translated. However, because the polygon and the molecule 2 are described by the same coordinates in their files, their images can be exactly superposed by executing ‘fit 3 2’ from the command line, where the ‘fit’ command performs the copy of the transform matrix. Finally, the image in Figure 4 appears.

[[File:Fig4.jpg|thumb|Figure4: An example of polygon images.|center|600px]]

You can control the transparency rate of polygons. Try ’set transparency 0.5’ from the command line, where 0.5 stands for 50% transparency. To restore the image, execute ‘reset transparency’ or ‘set transparency 0’. In the same sense as each atom of a molecule, each vertex of a polygon is assigned either selected or not selected. All vertices are selected in the initial state. Execute a command ’displayvertex off’ and all vertices become invisible. Next execute ’selectvertex within(10.0, 1&amp;*H@2)’, where this means to select vertices that exist within 10 angstroms from each atom that belongs to the first residue of the ‘H’ chain of the molecule 2. Subsequently execute ’displayvertex on’. As a result, only the selected vertices are appeared. The usage of the selectvertex command is summarized in the [[Command List]].

== Working with xPSSS ==
Functional site information on a molecule stored at xPSSS (xml-based Protein Structure Search Service) is available in jV3. Before trying this, let us close the molecule 2 and the polygon 3 to make the situation simple. Select the [File] – [Close] – [2. 1yec.pdb] and [File] – [Close] – [3. 1yec.surface.gz] menu items sequentially. Then execute a ‘reset’ command and the transform of the molecule 1 and the position of the viewpoint are initialized. 
Next, confirm that the ‘select’ checkbox of the file 1 is checked, and try a ‘show xps3’ command. The functional site information of the molecule ‘12as’ is read from the xPSSS and ‘type’ and ‘subtype’ keywords for each functional site are listed. These keywords can be used to select a set of atoms. For example, if a keyword ‘CATRES’ exists (probably it does), the command ‘select xps3:CATRES’ selects the corresponding atoms. 
In addition, gene ontology information can be obtained from the xPSSS. The gene ontology information for the molecule 12as is displayed by the command ’show godata’. Similar operations can be applied to other external databases on the Internet provided that the external database supports the interface that jV3 requires. See the [[Functional site information for molecules]] for details.

== Animation ==
The animation of molecules can be performed in jV3. The animation file takes the PDB format, where the MODEL line divides each frame. Let us open an animation file ’http://ef-site.hgc.jp/eF-site/jV/anim.pdb.gz’ as an example from the open-remote dialog shown by selecting the [File] – [Open – Remote] – [Animation] menu item. When an animation file is loaded to the application, the first frame is automatically displayed in the wire frame model. You can start the animation by using the animation-control dialog that is shown by choosing the [Options] – [Animation] menu item. The dialog provides operations such as start and stop of the animation, selection of the animation mode, and adjustment of the speed. Some sample figures of the dialog are shown in the [[GUI#3]]

== Saving your work ==
While in your work, you can create a script file that contains a set of commands that reproduces the current work by using the [File] – [Save] – [Script] menu item. The script file can be loaded by the [File] – [Open – Local] – [Script] menu item. On the other hand, the [File] – [Save] – [PDB] menu item enables to save a molecule to a PDB format file with the coordinates of the atoms being transformed according to the current image. Here, only one molecule must be selected and only selected atoms in the molecule are saved. The other two menu items in the [File] – [Save] menu, [PNG] and [JPEG], save the current screen image to an image file in the PNG and JPEG format, respectively. The created image file has the same size as that of the 3D-display panel in the application.

== Terminating the application ==
The application is terminated when the [File] – [Exit] menu item is chosen or the application window is closed by the way your operation system provides. You can also quit the application by executing ‘exit’ or ‘quit’ command.</text>
    <sha1>3c14fd626113a419751e3d7cadce1d95857b34d0</sha1>
  </revision>
  <revision>
    <id>206</id>
    <parentid>205</parentid>
    <timestamp>2009-03-09T09:33:54Z</timestamp>
    <contributor>
      <username>JVuser</username>
      <id>2</id>
    </contributor>
    <comment>/* Displaying polygons */</comment>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="12255" xml:space="preserve">{| style="float:right"
 |__TOC__
 |}
== Starting up ==
It is assumed that Java Runtime Environment and JOGL have been appropriately installed. Once you extract the binary distribution file of jV3, the directory of the name, jV_(version), is generated (Ex. jV_3_6_2). The version is assumed to be 3_6_x hereafter. The application starts up by double-clicking the file ‘jv_3_6_x.jar’ in the jV_3_6_x directory or executing the following command from the command line interface.
 java –jar jv_3_6_x.jar
Figure 1 shows the start-up screen. The window has a 3-panel structure, and the upper-left panel with the black background is a 3D image display area. The status of files that have been loaded to the application is shown in the upper-right panel and the lower panel is a command-input and a message-output area.
[[File:Fig1.jpg|thumb|Figure 1: Start-up screen|center|600px]]

== Displaying molecules ==
If you are working in the environment that is getting on the Internet and know the PDB ID of the molecule that you want to display, the simplest way is as follows. A dialog shown in Figure 2 is opened by selecting the [File] – [Open – Remote] – [PDB ID] menu item. Enter a PDB ID '12as', for example, to the text field and click the 'OK' button, then the PDBML file is read through the Internet and the molecule is displayed. The URL where the PDBML file is retrieved from is specified in the 'properties.txt' file in the jV_3_3_x directory. A molecule is displayed in a wire frame model with colored by atom type in the initial state.

[[File:Fig2.jpg|thumb|Figure 2: Dialog to open the molecule specified by PDB ID|center|200px]]

Let us next attempt to load an arbitrary file on the Internet. Here we use 'http://ef-site.hgc.jp/eF-site/jV/1yec.pdb' as an example. The file is a conventional PDB file whose PDB ID is 1yec. In this case we choose the [File] – [Open – Remote] – [PDB] menu item. Then the open-remote dialog is appeared. Enter the above URL to the text field at the top of the dialog and click the 'OK' button and the molecule is read in and displayed. In jV3, each molecule is displayed according to the space coordination described in its file. Therefore, when loading and displaying more than one molecule together, they can be viewed with an appropriate separation in some cases; however, they may be displayed far separately or may be overlapped depending on the combination. In any case, when adding a new file, the position of the viewpoint is automatically controlled for the whole to be displayed.

The coordinate system is the right hand system with the x-y plane being on the screen (the x-axis is a horizontal line with positive values to the right and the y-axis is a vertical line with positive values up). Although, the above examples are about operations for remote files, a PDB file on your local hard disk can also be opened from the [File] – [Open – Local] – [PDB] menu item.

== Operating molecules ==
Interactive mouse operations are possible for 3D images. By left-dragging the mouse on the 3D-display panel, molecules are rotated around the x-axis or y-axis. By left-dragging the mouse while holding the Shift key or Alt key on the keyboard, molecules are translated along the z-axis. All mouse operations are as follows (as for the Macintosh environment, the Command key + left-drag substitutes for the right-drag).

{| border="1"
 ! Mouse operations !! Actions
 |-
 | Left-drag || The image is rotated around the x (for a vertical motion) and y (for a horizontal motion) axes.
 |-
 | Right-drag || The image is translated on the x-y plane.
 |-
 | [Alt or Shift] + left-drag || The image is translated along the z-axis.
 |-
 | [Alt or Shift] + right-drag || The image is rotated around the z-axis.
 |-
 | [Ctrl] + left-drag || The z-clipping plane is shifted when [Option]-[Slab] is checked.
 |-
 | Left-click || An atom of the molecule displayed on the screen is picked.
 |}

In the upper-right panel in the application window (see Figure 3), the file names that have been loaded to the application are listed, where sequential integers are automatically assigned to the individual file. Each integer is a file ID that can be used to specify the file in the command line interface. In addition, two checkboxes are attached to each file. If you change the status of a ‘display’ checkbox, the corresponding molecule is switched to be displayed or not to be displayed. If you change the status of a ‘select’ checkbox, the corresponding molecule is switched to be a target of the mouse operations or not. For example, set the both ‘display’ checkboxes on, and the both ‘select’ checkboxes off. In this case, either molecule does not move against mouse operations. 

Subsequently set the ‘select’ checkbox of file 1 on. In this case, mouse operations work for the molecule 1. Thus, each file is assigned either selected or not selected, and transform operations, such as rotation or translation, act only on selected files. On the other hand, every atom in a molecule is also assigned either selected or not selected, independently of whether the molecule itself is selected or not. Operations that modify display models or colors work for selected atoms. To see this, choose the [Display] – [Spacefill] menu item. Then the both molecules are displayed with the space fill model because all atoms are initially selected. In the same way, if you choose the [Colors] – [Monochrome] menu item, the both molecules are colored white. These operations are independent of the status of ‘select’ checkboxes mentioned above. 

Let us next try a more detailed operation. Type ‘select *@2’ in the command line area and press Enter key. This command means to select all atoms contained in the file 2 (the usage of the select command is summarized in the reference manual included in the binary distribution of jV3). Subsequently, choose the [Display] – [Cartoon] menu item. As a result, only the molecule 2 is displayed in the cartoon model. Furthermore select the [Colors] – [Structure] menu item, and each residue of the molecule 2 is colored according to its secondary structure type (see Figure 3). 

In order to reproduce the same view as that in Figure 3, first execute ‘reset’ command. It restores the position of the viewpoint and the transform of every file to the initial state. Note that the command line interface tries to complement a command word when the Tab key is pressed. If you enter ‘res’ to the command line and subsequently press the Tab key, the command ‘reset’ is automatically entered. Next set the both ‘select’ checkboxes on, and execute ‘translate z 100’ command. This command means to translate the molecules along the z-axis by 100 angstroms.

[[File:Fig3.jpg|thumb|Figure 3: An example of molecular images.|center|600px]]

== Displaying polygons ==
In addition to molecules, arbitrary shapes described by polygons can be read in and displayed together, where the polygon file is an XML file, whose document type is described in the section 6. Here, we use ’http://ef-site.hgc.jp/eF-site/jV/1yec.surface.gz’ as an example. This polygon file represents a molecular surface of the molecule 2 (1yec) and the surface is colored according to the electrostatic potential and the hydrophobicity. It is assumed that the current image is the same as that in Figure 3. Then, open the open-remote dialog by choosing the [File] – [Open – Remote] – [Polygon] menu item, enter the above URL to the text field at the top of the dialog, and click the 'OK' button. As a result, the polygon is loaded, displayed and assigned file ID 3. 

Note that the polygon is displayed at the different position from the molecule 2 since the molecule 2 is translated. However, because the polygon and the molecule 2 are described by the same coordinates in their files, their images can be exactly superposed by executing ‘fit 3 2’ from the command line, where the ‘fit’ command performs the copy of the transform matrix. Finally, the image in Figure 4 appears.

[[File:Fig4.jpg|thumb|Figure4: An example of polygon images.|center|600px]]

You can control the transparency rate of polygons. Try ’set transparency 0.5’ from the command line, where 0.5 stands for 50% transparency. To restore the image, execute ‘reset transparency’ or ‘set transparency 0’. In the same sense as each atom of a molecule, each vertex of a polygon is assigned either selected or not selected. All vertices are selected in the initial state. Execute a command ’displayvertex off’ and all vertices become invisible. Next execute ’selectvertex within(10.0, 1&amp;*H@2)’, where this means to select vertices that exist within 10 angstroms from each atom that belongs to the first residue of the ‘H’ chain of the molecule 2. Subsequently execute ’displayvertex on’. As a result, only the selected vertices are appeared. The usage of the selectvertex command is summarized in the [[Command List]].

== Working with xPSSS ==
Functional site information on a molecule stored at xPSSS (xml-based Protein Structure Search Service) is available in jV3. Before trying this, let us close the molecule 2 and the polygon 3 to make the situation simple. Select the [File] – [Close] – [2. 1yec.pdb] and [File] – [Close] – [3. 1yec.surface.gz] menu items sequentially. Then execute a ‘reset’ command and the transform of the molecule 1 and the position of the viewpoint are initialized. 
Next, confirm that the ‘select’ checkbox of the file 1 is checked, and try a ‘show xps3’ command. The functional site information of the molecule ‘12as’ is read from the xPSSS and ‘type’ and ‘subtype’ keywords for each functional site are listed. These keywords can be used to select a set of atoms. For example, if a keyword ‘CATRES’ exists (probably it does), the command ‘select xps3:CATRES’ selects the corresponding atoms. 
In addition, gene ontology information can be obtained from the xPSSS. The gene ontology information for the molecule 12as is displayed by the command ’show godata’. Similar operations can be applied to other external databases on the Internet provided that the external database supports the interface that jV3 requires. See the [[Functional site information for molecules]] for details.

== Animation ==
The animation of molecules can be performed in jV3. The animation file takes the PDB format, where the MODEL line divides each frame. Let us open an animation file ’http://ef-site.hgc.jp/eF-site/jV/anim.pdb.gz’ as an example from the open-remote dialog shown by selecting the [File] – [Open – Remote] – [Animation] menu item. When an animation file is loaded to the application, the first frame is automatically displayed in the wire frame model. You can start the animation by using the animation-control dialog that is shown by choosing the [Options] – [Animation] menu item. The dialog provides operations such as start and stop of the animation, selection of the animation mode, and adjustment of the speed. Some sample figures of the dialog are shown in the [[GUI#3]]

== Saving your work ==
While in your work, you can create a script file that contains a set of commands that reproduces the current work by using the [File] – [Save] – [Script] menu item. The script file can be loaded by the [File] – [Open – Local] – [Script] menu item. On the other hand, the [File] – [Save] – [PDB] menu item enables to save a molecule to a PDB format file with the coordinates of the atoms being transformed according to the current image. Here, only one molecule must be selected and only selected atoms in the molecule are saved. The other two menu items in the [File] – [Save] menu, [PNG] and [JPEG], save the current screen image to an image file in the PNG and JPEG format, respectively. The created image file has the same size as that of the 3D-display panel in the application.

== Terminating the application ==
The application is terminated when the [File] – [Exit] menu item is chosen or the application window is closed by the way your operation system provides. You can also quit the application by executing ‘exit’ or ‘quit’ command.</text>
    <sha1>95f11e329a603a6199b5e9f6cd58d89dc39fb0d0</sha1>
  </revision>
  <revision>
    <id>207</id>
    <parentid>206</parentid>
    <timestamp>2009-03-09T09:34:10Z</timestamp>
    <contributor>
      <username>JVuser</username>
      <id>2</id>
    </contributor>
    <comment>/* Working with xPSSS */</comment>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="12257" xml:space="preserve">{| style="float:right"
 |__TOC__
 |}
== Starting up ==
It is assumed that Java Runtime Environment and JOGL have been appropriately installed. Once you extract the binary distribution file of jV3, the directory of the name, jV_(version), is generated (Ex. jV_3_6_2). The version is assumed to be 3_6_x hereafter. The application starts up by double-clicking the file ‘jv_3_6_x.jar’ in the jV_3_6_x directory or executing the following command from the command line interface.
 java –jar jv_3_6_x.jar
Figure 1 shows the start-up screen. The window has a 3-panel structure, and the upper-left panel with the black background is a 3D image display area. The status of files that have been loaded to the application is shown in the upper-right panel and the lower panel is a command-input and a message-output area.
[[File:Fig1.jpg|thumb|Figure 1: Start-up screen|center|600px]]

== Displaying molecules ==
If you are working in the environment that is getting on the Internet and know the PDB ID of the molecule that you want to display, the simplest way is as follows. A dialog shown in Figure 2 is opened by selecting the [File] – [Open – Remote] – [PDB ID] menu item. Enter a PDB ID '12as', for example, to the text field and click the 'OK' button, then the PDBML file is read through the Internet and the molecule is displayed. The URL where the PDBML file is retrieved from is specified in the 'properties.txt' file in the jV_3_3_x directory. A molecule is displayed in a wire frame model with colored by atom type in the initial state.

[[File:Fig2.jpg|thumb|Figure 2: Dialog to open the molecule specified by PDB ID|center|200px]]

Let us next attempt to load an arbitrary file on the Internet. Here we use 'http://ef-site.hgc.jp/eF-site/jV/1yec.pdb' as an example. The file is a conventional PDB file whose PDB ID is 1yec. In this case we choose the [File] – [Open – Remote] – [PDB] menu item. Then the open-remote dialog is appeared. Enter the above URL to the text field at the top of the dialog and click the 'OK' button and the molecule is read in and displayed. In jV3, each molecule is displayed according to the space coordination described in its file. Therefore, when loading and displaying more than one molecule together, they can be viewed with an appropriate separation in some cases; however, they may be displayed far separately or may be overlapped depending on the combination. In any case, when adding a new file, the position of the viewpoint is automatically controlled for the whole to be displayed.

The coordinate system is the right hand system with the x-y plane being on the screen (the x-axis is a horizontal line with positive values to the right and the y-axis is a vertical line with positive values up). Although, the above examples are about operations for remote files, a PDB file on your local hard disk can also be opened from the [File] – [Open – Local] – [PDB] menu item.

== Operating molecules ==
Interactive mouse operations are possible for 3D images. By left-dragging the mouse on the 3D-display panel, molecules are rotated around the x-axis or y-axis. By left-dragging the mouse while holding the Shift key or Alt key on the keyboard, molecules are translated along the z-axis. All mouse operations are as follows (as for the Macintosh environment, the Command key + left-drag substitutes for the right-drag).

{| border="1"
 ! Mouse operations !! Actions
 |-
 | Left-drag || The image is rotated around the x (for a vertical motion) and y (for a horizontal motion) axes.
 |-
 | Right-drag || The image is translated on the x-y plane.
 |-
 | [Alt or Shift] + left-drag || The image is translated along the z-axis.
 |-
 | [Alt or Shift] + right-drag || The image is rotated around the z-axis.
 |-
 | [Ctrl] + left-drag || The z-clipping plane is shifted when [Option]-[Slab] is checked.
 |-
 | Left-click || An atom of the molecule displayed on the screen is picked.
 |}

In the upper-right panel in the application window (see Figure 3), the file names that have been loaded to the application are listed, where sequential integers are automatically assigned to the individual file. Each integer is a file ID that can be used to specify the file in the command line interface. In addition, two checkboxes are attached to each file. If you change the status of a ‘display’ checkbox, the corresponding molecule is switched to be displayed or not to be displayed. If you change the status of a ‘select’ checkbox, the corresponding molecule is switched to be a target of the mouse operations or not. For example, set the both ‘display’ checkboxes on, and the both ‘select’ checkboxes off. In this case, either molecule does not move against mouse operations. 

Subsequently set the ‘select’ checkbox of file 1 on. In this case, mouse operations work for the molecule 1. Thus, each file is assigned either selected or not selected, and transform operations, such as rotation or translation, act only on selected files. On the other hand, every atom in a molecule is also assigned either selected or not selected, independently of whether the molecule itself is selected or not. Operations that modify display models or colors work for selected atoms. To see this, choose the [Display] – [Spacefill] menu item. Then the both molecules are displayed with the space fill model because all atoms are initially selected. In the same way, if you choose the [Colors] – [Monochrome] menu item, the both molecules are colored white. These operations are independent of the status of ‘select’ checkboxes mentioned above. 

Let us next try a more detailed operation. Type ‘select *@2’ in the command line area and press Enter key. This command means to select all atoms contained in the file 2 (the usage of the select command is summarized in the reference manual included in the binary distribution of jV3). Subsequently, choose the [Display] – [Cartoon] menu item. As a result, only the molecule 2 is displayed in the cartoon model. Furthermore select the [Colors] – [Structure] menu item, and each residue of the molecule 2 is colored according to its secondary structure type (see Figure 3). 

In order to reproduce the same view as that in Figure 3, first execute ‘reset’ command. It restores the position of the viewpoint and the transform of every file to the initial state. Note that the command line interface tries to complement a command word when the Tab key is pressed. If you enter ‘res’ to the command line and subsequently press the Tab key, the command ‘reset’ is automatically entered. Next set the both ‘select’ checkboxes on, and execute ‘translate z 100’ command. This command means to translate the molecules along the z-axis by 100 angstroms.

[[File:Fig3.jpg|thumb|Figure 3: An example of molecular images.|center|600px]]

== Displaying polygons ==
In addition to molecules, arbitrary shapes described by polygons can be read in and displayed together, where the polygon file is an XML file, whose document type is described in the section 6. Here, we use ’http://ef-site.hgc.jp/eF-site/jV/1yec.surface.gz’ as an example. This polygon file represents a molecular surface of the molecule 2 (1yec) and the surface is colored according to the electrostatic potential and the hydrophobicity. It is assumed that the current image is the same as that in Figure 3. Then, open the open-remote dialog by choosing the [File] – [Open – Remote] – [Polygon] menu item, enter the above URL to the text field at the top of the dialog, and click the 'OK' button. As a result, the polygon is loaded, displayed and assigned file ID 3. 

Note that the polygon is displayed at the different position from the molecule 2 since the molecule 2 is translated. However, because the polygon and the molecule 2 are described by the same coordinates in their files, their images can be exactly superposed by executing ‘fit 3 2’ from the command line, where the ‘fit’ command performs the copy of the transform matrix. Finally, the image in Figure 4 appears.

[[File:Fig4.jpg|thumb|Figure4: An example of polygon images.|center|600px]]

You can control the transparency rate of polygons. Try ’set transparency 0.5’ from the command line, where 0.5 stands for 50% transparency. To restore the image, execute ‘reset transparency’ or ‘set transparency 0’. In the same sense as each atom of a molecule, each vertex of a polygon is assigned either selected or not selected. All vertices are selected in the initial state. Execute a command ’displayvertex off’ and all vertices become invisible. Next execute ’selectvertex within(10.0, 1&amp;*H@2)’, where this means to select vertices that exist within 10 angstroms from each atom that belongs to the first residue of the ‘H’ chain of the molecule 2. Subsequently execute ’displayvertex on’. As a result, only the selected vertices are appeared. The usage of the selectvertex command is summarized in the [[Command List]].

== Working with xPSSS ==
Functional site information on a molecule stored at xPSSS (xml-based Protein Structure Search Service) is available in jV3. Before trying this, let us close the molecule 2 and the polygon 3 to make the situation simple. Select the [File] – [Close] – [2. 1yec.pdb] and [File] – [Close] – [3. 1yec.surface.gz] menu items sequentially. Then execute a ‘reset’ command and the transform of the molecule 1 and the position of the viewpoint are initialized. 

Next, confirm that the ‘select’ checkbox of the file 1 is checked, and try a ‘show xps3’ command. The functional site information of the molecule ‘12as’ is read from the xPSSS and ‘type’ and ‘subtype’ keywords for each functional site are listed. These keywords can be used to select a set of atoms. For example, if a keyword ‘CATRES’ exists (probably it does), the command ‘select xps3:CATRES’ selects the corresponding atoms. 

In addition, gene ontology information can be obtained from the xPSSS. The gene ontology information for the molecule 12as is displayed by the command ’show godata’. Similar operations can be applied to other external databases on the Internet provided that the external database supports the interface that jV3 requires. See the [[Functional site information for molecules]] for details.

== Animation ==
The animation of molecules can be performed in jV3. The animation file takes the PDB format, where the MODEL line divides each frame. Let us open an animation file ’http://ef-site.hgc.jp/eF-site/jV/anim.pdb.gz’ as an example from the open-remote dialog shown by selecting the [File] – [Open – Remote] – [Animation] menu item. When an animation file is loaded to the application, the first frame is automatically displayed in the wire frame model. You can start the animation by using the animation-control dialog that is shown by choosing the [Options] – [Animation] menu item. The dialog provides operations such as start and stop of the animation, selection of the animation mode, and adjustment of the speed. Some sample figures of the dialog are shown in the [[GUI#3]]

== Saving your work ==
While in your work, you can create a script file that contains a set of commands that reproduces the current work by using the [File] – [Save] – [Script] menu item. The script file can be loaded by the [File] – [Open – Local] – [Script] menu item. On the other hand, the [File] – [Save] – [PDB] menu item enables to save a molecule to a PDB format file with the coordinates of the atoms being transformed according to the current image. Here, only one molecule must be selected and only selected atoms in the molecule are saved. The other two menu items in the [File] – [Save] menu, [PNG] and [JPEG], save the current screen image to an image file in the PNG and JPEG format, respectively. The created image file has the same size as that of the 3D-display panel in the application.

== Terminating the application ==
The application is terminated when the [File] – [Exit] menu item is chosen or the application window is closed by the way your operation system provides. You can also quit the application by executing ‘exit’ or ‘quit’ command.</text>
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    <id>208</id>
    <parentid>207</parentid>
    <timestamp>2009-03-09T09:35:45Z</timestamp>
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    <text bytes="12257" xml:space="preserve">{| style="float:right"
 |__TOC__
 |}
== Starting up ==
It is assumed that Java Runtime Environment and JOGL have been appropriately installed. Once you extract the binary distribution file of jV3, the directory of the name, jV_(version), is generated (Ex. jV_3_6_2). The version is assumed to be 3_6_x hereafter. The application starts up by double-clicking the file ‘jv_3_6_x.jar’ in the jV_3_6_x directory or executing the following command from the command line interface.
 java –jar jv_3_6_x.jar
Figure 1 shows the start-up screen. The window has a 3-panel structure, and the upper-left panel with the black background is a 3D image display area. The status of files that have been loaded to the application is shown in the upper-right panel and the lower panel is a command-input and a message-output area.
[[File:Fig1.jpg|thumb|Figure 1: Start-up screen|center|500px]]

== Displaying molecules ==
If you are working in the environment that is getting on the Internet and know the PDB ID of the molecule that you want to display, the simplest way is as follows. A dialog shown in Figure 2 is opened by selecting the [File] – [Open – Remote] – [PDB ID] menu item. Enter a PDB ID '12as', for example, to the text field and click the 'OK' button, then the PDBML file is read through the Internet and the molecule is displayed. The URL where the PDBML file is retrieved from is specified in the 'properties.txt' file in the jV_3_3_x directory. A molecule is displayed in a wire frame model with colored by atom type in the initial state.

[[File:Fig2.jpg|thumb|Figure 2: Dialog to open the molecule specified by PDB ID|center|200px]]

Let us next attempt to load an arbitrary file on the Internet. Here we use 'http://ef-site.hgc.jp/eF-site/jV/1yec.pdb' as an example. The file is a conventional PDB file whose PDB ID is 1yec. In this case we choose the [File] – [Open – Remote] – [PDB] menu item. Then the open-remote dialog is appeared. Enter the above URL to the text field at the top of the dialog and click the 'OK' button and the molecule is read in and displayed. In jV3, each molecule is displayed according to the space coordination described in its file. Therefore, when loading and displaying more than one molecule together, they can be viewed with an appropriate separation in some cases; however, they may be displayed far separately or may be overlapped depending on the combination. In any case, when adding a new file, the position of the viewpoint is automatically controlled for the whole to be displayed.

The coordinate system is the right hand system with the x-y plane being on the screen (the x-axis is a horizontal line with positive values to the right and the y-axis is a vertical line with positive values up). Although, the above examples are about operations for remote files, a PDB file on your local hard disk can also be opened from the [File] – [Open – Local] – [PDB] menu item.

== Operating molecules ==
Interactive mouse operations are possible for 3D images. By left-dragging the mouse on the 3D-display panel, molecules are rotated around the x-axis or y-axis. By left-dragging the mouse while holding the Shift key or Alt key on the keyboard, molecules are translated along the z-axis. All mouse operations are as follows (as for the Macintosh environment, the Command key + left-drag substitutes for the right-drag).

{| border="1"
 ! Mouse operations !! Actions
 |-
 | Left-drag || The image is rotated around the x (for a vertical motion) and y (for a horizontal motion) axes.
 |-
 | Right-drag || The image is translated on the x-y plane.
 |-
 | [Alt or Shift] + left-drag || The image is translated along the z-axis.
 |-
 | [Alt or Shift] + right-drag || The image is rotated around the z-axis.
 |-
 | [Ctrl] + left-drag || The z-clipping plane is shifted when [Option]-[Slab] is checked.
 |-
 | Left-click || An atom of the molecule displayed on the screen is picked.
 |}

In the upper-right panel in the application window (see Figure 3), the file names that have been loaded to the application are listed, where sequential integers are automatically assigned to the individual file. Each integer is a file ID that can be used to specify the file in the command line interface. In addition, two checkboxes are attached to each file. If you change the status of a ‘display’ checkbox, the corresponding molecule is switched to be displayed or not to be displayed. If you change the status of a ‘select’ checkbox, the corresponding molecule is switched to be a target of the mouse operations or not. For example, set the both ‘display’ checkboxes on, and the both ‘select’ checkboxes off. In this case, either molecule does not move against mouse operations. 

Subsequently set the ‘select’ checkbox of file 1 on. In this case, mouse operations work for the molecule 1. Thus, each file is assigned either selected or not selected, and transform operations, such as rotation or translation, act only on selected files. On the other hand, every atom in a molecule is also assigned either selected or not selected, independently of whether the molecule itself is selected or not. Operations that modify display models or colors work for selected atoms. To see this, choose the [Display] – [Spacefill] menu item. Then the both molecules are displayed with the space fill model because all atoms are initially selected. In the same way, if you choose the [Colors] – [Monochrome] menu item, the both molecules are colored white. These operations are independent of the status of ‘select’ checkboxes mentioned above. 

Let us next try a more detailed operation. Type ‘select *@2’ in the command line area and press Enter key. This command means to select all atoms contained in the file 2 (the usage of the select command is summarized in the reference manual included in the binary distribution of jV3). Subsequently, choose the [Display] – [Cartoon] menu item. As a result, only the molecule 2 is displayed in the cartoon model. Furthermore select the [Colors] – [Structure] menu item, and each residue of the molecule 2 is colored according to its secondary structure type (see Figure 3). 

In order to reproduce the same view as that in Figure 3, first execute ‘reset’ command. It restores the position of the viewpoint and the transform of every file to the initial state. Note that the command line interface tries to complement a command word when the Tab key is pressed. If you enter ‘res’ to the command line and subsequently press the Tab key, the command ‘reset’ is automatically entered. Next set the both ‘select’ checkboxes on, and execute ‘translate z 100’ command. This command means to translate the molecules along the z-axis by 100 angstroms.

[[File:Fig3.jpg|thumb|Figure 3: An example of molecular images.|center|500px]]

== Displaying polygons ==
In addition to molecules, arbitrary shapes described by polygons can be read in and displayed together, where the polygon file is an XML file, whose document type is described in the section 6. Here, we use ’http://ef-site.hgc.jp/eF-site/jV/1yec.surface.gz’ as an example. This polygon file represents a molecular surface of the molecule 2 (1yec) and the surface is colored according to the electrostatic potential and the hydrophobicity. It is assumed that the current image is the same as that in Figure 3. Then, open the open-remote dialog by choosing the [File] – [Open – Remote] – [Polygon] menu item, enter the above URL to the text field at the top of the dialog, and click the 'OK' button. As a result, the polygon is loaded, displayed and assigned file ID 3. 

Note that the polygon is displayed at the different position from the molecule 2 since the molecule 2 is translated. However, because the polygon and the molecule 2 are described by the same coordinates in their files, their images can be exactly superposed by executing ‘fit 3 2’ from the command line, where the ‘fit’ command performs the copy of the transform matrix. Finally, the image in Figure 4 appears.

[[File:Fig4.jpg|thumb|Figure4: An example of polygon images.|center|500px]]

You can control the transparency rate of polygons. Try ’set transparency 0.5’ from the command line, where 0.5 stands for 50% transparency. To restore the image, execute ‘reset transparency’ or ‘set transparency 0’. In the same sense as each atom of a molecule, each vertex of a polygon is assigned either selected or not selected. All vertices are selected in the initial state. Execute a command ’displayvertex off’ and all vertices become invisible. Next execute ’selectvertex within(10.0, 1&amp;*H@2)’, where this means to select vertices that exist within 10 angstroms from each atom that belongs to the first residue of the ‘H’ chain of the molecule 2. Subsequently execute ’displayvertex on’. As a result, only the selected vertices are appeared. The usage of the selectvertex command is summarized in the [[Command List]].

== Working with xPSSS ==
Functional site information on a molecule stored at xPSSS (xml-based Protein Structure Search Service) is available in jV3. Before trying this, let us close the molecule 2 and the polygon 3 to make the situation simple. Select the [File] – [Close] – [2. 1yec.pdb] and [File] – [Close] – [3. 1yec.surface.gz] menu items sequentially. Then execute a ‘reset’ command and the transform of the molecule 1 and the position of the viewpoint are initialized. 

Next, confirm that the ‘select’ checkbox of the file 1 is checked, and try a ‘show xps3’ command. The functional site information of the molecule ‘12as’ is read from the xPSSS and ‘type’ and ‘subtype’ keywords for each functional site are listed. These keywords can be used to select a set of atoms. For example, if a keyword ‘CATRES’ exists (probably it does), the command ‘select xps3:CATRES’ selects the corresponding atoms. 

In addition, gene ontology information can be obtained from the xPSSS. The gene ontology information for the molecule 12as is displayed by the command ’show godata’. Similar operations can be applied to other external databases on the Internet provided that the external database supports the interface that jV3 requires. See the [[Functional site information for molecules]] for details.

== Animation ==
The animation of molecules can be performed in jV3. The animation file takes the PDB format, where the MODEL line divides each frame. Let us open an animation file ’http://ef-site.hgc.jp/eF-site/jV/anim.pdb.gz’ as an example from the open-remote dialog shown by selecting the [File] – [Open – Remote] – [Animation] menu item. When an animation file is loaded to the application, the first frame is automatically displayed in the wire frame model. You can start the animation by using the animation-control dialog that is shown by choosing the [Options] – [Animation] menu item. The dialog provides operations such as start and stop of the animation, selection of the animation mode, and adjustment of the speed. Some sample figures of the dialog are shown in the [[GUI#3]]

== Saving your work ==
While in your work, you can create a script file that contains a set of commands that reproduces the current work by using the [File] – [Save] – [Script] menu item. The script file can be loaded by the [File] – [Open – Local] – [Script] menu item. On the other hand, the [File] – [Save] – [PDB] menu item enables to save a molecule to a PDB format file with the coordinates of the atoms being transformed according to the current image. Here, only one molecule must be selected and only selected atoms in the molecule are saved. The other two menu items in the [File] – [Save] menu, [PNG] and [JPEG], save the current screen image to an image file in the PNG and JPEG format, respectively. The created image file has the same size as that of the 3D-display panel in the application.

== Terminating the application ==
The application is terminated when the [File] – [Exit] menu item is chosen or the application window is closed by the way your operation system provides. You can also quit the application by executing ‘exit’ or ‘quit’ command.</text>
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    <text bytes="12280" xml:space="preserve">{| style="float:right"
 |__TOC__
 |}
== Starting up ==
It is assumed that Java Runtime Environment and JOGL have been appropriately installed. Once you extract the binary distribution file of jV3, the directory of the name, jV_(version), is generated (Ex. jV_3_6_2). The version is assumed to be 3_6_x hereafter. The application starts up by double-clicking the file ‘jv_3_6_x.jar’ in the jV_3_6_x directory or executing the following command from the command line interface.
 java –jar jv_3_6_x.jar
Figure 1 shows the start-up screen. The window has a 3-panel structure, and the upper-left panel with the black background is a 3D image display area. The status of files that have been loaded to the application is shown in the upper-right panel and the lower panel is a command-input and a message-output area.
[[File:Fig1.jpg|thumb|Figure 1: Start-up screen|center|500px]]

== Displaying molecules ==
If you are working in the environment that is getting on the Internet and know the PDB ID of the molecule that you want to display, the simplest way is as follows. A dialog shown in Figure 2 is opened by selecting the [File] – [Open – Remote] – [PDB ID] menu item. Enter a PDB ID '12as', for example, to the text field and click the 'OK' button, then the PDBML file is read through the Internet and the molecule is displayed. The URL where the PDBML file is retrieved from is specified in the 'properties.txt' file in the jV_3_3_x directory. A molecule is displayed in a wire frame model with colored by atom type in the initial state.

[[File:Fig2.jpg|thumb|Figure 2: Dialog to open the molecule specified by PDB ID|center|200px]]

Let us next attempt to load an arbitrary file on the Internet. Here we use 'http://ef-site.hgc.jp/eF-site/jV/1yec.pdb' as an example. The file is a conventional PDB file whose PDB ID is 1yec. In this case we choose the [File] – [Open – Remote] – [PDB] menu item. Then the open-remote dialog is appeared. Enter the above URL to the text field at the top of the dialog and click the 'OK' button and the molecule is read in and displayed. In jV3, each molecule is displayed according to the space coordination described in its file. Therefore, when loading and displaying more than one molecule together, they can be viewed with an appropriate separation in some cases; however, they may be displayed far separately or may be overlapped depending on the combination. In any case, when adding a new file, the position of the viewpoint is automatically controlled for the whole to be displayed.

The coordinate system is the right hand system with the x-y plane being on the screen (the x-axis is a horizontal line with positive values to the right and the y-axis is a vertical line with positive values up). Although, the above examples are about operations for remote files, a PDB file on your local hard disk can also be opened from the [File] – [Open – Local] – [PDB] menu item.

== Operating molecules ==
Interactive mouse operations are possible for 3D images. By left-dragging the mouse on the 3D-display panel, molecules are rotated around the x-axis or y-axis. By left-dragging the mouse while holding the Shift key or Alt key on the keyboard, molecules are translated along the z-axis. All mouse operations are as follows (as for the Macintosh environment, the Command key + left-drag substitutes for the right-drag).

{| border="1"
 ! Mouse operations !! Actions
 |-
 | Left-drag || The image is rotated around the x (for a vertical motion) and y (for a horizontal motion) axes.
 |-
 | Right-drag || The image is translated on the x-y plane.
 |-
 | [Alt or Shift] + left-drag || The image is translated along the z-axis.
 |-
 | [Alt or Shift] + right-drag || The image is rotated around the z-axis.
 |-
 | [Ctrl] + left-drag || The z-clipping plane is shifted when [Option]-[Slab] is checked.
 |-
 | Left-click || An atom of the molecule displayed on the screen is picked.
 |}

In the upper-right panel in the application window (see Figure 3), the file names that have been loaded to the application are listed, where sequential integers are automatically assigned to the individual file. Each integer is a file ID that can be used to specify the file in the command line interface. In addition, two checkboxes are attached to each file. If you change the status of a ‘display’ checkbox, the corresponding molecule is switched to be displayed or not to be displayed. If you change the status of a ‘select’ checkbox, the corresponding molecule is switched to be a target of the mouse operations or not. For example, set the both ‘display’ checkboxes on, and the both ‘select’ checkboxes off. In this case, either molecule does not move against mouse operations. 

Subsequently set the ‘select’ checkbox of file 1 on. In this case, mouse operations work for the molecule 1. Thus, each file is assigned either selected or not selected, and transform operations, such as rotation or translation, act only on selected files. On the other hand, every atom in a molecule is also assigned either selected or not selected, independently of whether the molecule itself is selected or not. Operations that modify display models or colors work for selected atoms. To see this, choose the [Display] – [Spacefill] menu item. Then the both molecules are displayed with the space fill model because all atoms are initially selected. In the same way, if you choose the [Colors] – [Monochrome] menu item, the both molecules are colored white. These operations are independent of the status of ‘select’ checkboxes mentioned above. 

Let us next try a more detailed operation. Type ‘select *@2’ in the command line area and press Enter key. This command means to select all atoms contained in the file 2 (the usage of the select command is summarized in the reference manual included in the binary distribution of jV3). Subsequently, choose the [Display] – [Cartoon] menu item. As a result, only the molecule 2 is displayed in the cartoon model. Furthermore select the [Colors] – [Structure] menu item, and each residue of the molecule 2 is colored according to its secondary structure type (see Figure 3). 

In order to reproduce the same view as that in Figure 3, first execute ‘reset’ command. It restores the position of the viewpoint and the transform of every file to the initial state. Note that the command line interface tries to complement a command word when the Tab key is pressed. If you enter ‘res’ to the command line and subsequently press the Tab key, the command ‘reset’ is automatically entered. Next set the both ‘select’ checkboxes on, and execute ‘translate z 100’ command. This command means to translate the molecules along the z-axis by 100 angstroms.

[[File:Fig3.jpg|thumb|Figure 3: An example of molecular images.|center|500px]]

== Displaying polygons ==
In addition to molecules, arbitrary shapes described by polygons can be read in and displayed together, where the polygon file is an XML file, whose document type is described in the section 6. Here, we use ’http://ef-site.hgc.jp/eF-site/jV/1yec.surface.gz’ as an example. This polygon file represents a molecular surface of the molecule 2 (1yec) and the surface is colored according to the electrostatic potential and the hydrophobicity. It is assumed that the current image is the same as that in Figure 3. Then, open the open-remote dialog by choosing the [File] – [Open – Remote] – [Polygon] menu item, enter the above URL to the text field at the top of the dialog, and click the 'OK' button. As a result, the polygon is loaded, displayed and assigned file ID 3. 

Note that the polygon is displayed at the different position from the molecule 2 since the molecule 2 is translated. However, because the polygon and the molecule 2 are described by the same coordinates in their files, their images can be exactly superposed by executing ‘fit 3 2’ from the command line, where the ‘fit’ command performs the copy of the transform matrix. Finally, the image in Figure 4 appears.

[[File:Fig4.jpg|thumb|Figure4: An example of polygon images.|center|500px]]

You can control the transparency rate of polygons. Try ’set transparency 0.5’ from the command line, where 0.5 stands for 50% transparency. To restore the image, execute ‘reset transparency’ or ‘set transparency 0’. In the same sense as each atom of a molecule, each vertex of a polygon is assigned either selected or not selected. All vertices are selected in the initial state. Execute a command ’displayvertex off’ and all vertices become invisible. Next execute ’selectvertex within(10.0, 1&amp;*H@2)’, where this means to select vertices that exist within 10 angstroms from each atom that belongs to the first residue of the ‘H’ chain of the molecule 2. Subsequently execute ’displayvertex on’. As a result, only the selected vertices are appeared. The usage of the selectvertex command is summarized in the [[Command List]].

== Working with xPSSS ==
Functional site information on a molecule stored at xPSSS (xml-based Protein Structure Search Service) is available in jV3. Before trying this, let us close the molecule 2 and the polygon 3 to make the situation simple. Select the [File] – [Close] – [2. 1yec.pdb] and [File] – [Close] – [3. 1yec.surface.gz] menu items sequentially. Then execute a ‘reset’ command and the transform of the molecule 1 and the position of the viewpoint are initialized. 

Next, confirm that the ‘select’ checkbox of the file 1 is checked, and try a ‘show xps3’ command. The functional site information of the molecule ‘12as’ is read from the xPSSS and ‘type’ and ‘subtype’ keywords for each functional site are listed. These keywords can be used to select a set of atoms. For example, if a keyword ‘CATRES’ exists (probably it does), the command ‘select xps3:CATRES’ selects the corresponding atoms. 

In addition, gene ontology information can be obtained from the xPSSS. The gene ontology information for the molecule 12as is displayed by the command ’show godata’. Similar operations can be applied to other external databases on the Internet provided that the external database supports the interface that jV3 requires. See the [[Functional site information for molecules]] for details.

== Animation ==
The animation of molecules can be performed in jV3. The animation file takes the PDB format, where the MODEL line divides each frame. Let us open an animation file ’http://ef-site.hgc.jp/eF-site/jV/anim.pdb.gz’ as an example from the open-remote dialog shown by selecting the [File] – [Open – Remote] – [Animation] menu item. When an animation file is loaded to the application, the first frame is automatically displayed in the wire frame model. You can start the animation by using the animation-control dialog that is shown by choosing the [Options] – [Animation] menu item. The dialog provides operations such as start and stop of the animation, selection of the animation mode, and adjustment of the speed. Some sample figures of the dialog are shown in the [[GUI#Animation_control_dialog]]

== Saving your work ==
While in your work, you can create a script file that contains a set of commands that reproduces the current work by using the [File] – [Save] – [Script] menu item. The script file can be loaded by the [File] – [Open – Local] – [Script] menu item. On the other hand, the [File] – [Save] – [PDB] menu item enables to save a molecule to a PDB format file with the coordinates of the atoms being transformed according to the current image. Here, only one molecule must be selected and only selected atoms in the molecule are saved. The other two menu items in the [File] – [Save] menu, [PNG] and [JPEG], save the current screen image to an image file in the PNG and JPEG format, respectively. The created image file has the same size as that of the 3D-display panel in the application.

== Terminating the application ==
The application is terminated when the [File] – [Exit] menu item is chosen or the application window is closed by the way your operation system provides. You can also quit the application by executing ‘exit’ or ‘quit’ command.</text>
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  <title>GUI</title>
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    <comment>Created page with '{| style="float:right"  |__TOC__  |} == Menu bar == The organization of the menu bar and the function of its components are shown below.  ;1) File menu {| class="wikitable" borde...'</comment>
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 |__TOC__
 |}
== Menu bar ==
The organization of the menu bar and the function of its components are shown below.

;1) File menu
{| class="wikitable" border="1"
 |-
 ! Component || Function
 |-
 | rowspan="5" | Open - Local
 | PDBML
 | A local PDBML file is opened.
 |-
 | PDB
 | A local PDB file is opened.
 |-
 | Polygon
 | A local polygon file is opened.
 |-
 | Script 
 | A local script file is opened.
 |-
 | Animation
 | A local animation file is opened.
 |-
 | rowspan="7" | Open-Remote
 |-
 | PDBML
 | A remote PDBML file is opened.
 |-
 | PDB
 | A remote PDB file is opened.
 |-
 | Polygon
 | A remote polygon file is opened.
 |- 
 | Script
 | A remote script file is opened.
 |-
 | Animation
 | A remote animation file is opened.
 |-
 | PDB ID
 | A PDBML file at the PDBML FTP site is opened.
 |-
 | eF-site ID
 | A set of molecular and polygon files stored in eF-site database are opened.
 |-
 | colspan="2" | Information
 | Information about the selected files are shown.
 |-
 | colspan="2" | Close
 | The specified file is closed.
 |}</text>
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    <timestamp>2009-03-09T09:45:44Z</timestamp>
    <contributor>
      <username>JVuser</username>
      <id>2</id>
    </contributor>
    <comment>/* Menu bar */</comment>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="1082" xml:space="preserve">{| style="float:right"
 |__TOC__
 |}
== Menu bar ==
The organization of the menu bar and the function of its components are shown below.

;1) File menu
{| class="wikitable" border="1"
 |-
 ! colspan="2" Component || Function
 |-
 | rowspan="5" | Open - Local
 | PDBML
 | A local PDBML file is opened.
 |-
 | PDB
 | A local PDB file is opened.
 |-
 | Polygon
 | A local polygon file is opened.
 |-
 | Script 
 | A local script file is opened.
 |-
 | Animation
 | A local animation file is opened.
 |-
 | rowspan="7" | Open-Remote
 |-
 | PDBML
 | A remote PDBML file is opened.
 |-
 | PDB
 | A remote PDB file is opened.
 |-
 | Polygon
 | A remote polygon file is opened.
 |- 
 | Script
 | A remote script file is opened.
 |-
 | Animation
 | A remote animation file is opened.
 |-
 | PDB ID
 | A PDBML file at the PDBML FTP site is opened.
 |-
 | eF-site ID
 | A set of molecular and polygon files stored in eF-site database are opened.
 |-
 | colspan="2" | Information
 | Information about the selected files are shown.
 |-
 | colspan="2" | Close
 | The specified file is closed.
 |}</text>
    <sha1>3a6552bd25366a339c97267c25ddd2ee36dffaf2</sha1>
  </revision>
  <revision>
    <id>211</id>
    <parentid>210</parentid>
    <timestamp>2009-03-09T09:47:24Z</timestamp>
    <contributor>
      <username>JVuser</username>
      <id>2</id>
    </contributor>
    <comment>/* Menu bar */</comment>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="1084" xml:space="preserve">{| style="float:right"
 |__TOC__
 |}
== Menu bar ==
The organization of the menu bar and the function of its components are shown below.

;1) File menu
{| class="wikitable" border="1"
 |-
 | colspan="2" | Component
 | Function
 |-
 | rowspan="5" | Open - Local
 | PDBML
 | A local PDBML file is opened.
 |-
 | PDB
 | A local PDB file is opened.
 |-
 | Polygon
 | A local polygon file is opened.
 |-
 | Script 
 | A local script file is opened.
 |-
 | Animation
 | A local animation file is opened.
 |-
 | rowspan="7" | Open-Remote
 |-
 | PDBML
 | A remote PDBML file is opened.
 |-
 | PDB
 | A remote PDB file is opened.
 |-
 | Polygon
 | A remote polygon file is opened.
 |- 
 | Script
 | A remote script file is opened.
 |-
 | Animation
 | A remote animation file is opened.
 |-
 | PDB ID
 | A PDBML file at the PDBML FTP site is opened.
 |-
 | eF-site ID
 | A set of molecular and polygon files stored in eF-site database are opened.
 |-
 | colspan="2" | Information
 | Information about the selected files are shown.
 |-
 | colspan="2" | Close
 | The specified file is closed.
 |}</text>
    <sha1>be8abf9907f72ded9075442f030d3e1e83231c76</sha1>
  </revision>
  <revision>
    <id>212</id>
    <parentid>211</parentid>
    <timestamp>2009-03-09T09:50:38Z</timestamp>
    <contributor>
      <username>JVuser</username>
      <id>2</id>
    </contributor>
    <comment>/* Menu bar */</comment>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="1432" xml:space="preserve">{| style="float:right"
 |__TOC__
 |}
== Menu bar ==
The organization of the menu bar and the function of its components are shown below.

;1) File menu
{| class="wikitable" border="1"
 |-
 | colspan="2" | Component
 | Function
 |-
 | rowspan="5" | Open - Local
 | PDBML
 | A local PDBML file is opened.
 |-
 | PDB
 | A local PDB file is opened.
 |-
 | Polygon
 | A local polygon file is opened.
 |-
 | Script 
 | A local script file is opened.
 |-
 | Animation
 | A local animation file is opened.
 |-
 | rowspan="7" | Open-Remote
 | PDBML
 | A remote PDBML file is opened.
 |-
 | PDB
 | A remote PDB file is opened.
 |-
 | Polygon
 | A remote polygon file is opened.
 |- 
 | Script
 | A remote script file is opened.
 |-
 | Animation
 | A remote animation file is opened.
 |-
 | PDB ID
 | A PDBML file at the PDBML FTP site is opened.
 |-
 | eF-site ID
 | A set of molecular and polygon files stored in eF-site database are opened.
 |-
 | colspan="2" | Information
 | Information about the selected files are shown.
 |-
 | colspan="2" | Close
 | The specified file is closed.
 |-
 | rowspan="4" | Save
 | PDB
 | A PDB format file that contains the current atom coordinates is created.
 |-
 | Script
 | A script by which the present condition is reproduced is created.
 |-
 | PNG
 | The current image is saved as PNG.
 |-
 | JPEG
 | The current image is saved as JPEG.
 |-
 | colspan="2" | Exit
 | The application is terminated.
 |}</text>
    <sha1>e50b588ceac3e1e5254cf0ab9d072a6bd6b5b2cc</sha1>
  </revision>
  <revision>
    <id>213</id>
    <parentid>212</parentid>
    <timestamp>2009-03-09T09:53:59Z</timestamp>
    <contributor>
      <username>JVuser</username>
      <id>2</id>
    </contributor>
    <comment>/* Menu bar */</comment>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="1462" xml:space="preserve">{| style="float:right"
 |__TOC__
 |}
== Menu bar ==
The organization of the menu bar and the function of its components are shown below.

;1) File menu
{| class="wikitable" border="1"
 |-
 | style="background-color:#dfd" colspan="2" | Component
 | Function
 |-
 | rowspan="5" | Open - Local
 | PDBML
 | A local PDBML file is opened.
 |-
 | PDB
 | A local PDB file is opened.
 |-
 | Polygon
 | A local polygon file is opened.
 |-
 | Script 
 | A local script file is opened.
 |-
 | Animation
 | A local animation file is opened.
 |-
 | rowspan="7" | Open-Remote
 | PDBML
 | A remote PDBML file is opened.
 |-
 | PDB
 | A remote PDB file is opened.
 |-
 | Polygon
 | A remote polygon file is opened.
 |- 
 | Script
 | A remote script file is opened.
 |-
 | Animation
 | A remote animation file is opened.
 |-
 | PDB ID
 | A PDBML file at the PDBML FTP site is opened.
 |-
 | eF-site ID
 | A set of molecular and polygon files stored in eF-site database are opened.
 |-
 | colspan="2" | Information
 | Information about the selected files are shown.
 |-
 | colspan="2" | Close
 | The specified file is closed.
 |-
 | rowspan="4" | Save
 | PDB
 | A PDB format file that contains the current atom coordinates is created.
 |-
 | Script
 | A script by which the present condition is reproduced is created.
 |-
 | PNG
 | The current image is saved as PNG.
 |-
 | JPEG
 | The current image is saved as JPEG.
 |-
 | colspan="2" | Exit
 | The application is terminated.
 |}</text>
    <sha1>f7b303a2d07a2cea8c32c0b291712b8727d78eca</sha1>
  </revision>
  <revision>
    <id>214</id>
    <parentid>213</parentid>
    <timestamp>2009-03-09T09:54:14Z</timestamp>
    <contributor>
      <username>JVuser</username>
      <id>2</id>
    </contributor>
    <comment>/* Menu bar */</comment>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="1462" xml:space="preserve">{| style="float:right"
 |__TOC__
 |}
== Menu bar ==
The organization of the menu bar and the function of its components are shown below.

;1) File menu
{| class="wikitable" border="1"
 |-
 | style="background-color:#fdd" colspan="2" | Component
 | Function
 |-
 | rowspan="5" | Open - Local
 | PDBML
 | A local PDBML file is opened.
 |-
 | PDB
 | A local PDB file is opened.
 |-
 | Polygon
 | A local polygon file is opened.
 |-
 | Script 
 | A local script file is opened.
 |-
 | Animation
 | A local animation file is opened.
 |-
 | rowspan="7" | Open-Remote
 | PDBML
 | A remote PDBML file is opened.
 |-
 | PDB
 | A remote PDB file is opened.
 |-
 | Polygon
 | A remote polygon file is opened.
 |- 
 | Script
 | A remote script file is opened.
 |-
 | Animation
 | A remote animation file is opened.
 |-
 | PDB ID
 | A PDBML file at the PDBML FTP site is opened.
 |-
 | eF-site ID
 | A set of molecular and polygon files stored in eF-site database are opened.
 |-
 | colspan="2" | Information
 | Information about the selected files are shown.
 |-
 | colspan="2" | Close
 | The specified file is closed.
 |-
 | rowspan="4" | Save
 | PDB
 | A PDB format file that contains the current atom coordinates is created.
 |-
 | Script
 | A script by which the present condition is reproduced is created.
 |-
 | PNG
 | The current image is saved as PNG.
 |-
 | JPEG
 | The current image is saved as JPEG.
 |-
 | colspan="2" | Exit
 | The application is terminated.
 |}</text>
    <sha1>d7efe5898576ccc64a94eb8483d4c4d11085acb7</sha1>
  </revision>
  <revision>
    <id>215</id>
    <parentid>214</parentid>
    <timestamp>2009-03-09T09:57:20Z</timestamp>
    <contributor>
      <username>JVuser</username>
      <id>2</id>
    </contributor>
    <comment>/* Menu bar */</comment>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="1467" xml:space="preserve">{| style="float:right"
 |__TOC__
 |}
== Menu bar ==
The organization of the menu bar and the function of its components are shown below.

;1) File menu
{| class="wikitable" border="1"
 |-
 | style="background-color:LightGrey" colspan="2" | Component
 | Function
 |-
 | rowspan="5" | Open - Local
 | PDBML
 | A local PDBML file is opened.
 |-
 | PDB
 | A local PDB file is opened.
 |-
 | Polygon
 | A local polygon file is opened.
 |-
 | Script 
 | A local script file is opened.
 |-
 | Animation
 | A local animation file is opened.
 |-
 | rowspan="7" | Open-Remote
 | PDBML
 | A remote PDBML file is opened.
 |-
 | PDB
 | A remote PDB file is opened.
 |-
 | Polygon
 | A remote polygon file is opened.
 |- 
 | Script
 | A remote script file is opened.
 |-
 | Animation
 | A remote animation file is opened.
 |-
 | PDB ID
 | A PDBML file at the PDBML FTP site is opened.
 |-
 | eF-site ID
 | A set of molecular and polygon files stored in eF-site database are opened.
 |-
 | colspan="2" | Information
 | Information about the selected files are shown.
 |-
 | colspan="2" | Close
 | The specified file is closed.
 |-
 | rowspan="4" | Save
 | PDB
 | A PDB format file that contains the current atom coordinates is created.
 |-
 | Script
 | A script by which the present condition is reproduced is created.
 |-
 | PNG
 | The current image is saved as PNG.
 |-
 | JPEG
 | The current image is saved as JPEG.
 |-
 | colspan="2" | Exit
 | The application is terminated.
 |}</text>
    <sha1>39d3e21c6c65275a924cff645778925035531dfe</sha1>
  </revision>
  <revision>
    <id>216</id>
    <parentid>215</parentid>
    <timestamp>2009-03-09T09:58:18Z</timestamp>
    <contributor>
      <username>JVuser</username>
      <id>2</id>
    </contributor>
    <comment>/* Menu bar */</comment>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="1467" xml:space="preserve">{| style="float:right"
 |__TOC__
 |}
== Menu bar ==
The organization of the menu bar and the function of its components are shown below.

;1) File menu
{| class="wikitable" border="1"
 |-
 | style="background-color:gainsboro" colspan="2" | Component
 | Function
 |-
 | rowspan="5" | Open - Local
 | PDBML
 | A local PDBML file is opened.
 |-
 | PDB
 | A local PDB file is opened.
 |-
 | Polygon
 | A local polygon file is opened.
 |-
 | Script 
 | A local script file is opened.
 |-
 | Animation
 | A local animation file is opened.
 |-
 | rowspan="7" | Open-Remote
 | PDBML
 | A remote PDBML file is opened.
 |-
 | PDB
 | A remote PDB file is opened.
 |-
 | Polygon
 | A remote polygon file is opened.
 |- 
 | Script
 | A remote script file is opened.
 |-
 | Animation
 | A remote animation file is opened.
 |-
 | PDB ID
 | A PDBML file at the PDBML FTP site is opened.
 |-
 | eF-site ID
 | A set of molecular and polygon files stored in eF-site database are opened.
 |-
 | colspan="2" | Information
 | Information about the selected files are shown.
 |-
 | colspan="2" | Close
 | The specified file is closed.
 |-
 | rowspan="4" | Save
 | PDB
 | A PDB format file that contains the current atom coordinates is created.
 |-
 | Script
 | A script by which the present condition is reproduced is created.
 |-
 | PNG
 | The current image is saved as PNG.
 |-
 | JPEG
 | The current image is saved as JPEG.
 |-
 | colspan="2" | Exit
 | The application is terminated.
 |}</text>
    <sha1>393d3af806f32ea5458a49b258e868038289a790</sha1>
  </revision>
  <revision>
    <id>217</id>
    <parentid>216</parentid>
    <timestamp>2009-03-09T09:58:37Z</timestamp>
    <contributor>
      <username>JVuser</username>
      <id>2</id>
    </contributor>
    <comment>/* Menu bar */</comment>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="1502" xml:space="preserve">{| style="float:right"
 |__TOC__
 |}
== Menu bar ==
The organization of the menu bar and the function of its components are shown below.

;1) File menu
{| class="wikitable" border="1"
 |-
 | style="background-color:gainsboro" colspan="2" | style="background-color:gainsboro" Component
 | Function
 |-
 | rowspan="5" | Open - Local
 | PDBML
 | A local PDBML file is opened.
 |-
 | PDB
 | A local PDB file is opened.
 |-
 | Polygon
 | A local polygon file is opened.
 |-
 | Script 
 | A local script file is opened.
 |-
 | Animation
 | A local animation file is opened.
 |-
 | rowspan="7" | Open-Remote
 | PDBML
 | A remote PDBML file is opened.
 |-
 | PDB
 | A remote PDB file is opened.
 |-
 | Polygon
 | A remote polygon file is opened.
 |- 
 | Script
 | A remote script file is opened.
 |-
 | Animation
 | A remote animation file is opened.
 |-
 | PDB ID
 | A PDBML file at the PDBML FTP site is opened.
 |-
 | eF-site ID
 | A set of molecular and polygon files stored in eF-site database are opened.
 |-
 | colspan="2" | Information
 | Information about the selected files are shown.
 |-
 | colspan="2" | Close
 | The specified file is closed.
 |-
 | rowspan="4" | Save
 | PDB
 | A PDB format file that contains the current atom coordinates is created.
 |-
 | Script
 | A script by which the present condition is reproduced is created.
 |-
 | PNG
 | The current image is saved as PNG.
 |-
 | JPEG
 | The current image is saved as JPEG.
 |-
 | colspan="2" | Exit
 | The application is terminated.
 |}</text>
    <sha1>93bc0057ac46c95b7274401ef13c87def1c6ee6d</sha1>
  </revision>
  <revision>
    <id>218</id>
    <parentid>217</parentid>
    <timestamp>2009-03-09T09:59:18Z</timestamp>
    <contributor>
      <username>JVuser</username>
      <id>2</id>
    </contributor>
    <comment>/* Menu bar */</comment>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="1502" xml:space="preserve">{| style="float:right"
 |__TOC__
 |}
== Menu bar ==
The organization of the menu bar and the function of its components are shown below.

;1) File menu
{| class="wikitable" border="1"
 |-
 | style="background-color:gainsboro" colspan="2" | Component
 | style="background-color:gainsboro" Function
 |-
 | rowspan="5" | Open - Local
 | PDBML
 | A local PDBML file is opened.
 |-
 | PDB
 | A local PDB file is opened.
 |-
 | Polygon
 | A local polygon file is opened.
 |-
 | Script 
 | A local script file is opened.
 |-
 | Animation
 | A local animation file is opened.
 |-
 | rowspan="7" | Open-Remote
 | PDBML
 | A remote PDBML file is opened.
 |-
 | PDB
 | A remote PDB file is opened.
 |-
 | Polygon
 | A remote polygon file is opened.
 |- 
 | Script
 | A remote script file is opened.
 |-
 | Animation
 | A remote animation file is opened.
 |-
 | PDB ID
 | A PDBML file at the PDBML FTP site is opened.
 |-
 | eF-site ID
 | A set of molecular and polygon files stored in eF-site database are opened.
 |-
 | colspan="2" | Information
 | Information about the selected files are shown.
 |-
 | colspan="2" | Close
 | The specified file is closed.
 |-
 | rowspan="4" | Save
 | PDB
 | A PDB format file that contains the current atom coordinates is created.
 |-
 | Script
 | A script by which the present condition is reproduced is created.
 |-
 | PNG
 | The current image is saved as PNG.
 |-
 | JPEG
 | The current image is saved as JPEG.
 |-
 | colspan="2" | Exit
 | The application is terminated.
 |}</text>
    <sha1>6f91b41f37a177dd86f99097f360986d45a7ba20</sha1>
  </revision>
  <revision>
    <id>219</id>
    <parentid>218</parentid>
    <timestamp>2009-03-09T09:59:31Z</timestamp>
    <contributor>
      <username>JVuser</username>
      <id>2</id>
    </contributor>
    <comment>/* Menu bar */</comment>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="1504" xml:space="preserve">{| style="float:right"
 |__TOC__
 |}
== Menu bar ==
The organization of the menu bar and the function of its components are shown below.

;1) File menu
{| class="wikitable" border="1"
 |-
 | style="background-color:gainsboro" colspan="2" | Component
 | style="background-color:gainsboro" | Function
 |-
 | rowspan="5" | Open - Local
 | PDBML
 | A local PDBML file is opened.
 |-
 | PDB
 | A local PDB file is opened.
 |-
 | Polygon
 | A local polygon file is opened.
 |-
 | Script 
 | A local script file is opened.
 |-
 | Animation
 | A local animation file is opened.
 |-
 | rowspan="7" | Open-Remote
 | PDBML
 | A remote PDBML file is opened.
 |-
 | PDB
 | A remote PDB file is opened.
 |-
 | Polygon
 | A remote polygon file is opened.
 |- 
 | Script
 | A remote script file is opened.
 |-
 | Animation
 | A remote animation file is opened.
 |-
 | PDB ID
 | A PDBML file at the PDBML FTP site is opened.
 |-
 | eF-site ID
 | A set of molecular and polygon files stored in eF-site database are opened.
 |-
 | colspan="2" | Information
 | Information about the selected files are shown.
 |-
 | colspan="2" | Close
 | The specified file is closed.
 |-
 | rowspan="4" | Save
 | PDB
 | A PDB format file that contains the current atom coordinates is created.
 |-
 | Script
 | A script by which the present condition is reproduced is created.
 |-
 | PNG
 | The current image is saved as PNG.
 |-
 | JPEG
 | The current image is saved as JPEG.
 |-
 | colspan="2" | Exit
 | The application is terminated.
 |}</text>
    <sha1>60272ef0cc714923a79369bb7c07070976138d58</sha1>
  </revision>
  <revision>
    <id>220</id>
    <parentid>219</parentid>
    <timestamp>2009-03-09T10:04:51Z</timestamp>
    <contributor>
      <username>JVuser</username>
      <id>2</id>
    </contributor>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="3478" xml:space="preserve">{| style="float:right"
 |__TOC__
 |}
== Menu bar ==
The organization of the menu bar and the function of its components are shown below.

;1) File menu
{| class="wikitable" border="1"
 |-
 | style="background-color:gainsboro" colspan="2" | Component
 | style="background-color:gainsboro" | Function
 |-
 | rowspan="5" | Open - Local
 | PDBML
 | A local PDBML file is opened.
 |-
 | PDB
 | A local PDB file is opened.
 |-
 | Polygon
 | A local polygon file is opened.
 |-
 | Script 
 | A local script file is opened.
 |-
 | Animation
 | A local animation file is opened.
 |-
 | rowspan="7" | Open-Remote
 | PDBML
 | A remote PDBML file is opened.
 |-
 | PDB
 | A remote PDB file is opened.
 |-
 | Polygon
 | A remote polygon file is opened.
 |- 
 | Script
 | A remote script file is opened.
 |-
 | Animation
 | A remote animation file is opened.
 |-
 | PDB ID
 | A PDBML file at the PDBML FTP site is opened.
 |-
 | eF-site ID
 | A set of molecular and polygon files stored in eF-site database are opened.
 |-
 | colspan="2" | Information
 | Information about the selected files are shown.
 |-
 | colspan="2" | Close
 | The specified file is closed.
 |-
 | rowspan="4" | Save
 | PDB
 | A PDB format file that contains the current atom coordinates is created.
 |-
 | Script
 | A script by which the present condition is reproduced is created.
 |-
 | PNG
 | The current image is saved as PNG.
 |-
 | JPEG
 | The current image is saved as JPEG.
 |-
 | colspan="2" | Exit
 | The application is terminated.
 |}

;2) Display menu
{| class="wikitable" border="1"
 |-
 | style="background-color:gainsboro" colspan="2" | Component
 | style="background-color:gainsboro" | Function
 |-
 | Wireframe
 | The selected atoms are displayed in a wire frame model.
 |-
 | Backbone
 | The selected atoms are displayed in a backbone model.
 |-
 | Sticks
 | The selected atoms are displayed in a stick model.
 |-
 | Spacefill
 | The selected atoms are displayed in a space-fill model.
 |-
 | Ball&amp;Stick
 | The selected atoms are displayed in a ball &amp; stick model.
 |-
 | Ribbons
 | The selected atoms are displayed in a ribbon model.
 |-
 | Cartoon
 | The selected atoms are displayed in a cartoon model.
 |}

;3) Colors menu
{| class="wikitable" border="1"
 |-
 | style="background-color:gainsboro" colspan="2" | Component
 | style="background-color:gainsboro" | Function
 |-
 | Monochrome
 | The selected atoms are colored in white.
 |-
 | CPK
 | The selected atoms are colored by CPK color scheme.
 |-
 | Shapely
 | The selected atoms are colored by the color scheme in which each amino acid and nucleic acid is assigned a unique color according to the amino acid and nucleic acid properties.
 |-
 | Group
 | The atoms of every chain are drawn as a smooth spectrum from red (N-terminal of the molecule) to blue (C-terminal).
 |-
 | Chain
 | The selected atoms are colored by the color scheme in which each chain is assigned a unique color.
 |-
 | Temperature
 | The selected atoms are drawn as a smooth spectrum from red (high value) to blue (low value) according to the value of the temperature factor.
 |-
 | Structure
 | The secondary structures are colored by the color scheme in which each secondary structure is assigned a unique color.
 |-
 | Charge
 | The selected atoms are drawn as a smooth spectrum from blue (positive) to red (negative) according to the charge.
 |-
 | Amino
 | The selected atoms are colored by the color scheme in which each amino acid is assigned a unique color.
 |}</text>
    <sha1>5cdc30ee4c91b64523bc77277de1995d35ee13d3</sha1>
  </revision>
  <revision>
    <id>221</id>
    <parentid>220</parentid>
    <timestamp>2009-03-09T10:05:32Z</timestamp>
    <contributor>
      <username>JVuser</username>
      <id>2</id>
    </contributor>
    <comment>/* Menu bar */</comment>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="3454" xml:space="preserve">{| style="float:right"
 |__TOC__
 |}
== Menu bar ==
The organization of the menu bar and the function of its components are shown below.

;1) File menu
{| class="wikitable" border="1"
 |-
 | style="background-color:gainsboro" colspan="2" | Component
 | style="background-color:gainsboro" | Function
 |-
 | rowspan="5" | Open - Local
 | PDBML
 | A local PDBML file is opened.
 |-
 | PDB
 | A local PDB file is opened.
 |-
 | Polygon
 | A local polygon file is opened.
 |-
 | Script 
 | A local script file is opened.
 |-
 | Animation
 | A local animation file is opened.
 |-
 | rowspan="7" | Open-Remote
 | PDBML
 | A remote PDBML file is opened.
 |-
 | PDB
 | A remote PDB file is opened.
 |-
 | Polygon
 | A remote polygon file is opened.
 |- 
 | Script
 | A remote script file is opened.
 |-
 | Animation
 | A remote animation file is opened.
 |-
 | PDB ID
 | A PDBML file at the PDBML FTP site is opened.
 |-
 | eF-site ID
 | A set of molecular and polygon files stored in eF-site database are opened.
 |-
 | colspan="2" | Information
 | Information about the selected files are shown.
 |-
 | colspan="2" | Close
 | The specified file is closed.
 |-
 | rowspan="4" | Save
 | PDB
 | A PDB format file that contains the current atom coordinates is created.
 |-
 | Script
 | A script by which the present condition is reproduced is created.
 |-
 | PNG
 | The current image is saved as PNG.
 |-
 | JPEG
 | The current image is saved as JPEG.
 |-
 | colspan="2" | Exit
 | The application is terminated.
 |}

;2) Display menu
{| class="wikitable" border="1"
 |-
 | style="background-color:gainsboro" | Component
 | style="background-color:gainsboro" | Function
 |-
 | Wireframe
 | The selected atoms are displayed in a wire frame model.
 |-
 | Backbone
 | The selected atoms are displayed in a backbone model.
 |-
 | Sticks
 | The selected atoms are displayed in a stick model.
 |-
 | Spacefill
 | The selected atoms are displayed in a space-fill model.
 |-
 | Ball&amp;Stick
 | The selected atoms are displayed in a ball &amp; stick model.
 |-
 | Ribbons
 | The selected atoms are displayed in a ribbon model.
 |-
 | Cartoon
 | The selected atoms are displayed in a cartoon model.
 |}

;3) Colors menu
{| class="wikitable" border="1"
 |-
 | style="background-color:gainsboro" | Component
 | style="background-color:gainsboro" | Function
 |-
 | Monochrome
 | The selected atoms are colored in white.
 |-
 | CPK
 | The selected atoms are colored by CPK color scheme.
 |-
 | Shapely
 | The selected atoms are colored by the color scheme in which each amino acid and nucleic acid is assigned a unique color according to the amino acid and nucleic acid properties.
 |-
 | Group
 | The atoms of every chain are drawn as a smooth spectrum from red (N-terminal of the molecule) to blue (C-terminal).
 |-
 | Chain
 | The selected atoms are colored by the color scheme in which each chain is assigned a unique color.
 |-
 | Temperature
 | The selected atoms are drawn as a smooth spectrum from red (high value) to blue (low value) according to the value of the temperature factor.
 |-
 | Structure
 | The secondary structures are colored by the color scheme in which each secondary structure is assigned a unique color.
 |-
 | Charge
 | The selected atoms are drawn as a smooth spectrum from blue (positive) to red (negative) according to the charge.
 |-
 | Amino
 | The selected atoms are colored by the color scheme in which each amino acid is assigned a unique color.
 |}</text>
    <sha1>6b41b156a54f8fee0c466b542817173cc47c0116</sha1>
  </revision>
  <revision>
    <id>222</id>
    <parentid>221</parentid>
    <timestamp>2009-03-09T10:09:06Z</timestamp>
    <contributor>
      <username>JVuser</username>
      <id>2</id>
    </contributor>
    <comment>/* Menu bar */</comment>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="5056" xml:space="preserve">{| style="float:right"
 |__TOC__
 |}
== Menu bar ==
The organization of the menu bar and the function of its components are shown below.

;1) File menu
{| class="wikitable" border="1"
 |-
 | style="background-color:gainsboro" colspan="2" | Component
 | style="background-color:gainsboro" | Function
 |-
 | rowspan="5" | Open - Local
 | PDBML
 | A local PDBML file is opened.
 |-
 | PDB
 | A local PDB file is opened.
 |-
 | Polygon
 | A local polygon file is opened.
 |-
 | Script 
 | A local script file is opened.
 |-
 | Animation
 | A local animation file is opened.
 |-
 | rowspan="7" | Open-Remote
 | PDBML
 | A remote PDBML file is opened.
 |-
 | PDB
 | A remote PDB file is opened.
 |-
 | Polygon
 | A remote polygon file is opened.
 |- 
 | Script
 | A remote script file is opened.
 |-
 | Animation
 | A remote animation file is opened.
 |-
 | PDB ID
 | A PDBML file at the PDBML FTP site is opened.
 |-
 | eF-site ID
 | A set of molecular and polygon files stored in eF-site database are opened.
 |-
 | colspan="2" | Information
 | Information about the selected files are shown.
 |-
 | colspan="2" | Close
 | The specified file is closed.
 |-
 | rowspan="4" | Save
 | PDB
 | A PDB format file that contains the current atom coordinates is created.
 |-
 | Script
 | A script by which the present condition is reproduced is created.
 |-
 | PNG
 | The current image is saved as PNG.
 |-
 | JPEG
 | The current image is saved as JPEG.
 |-
 | colspan="2" | Exit
 | The application is terminated.
 |}

;2) Display menu
{| class="wikitable" border="1"
 |-
 | style="background-color:gainsboro" | Component
 | style="background-color:gainsboro" | Function
 |-
 | Wireframe
 | The selected atoms are displayed in a wire frame model.
 |-
 | Backbone
 | The selected atoms are displayed in a backbone model.
 |-
 | Sticks
 | The selected atoms are displayed in a stick model.
 |-
 | Spacefill
 | The selected atoms are displayed in a space-fill model.
 |-
 | Ball&amp;Stick
 | The selected atoms are displayed in a ball &amp; stick model.
 |-
 | Ribbons
 | The selected atoms are displayed in a ribbon model.
 |-
 | Cartoon
 | The selected atoms are displayed in a cartoon model.
 |}

;3) Colors menu
{| class="wikitable" border="1"
 |-
 | style="background-color:gainsboro" | Component
 | style="background-color:gainsboro" | Function
 |-
 | Monochrome
 | The selected atoms are colored in white.
 |-
 | CPK
 | The selected atoms are colored by CPK color scheme.
 |-
 | Shapely
 | The selected atoms are colored by the color scheme in which each amino acid and nucleic acid is assigned a unique color according to the amino acid and nucleic acid properties.
 |-
 | Group
 | The atoms of every chain are drawn as a smooth spectrum from red (N-terminal of the molecule) to blue (C-terminal).
 |-
 | Chain
 | The selected atoms are colored by the color scheme in which each chain is assigned a unique color.
 |-
 | Temperature
 | The selected atoms are drawn as a smooth spectrum from red (high value) to blue (low value) according to the value of the temperature factor.
 |-
 | Structure
 | The secondary structures are colored by the color scheme in which each secondary structure is assigned a unique color.
 |-
 | Charge
 | The selected atoms are drawn as a smooth spectrum from blue (positive) to red (negative) according to the charge.
 |-
 | Amino
 | The selected atoms are colored by the color scheme in which each amino acid is assigned a unique color.
 |}

;4) Options menu
{| class="wikitable" border="1"
 |-
 | style="background-color:gainsboro" | Component
 | style="background-color:gainsboro" | Function
 |-
 | Hetero || Atoms	Users can choose whether the heterogeneous atoms described by ‘HETATM’ in PDB files are selected or not.
 |-
 | Hydrogens || Users can choose whether the hydrogen atoms are selected or not.
 |-
 | Slab || Users can choose whether the z-clipping plane is located on the default position or is shifted.
 |-
 | Stereo || Users can choose whether the stereo display is enabled or not.
 |-
 | Load To Center || Users can choose whether a new image is added to the center of screen or not when a new file is opened.
 |-
 | Pick Off || The mouse-pick is disabled. 
 |-
 | Pick Ident || The atom and residue names, their serial numbers, chain identifier and file ID of the object picked by mouse-click are represented.
 |-
 | Pick Coordinates || The atom and residue names, their serial numbers, chain identifier, file ID and coordinate of the object picked by mouse-click are represented.
 |-
 | Pick Distance || The distance between the first and second clicked atoms is calculated and shown.
 |-
 | Pick Center || The center of rotation and window are transferred to the clicked position.
 |-
 | Pick Select || Only clicked files are operated.
 |- 
 | Animation || The animation control dialog is opened.
 |}

;5) Help menu
{| class="wikitable" border="1"
 |-
 | style="background-color:gainsboro" | Component
 | style="background-color:gainsboro" | Function
 |-
 | About jV || Information about this application is shown.
 |}</text>
    <sha1>43ee9a9262b5ef6a3e89d050bbbd20032616cfdf</sha1>
  </revision>
  <revision>
    <id>223</id>
    <parentid>222</parentid>
    <timestamp>2009-03-09T10:21:18Z</timestamp>
    <contributor>
      <username>JVuser</username>
      <id>2</id>
    </contributor>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="8651" xml:space="preserve">{| style="float:right"
 |__TOC__
 |}
== Menu bar ==
The organization of the menu bar and the function of its components are shown below.

;1) File menu
{| class="wikitable" border="1"
 |-
 | style="background-color:gainsboro" colspan="2" | Component
 | style="background-color:gainsboro" | Function
 |-
 | rowspan="5" | Open - Local
 | PDBML
 | A local PDBML file is opened.
 |-
 | PDB
 | A local PDB file is opened.
 |-
 | Polygon
 | A local polygon file is opened.
 |-
 | Script 
 | A local script file is opened.
 |-
 | Animation
 | A local animation file is opened.
 |-
 | rowspan="7" | Open-Remote
 | PDBML
 | A remote PDBML file is opened.
 |-
 | PDB
 | A remote PDB file is opened.
 |-
 | Polygon
 | A remote polygon file is opened.
 |- 
 | Script
 | A remote script file is opened.
 |-
 | Animation
 | A remote animation file is opened.
 |-
 | PDB ID
 | A PDBML file at the PDBML FTP site is opened.
 |-
 | eF-site ID
 | A set of molecular and polygon files stored in eF-site database are opened.
 |-
 | colspan="2" | Information
 | Information about the selected files are shown.
 |-
 | colspan="2" | Close
 | The specified file is closed.
 |-
 | rowspan="4" | Save
 | PDB
 | A PDB format file that contains the current atom coordinates is created.
 |-
 | Script
 | A script by which the present condition is reproduced is created.
 |-
 | PNG
 | The current image is saved as PNG.
 |-
 | JPEG
 | The current image is saved as JPEG.
 |-
 | colspan="2" | Exit
 | The application is terminated.
 |}

;2) Display menu
{| class="wikitable" border="1"
 |-
 | style="background-color:gainsboro" | Component
 | style="background-color:gainsboro" | Function
 |-
 | Wireframe
 | The selected atoms are displayed in a wire frame model.
 |-
 | Backbone
 | The selected atoms are displayed in a backbone model.
 |-
 | Sticks
 | The selected atoms are displayed in a stick model.
 |-
 | Spacefill
 | The selected atoms are displayed in a space-fill model.
 |-
 | Ball&amp;Stick
 | The selected atoms are displayed in a ball &amp; stick model.
 |-
 | Ribbons
 | The selected atoms are displayed in a ribbon model.
 |-
 | Cartoon
 | The selected atoms are displayed in a cartoon model.
 |}

;3) Colors menu
{| class="wikitable" border="1"
 |-
 | style="background-color:gainsboro" | Component
 | style="background-color:gainsboro" | Function
 |-
 | Monochrome
 | The selected atoms are colored in white.
 |-
 | CPK
 | The selected atoms are colored by CPK color scheme.
 |-
 | Shapely
 | The selected atoms are colored by the color scheme in which each amino acid and nucleic acid is assigned a unique color according to the amino acid and nucleic acid properties.
 |-
 | Group
 | The atoms of every chain are drawn as a smooth spectrum from red (N-terminal of the molecule) to blue (C-terminal).
 |-
 | Chain
 | The selected atoms are colored by the color scheme in which each chain is assigned a unique color.
 |-
 | Temperature
 | The selected atoms are drawn as a smooth spectrum from red (high value) to blue (low value) according to the value of the temperature factor.
 |-
 | Structure
 | The secondary structures are colored by the color scheme in which each secondary structure is assigned a unique color.
 |-
 | Charge
 | The selected atoms are drawn as a smooth spectrum from blue (positive) to red (negative) according to the charge.
 |-
 | Amino
 | The selected atoms are colored by the color scheme in which each amino acid is assigned a unique color.
 |}

;4) Options menu
{| class="wikitable" border="1"
 |-
 | style="background-color:gainsboro" | Component
 | style="background-color:gainsboro" | Function
 |-
 | Hetero || Atoms	Users can choose whether the heterogeneous atoms described by ‘HETATM’ in PDB files are selected or not.
 |-
 | Hydrogens || Users can choose whether the hydrogen atoms are selected or not.
 |-
 | Slab || Users can choose whether the z-clipping plane is located on the default position or is shifted.
 |-
 | Stereo || Users can choose whether the stereo display is enabled or not.
 |-
 | Load To Center || Users can choose whether a new image is added to the center of screen or not when a new file is opened.
 |-
 | Pick Off || The mouse-pick is disabled. 
 |-
 | Pick Ident || The atom and residue names, their serial numbers, chain identifier and file ID of the object picked by mouse-click are represented.
 |-
 | Pick Coordinates || The atom and residue names, their serial numbers, chain identifier, file ID and coordinate of the object picked by mouse-click are represented.
 |-
 | Pick Distance || The distance between the first and second clicked atoms is calculated and shown.
 |-
 | Pick Center || The center of rotation and window are transferred to the clicked position.
 |-
 | Pick Select || Only clicked files are operated.
 |- 
 | Animation || The animation control dialog is opened.
 |}

;5) Help menu
{| class="wikitable" border="1"
 |-
 | style="background-color:gainsboro" | Component
 | style="background-color:gainsboro" | Function
 |-
 | About jV || Information about this application is shown.
 |}

== Open-Remode dialog ==
;1) URL with parameters
Selecting [PDBML], [PDB], [Polygon], [Script] or [Animation] menu item in the [File] – [Open – Remote] menu opens the open-remote dialog that can handle a URL with parameters. For example, Figure 5 shows a dialog opened by the [File] – [Open – Remote] – [PDBML] menu item.

[[File:Fig5.jpg|thumb|Figure5: The open-remote dialog|center|300px]]

When ‘Add’ button is clicked, a new parameter line is appended in the table at the center of the dialog. Figure 6 shows an example of a URL with one parameter. By clicking the ‘Add’ button the necessary number of times, you can attach multiple parameters. When ‘Remove’ button is clicked, a highlighted line in the parameter table is removed. When ‘Clear’ button is clicked, all parameters are removed.

[[File:Fig6.jpg|thumb|Figure6: Example of a URL with a parameter|center|400px]]

;2)'type' column and mouse pick
The ‘type’ column in the parameter table is selected from the follows.

{| class="wikitable" border="1"
 |-
 | style="background-color:gainsboro" | type
 | style="background-color:gainsboro" | values
 | style="background-color:gainsboro" | mouse pick
 |-
 | text || arbitrary value || does not work
 |-
 | atom ID || atom ID || work
 |-
 | atom || set of chain ID, residue ID and atom ID || work
 |-
 | residue || set of chain ID and residue ID || work
 |-
 | orig_coords || atom coordinates written in the molecule file || work
 |-
 | curr_coords || atom coordinates currently displayed || work
 |}

For the case of a type to which mouse pick works, selecting an atom in the screen by mouse pick sets the corresponding value to the ‘value’ column in a highlighted line in the parameter table. The value of the ‘delimiter’ field is used to delimit atom’s x, y, and z coordinate.

;3) Saving and loading the configuration
By clicking the ‘save’ button, a file chooser dialog is appeared and the current configuration can be saved to a file. In the same way, a configuration can be loaded by clicking the ‘load’ button. The contents of a configuration file are in XML format as follows.

 &lt;?xml version="1.0"?&gt;
 &lt;remote_file url="http://example.com"&gt;
  &lt;params attach="true" coordinates_delimiter=","&gt;
    &lt;param name="param1" value="value1" type="text"/&gt;
  &lt;/params&gt;
 &lt;/remote_file&gt;

;4) Copy of the transform
When a file ID that currently exists is entered to the ‘fit to’ field, the transform of the newly opened file is set identical to that of the specified file.

;5) Execution
When the ‘OK’ button is clicked, a new file is loaded and the dialog is closed. When you use ‘Submit’ button, on the other hand, the dialog remains visible even after a new file is loaded.

== Animation control dialog ==
The animation control dialog is visible only if [Options] - [Animation] menu is checked. When there is no animation file loaded, the animation control dialog is as Figure 7. If some animation files are opened, the animation control dialog is altered according to the number of the files. Figure 8 indicates the dialog in the presence of two files.

[[File:Fig7.jpg|thumb|Figure7: The animation control dialog in the absence of files.|center|300px]]

[[File:Fig8.jpg|thumb|Figure8: The animation control dialog in the presence of two files.|center|300px]]

Users can select which files are controlled by their checkbox. The frame position and playback and stop of the animation can be controlled individually to each file. The playback-speed and the selection of ‘loop’ and ‘swing’ modes are common for all files.</text>
    <sha1>6484a4a07de4a3ddd19278e2a7d62a938f03a3de</sha1>
  </revision>
  <revision>
    <id>224</id>
    <parentid>223</parentid>
    <timestamp>2009-03-09T10:21:53Z</timestamp>
    <contributor>
      <username>JVuser</username>
      <id>2</id>
    </contributor>
    <comment>/* Open-Remode dialog */</comment>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="8651" xml:space="preserve">{| style="float:right"
 |__TOC__
 |}
== Menu bar ==
The organization of the menu bar and the function of its components are shown below.

;1) File menu
{| class="wikitable" border="1"
 |-
 | style="background-color:gainsboro" colspan="2" | Component
 | style="background-color:gainsboro" | Function
 |-
 | rowspan="5" | Open - Local
 | PDBML
 | A local PDBML file is opened.
 |-
 | PDB
 | A local PDB file is opened.
 |-
 | Polygon
 | A local polygon file is opened.
 |-
 | Script 
 | A local script file is opened.
 |-
 | Animation
 | A local animation file is opened.
 |-
 | rowspan="7" | Open-Remote
 | PDBML
 | A remote PDBML file is opened.
 |-
 | PDB
 | A remote PDB file is opened.
 |-
 | Polygon
 | A remote polygon file is opened.
 |- 
 | Script
 | A remote script file is opened.
 |-
 | Animation
 | A remote animation file is opened.
 |-
 | PDB ID
 | A PDBML file at the PDBML FTP site is opened.
 |-
 | eF-site ID
 | A set of molecular and polygon files stored in eF-site database are opened.
 |-
 | colspan="2" | Information
 | Information about the selected files are shown.
 |-
 | colspan="2" | Close
 | The specified file is closed.
 |-
 | rowspan="4" | Save
 | PDB
 | A PDB format file that contains the current atom coordinates is created.
 |-
 | Script
 | A script by which the present condition is reproduced is created.
 |-
 | PNG
 | The current image is saved as PNG.
 |-
 | JPEG
 | The current image is saved as JPEG.
 |-
 | colspan="2" | Exit
 | The application is terminated.
 |}

;2) Display menu
{| class="wikitable" border="1"
 |-
 | style="background-color:gainsboro" | Component
 | style="background-color:gainsboro" | Function
 |-
 | Wireframe
 | The selected atoms are displayed in a wire frame model.
 |-
 | Backbone
 | The selected atoms are displayed in a backbone model.
 |-
 | Sticks
 | The selected atoms are displayed in a stick model.
 |-
 | Spacefill
 | The selected atoms are displayed in a space-fill model.
 |-
 | Ball&amp;Stick
 | The selected atoms are displayed in a ball &amp; stick model.
 |-
 | Ribbons
 | The selected atoms are displayed in a ribbon model.
 |-
 | Cartoon
 | The selected atoms are displayed in a cartoon model.
 |}

;3) Colors menu
{| class="wikitable" border="1"
 |-
 | style="background-color:gainsboro" | Component
 | style="background-color:gainsboro" | Function
 |-
 | Monochrome
 | The selected atoms are colored in white.
 |-
 | CPK
 | The selected atoms are colored by CPK color scheme.
 |-
 | Shapely
 | The selected atoms are colored by the color scheme in which each amino acid and nucleic acid is assigned a unique color according to the amino acid and nucleic acid properties.
 |-
 | Group
 | The atoms of every chain are drawn as a smooth spectrum from red (N-terminal of the molecule) to blue (C-terminal).
 |-
 | Chain
 | The selected atoms are colored by the color scheme in which each chain is assigned a unique color.
 |-
 | Temperature
 | The selected atoms are drawn as a smooth spectrum from red (high value) to blue (low value) according to the value of the temperature factor.
 |-
 | Structure
 | The secondary structures are colored by the color scheme in which each secondary structure is assigned a unique color.
 |-
 | Charge
 | The selected atoms are drawn as a smooth spectrum from blue (positive) to red (negative) according to the charge.
 |-
 | Amino
 | The selected atoms are colored by the color scheme in which each amino acid is assigned a unique color.
 |}

;4) Options menu
{| class="wikitable" border="1"
 |-
 | style="background-color:gainsboro" | Component
 | style="background-color:gainsboro" | Function
 |-
 | Hetero || Atoms	Users can choose whether the heterogeneous atoms described by ‘HETATM’ in PDB files are selected or not.
 |-
 | Hydrogens || Users can choose whether the hydrogen atoms are selected or not.
 |-
 | Slab || Users can choose whether the z-clipping plane is located on the default position or is shifted.
 |-
 | Stereo || Users can choose whether the stereo display is enabled or not.
 |-
 | Load To Center || Users can choose whether a new image is added to the center of screen or not when a new file is opened.
 |-
 | Pick Off || The mouse-pick is disabled. 
 |-
 | Pick Ident || The atom and residue names, their serial numbers, chain identifier and file ID of the object picked by mouse-click are represented.
 |-
 | Pick Coordinates || The atom and residue names, their serial numbers, chain identifier, file ID and coordinate of the object picked by mouse-click are represented.
 |-
 | Pick Distance || The distance between the first and second clicked atoms is calculated and shown.
 |-
 | Pick Center || The center of rotation and window are transferred to the clicked position.
 |-
 | Pick Select || Only clicked files are operated.
 |- 
 | Animation || The animation control dialog is opened.
 |}

;5) Help menu
{| class="wikitable" border="1"
 |-
 | style="background-color:gainsboro" | Component
 | style="background-color:gainsboro" | Function
 |-
 | About jV || Information about this application is shown.
 |}

== Open-Remode dialog ==
;1) URL with parameters
Selecting [PDBML], [PDB], [Polygon], [Script] or [Animation] menu item in the [File] – [Open – Remote] menu opens the open-remote dialog that can handle a URL with parameters. For example, Figure 5 shows a dialog opened by the [File] – [Open – Remote] – [PDBML] menu item.

[[File:Fig5.jpg|thumb|Figure5: The open-remote dialog|center|300px]]

When ‘Add’ button is clicked, a new parameter line is appended in the table at the center of the dialog. Figure 6 shows an example of a URL with one parameter. By clicking the ‘Add’ button the necessary number of times, you can attach multiple parameters. When ‘Remove’ button is clicked, a highlighted line in the parameter table is removed. When ‘Clear’ button is clicked, all parameters are removed.

[[File:Fig6.jpg|thumb|Figure6: Example of a URL with a parameter|center|300px]]

;2)'type' column and mouse pick
The ‘type’ column in the parameter table is selected from the follows.

{| class="wikitable" border="1"
 |-
 | style="background-color:gainsboro" | type
 | style="background-color:gainsboro" | values
 | style="background-color:gainsboro" | mouse pick
 |-
 | text || arbitrary value || does not work
 |-
 | atom ID || atom ID || work
 |-
 | atom || set of chain ID, residue ID and atom ID || work
 |-
 | residue || set of chain ID and residue ID || work
 |-
 | orig_coords || atom coordinates written in the molecule file || work
 |-
 | curr_coords || atom coordinates currently displayed || work
 |}

For the case of a type to which mouse pick works, selecting an atom in the screen by mouse pick sets the corresponding value to the ‘value’ column in a highlighted line in the parameter table. The value of the ‘delimiter’ field is used to delimit atom’s x, y, and z coordinate.

;3) Saving and loading the configuration
By clicking the ‘save’ button, a file chooser dialog is appeared and the current configuration can be saved to a file. In the same way, a configuration can be loaded by clicking the ‘load’ button. The contents of a configuration file are in XML format as follows.

 &lt;?xml version="1.0"?&gt;
 &lt;remote_file url="http://example.com"&gt;
  &lt;params attach="true" coordinates_delimiter=","&gt;
    &lt;param name="param1" value="value1" type="text"/&gt;
  &lt;/params&gt;
 &lt;/remote_file&gt;

;4) Copy of the transform
When a file ID that currently exists is entered to the ‘fit to’ field, the transform of the newly opened file is set identical to that of the specified file.

;5) Execution
When the ‘OK’ button is clicked, a new file is loaded and the dialog is closed. When you use ‘Submit’ button, on the other hand, the dialog remains visible even after a new file is loaded.

== Animation control dialog ==
The animation control dialog is visible only if [Options] - [Animation] menu is checked. When there is no animation file loaded, the animation control dialog is as Figure 7. If some animation files are opened, the animation control dialog is altered according to the number of the files. Figure 8 indicates the dialog in the presence of two files.

[[File:Fig7.jpg|thumb|Figure7: The animation control dialog in the absence of files.|center|300px]]

[[File:Fig8.jpg|thumb|Figure8: The animation control dialog in the presence of two files.|center|300px]]

Users can select which files are controlled by their checkbox. The frame position and playback and stop of the animation can be controlled individually to each file. The playback-speed and the selection of ‘loop’ and ‘swing’ modes are common for all files.</text>
    <sha1>0e1db41f9060d29a9c59b86d1ad6d39a1e61670f</sha1>
  </revision>
  <revision>
    <id>229</id>
    <parentid>224</parentid>
    <timestamp>2009-03-09T10:25:43Z</timestamp>
    <contributor>
      <username>JVuser</username>
      <id>2</id>
    </contributor>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="8651" xml:space="preserve">{| style="float:right"
 |__TOC__
 |}
== Menu bar ==
The organization of the menu bar and the function of its components are shown below.

;1) File menu
{| class="wikitable" border="1"
 |-
 | style="background-color:gainsboro" colspan="2" | Component
 | style="background-color:gainsboro" | Function
 |-
 | rowspan="5" | Open - Local
 | PDBML
 | A local PDBML file is opened.
 |-
 | PDB
 | A local PDB file is opened.
 |-
 | Polygon
 | A local polygon file is opened.
 |-
 | Script 
 | A local script file is opened.
 |-
 | Animation
 | A local animation file is opened.
 |-
 | rowspan="7" | Open-Remote
 | PDBML
 | A remote PDBML file is opened.
 |-
 | PDB
 | A remote PDB file is opened.
 |-
 | Polygon
 | A remote polygon file is opened.
 |- 
 | Script
 | A remote script file is opened.
 |-
 | Animation
 | A remote animation file is opened.
 |-
 | PDB ID
 | A PDBML file at the PDBML FTP site is opened.
 |-
 | eF-site ID
 | A set of molecular and polygon files stored in eF-site database are opened.
 |-
 | colspan="2" | Information
 | Information about the selected files are shown.
 |-
 | colspan="2" | Close
 | The specified file is closed.
 |-
 | rowspan="4" | Save
 | PDB
 | A PDB format file that contains the current atom coordinates is created.
 |-
 | Script
 | A script by which the present condition is reproduced is created.
 |-
 | PNG
 | The current image is saved as PNG.
 |-
 | JPEG
 | The current image is saved as JPEG.
 |-
 | colspan="2" | Exit
 | The application is terminated.
 |}

;2) Display menu
{| class="wikitable" border="1"
 |-
 | style="background-color:gainsboro" | Component
 | style="background-color:gainsboro" | Function
 |-
 | Wireframe
 | The selected atoms are displayed in a wire frame model.
 |-
 | Backbone
 | The selected atoms are displayed in a backbone model.
 |-
 | Sticks
 | The selected atoms are displayed in a stick model.
 |-
 | Spacefill
 | The selected atoms are displayed in a space-fill model.
 |-
 | Ball&amp;Stick
 | The selected atoms are displayed in a ball &amp; stick model.
 |-
 | Ribbons
 | The selected atoms are displayed in a ribbon model.
 |-
 | Cartoon
 | The selected atoms are displayed in a cartoon model.
 |}

;3) Colors menu
{| class="wikitable" border="1"
 |-
 | style="background-color:gainsboro" | Component
 | style="background-color:gainsboro" | Function
 |-
 | Monochrome
 | The selected atoms are colored in white.
 |-
 | CPK
 | The selected atoms are colored by CPK color scheme.
 |-
 | Shapely
 | The selected atoms are colored by the color scheme in which each amino acid and nucleic acid is assigned a unique color according to the amino acid and nucleic acid properties.
 |-
 | Group
 | The atoms of every chain are drawn as a smooth spectrum from red (N-terminal of the molecule) to blue (C-terminal).
 |-
 | Chain
 | The selected atoms are colored by the color scheme in which each chain is assigned a unique color.
 |-
 | Temperature
 | The selected atoms are drawn as a smooth spectrum from red (high value) to blue (low value) according to the value of the temperature factor.
 |-
 | Structure
 | The secondary structures are colored by the color scheme in which each secondary structure is assigned a unique color.
 |-
 | Charge
 | The selected atoms are drawn as a smooth spectrum from blue (positive) to red (negative) according to the charge.
 |-
 | Amino
 | The selected atoms are colored by the color scheme in which each amino acid is assigned a unique color.
 |}

;4) Options menu
{| class="wikitable" border="1"
 |-
 | style="background-color:gainsboro" | Component
 | style="background-color:gainsboro" | Function
 |-
 | Hetero || Atoms	Users can choose whether the heterogeneous atoms described by ‘HETATM’ in PDB files are selected or not.
 |-
 | Hydrogens || Users can choose whether the hydrogen atoms are selected or not.
 |-
 | Slab || Users can choose whether the z-clipping plane is located on the default position or is shifted.
 |-
 | Stereo || Users can choose whether the stereo display is enabled or not.
 |-
 | Load To Center || Users can choose whether a new image is added to the center of screen or not when a new file is opened.
 |-
 | Pick Off || The mouse-pick is disabled. 
 |-
 | Pick Ident || The atom and residue names, their serial numbers, chain identifier and file ID of the object picked by mouse-click are represented.
 |-
 | Pick Coordinates || The atom and residue names, their serial numbers, chain identifier, file ID and coordinate of the object picked by mouse-click are represented.
 |-
 | Pick Distance || The distance between the first and second clicked atoms is calculated and shown.
 |-
 | Pick Center || The center of rotation and window are transferred to the clicked position.
 |-
 | Pick Select || Only clicked files are operated.
 |- 
 | Animation || The animation control dialog is opened.
 |}

;5) Help menu
{| class="wikitable" border="1"
 |-
 | style="background-color:gainsboro" | Component
 | style="background-color:gainsboro" | Function
 |-
 | About jV || Information about this application is shown.
 |}

== Open-Remode dialog ==
;1) URL with parameters
Selecting [PDBML], [PDB], [Polygon], [Script] or [Animation] menu item in the [File] – [Open – Remote] menu opens the open-remote dialog that can handle a URL with parameters. For example, Figure 5 shows a dialog opened by the [File] – [Open – Remote] – [PDBML] menu item.

[[File:Fig5.jpg|thumb|Figure5: The open-remote dialog|center|400px]]

When ‘Add’ button is clicked, a new parameter line is appended in the table at the center of the dialog. Figure 6 shows an example of a URL with one parameter. By clicking the ‘Add’ button the necessary number of times, you can attach multiple parameters. When ‘Remove’ button is clicked, a highlighted line in the parameter table is removed. When ‘Clear’ button is clicked, all parameters are removed.

[[File:Fig6.jpg|thumb|Figure6: Example of a URL with a parameter|center|400px]]

;2)'type' column and mouse pick
The ‘type’ column in the parameter table is selected from the follows.

{| class="wikitable" border="1"
 |-
 | style="background-color:gainsboro" | type
 | style="background-color:gainsboro" | values
 | style="background-color:gainsboro" | mouse pick
 |-
 | text || arbitrary value || does not work
 |-
 | atom ID || atom ID || work
 |-
 | atom || set of chain ID, residue ID and atom ID || work
 |-
 | residue || set of chain ID and residue ID || work
 |-
 | orig_coords || atom coordinates written in the molecule file || work
 |-
 | curr_coords || atom coordinates currently displayed || work
 |}

For the case of a type to which mouse pick works, selecting an atom in the screen by mouse pick sets the corresponding value to the ‘value’ column in a highlighted line in the parameter table. The value of the ‘delimiter’ field is used to delimit atom’s x, y, and z coordinate.

;3) Saving and loading the configuration
By clicking the ‘save’ button, a file chooser dialog is appeared and the current configuration can be saved to a file. In the same way, a configuration can be loaded by clicking the ‘load’ button. The contents of a configuration file are in XML format as follows.

 &lt;?xml version="1.0"?&gt;
 &lt;remote_file url="http://example.com"&gt;
  &lt;params attach="true" coordinates_delimiter=","&gt;
    &lt;param name="param1" value="value1" type="text"/&gt;
  &lt;/params&gt;
 &lt;/remote_file&gt;

;4) Copy of the transform
When a file ID that currently exists is entered to the ‘fit to’ field, the transform of the newly opened file is set identical to that of the specified file.

;5) Execution
When the ‘OK’ button is clicked, a new file is loaded and the dialog is closed. When you use ‘Submit’ button, on the other hand, the dialog remains visible even after a new file is loaded.

== Animation control dialog ==
The animation control dialog is visible only if [Options] - [Animation] menu is checked. When there is no animation file loaded, the animation control dialog is as Figure 7. If some animation files are opened, the animation control dialog is altered according to the number of the files. Figure 8 indicates the dialog in the presence of two files.

[[File:Fig7.jpg|thumb|Figure7: The animation control dialog in the absence of files.|center|400px]]

[[File:Fig8.jpg|thumb|Figure8: The animation control dialog in the presence of two files.|center|400px]]

Users can select which files are controlled by their checkbox. The frame position and playback and stop of the animation can be controlled individually to each file. The playback-speed and the selection of ‘loop’ and ‘swing’ modes are common for all files.</text>
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  <revision>
    <id>230</id>
    <parentid>229</parentid>
    <timestamp>2009-03-09T10:26:32Z</timestamp>
    <contributor>
      <username>JVuser</username>
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    <text bytes="8667" xml:space="preserve">{| style="float:right"
 |__TOC__
 |}
== Menu bar ==
The organization of the menu bar and the function of its components are shown below.

;1) File menu
{| class="wikitable" border="1"
 |-
 | style="background-color:gainsboro" colspan="2" | Component
 | style="background-color:gainsboro" | Function
 |-
 | rowspan="5" | Open - Local
 | PDBML
 | A local PDBML file is opened.
 |-
 | PDB
 | A local PDB file is opened.
 |-
 | Polygon
 | A local polygon file is opened.
 |-
 | Script 
 | A local script file is opened.
 |-
 | Animation
 | A local animation file is opened.
 |-
 | rowspan="7" | Open-Remote
 | PDBML
 | A remote PDBML file is opened.
 |-
 | PDB
 | A remote PDB file is opened.
 |-
 | Polygon
 | A remote polygon file is opened.
 |- 
 | Script
 | A remote script file is opened.
 |-
 | Animation
 | A remote animation file is opened.
 |-
 | PDB ID
 | A PDBML file at the PDBML FTP site is opened.
 |-
 | eF-site ID
 | A set of molecular and polygon files stored in eF-site database are opened.
 |-
 | colspan="2" | Information
 | Information about the selected files are shown.
 |-
 | colspan="2" | Close
 | The specified file is closed.
 |-
 | rowspan="4" | Save
 | PDB
 | A PDB format file that contains the current atom coordinates is created.
 |-
 | Script
 | A script by which the present condition is reproduced is created.
 |-
 | PNG
 | The current image is saved as PNG.
 |-
 | JPEG
 | The current image is saved as JPEG.
 |-
 | colspan="2" | Exit
 | The application is terminated.
 |}

;2) Display menu
{| class="wikitable" border="1"
 |-
 | style="background-color:gainsboro" | Component
 | style="background-color:gainsboro" | Function
 |-
 | Wireframe
 | The selected atoms are displayed in a wire frame model.
 |-
 | Backbone
 | The selected atoms are displayed in a backbone model.
 |-
 | Sticks
 | The selected atoms are displayed in a stick model.
 |-
 | Spacefill
 | The selected atoms are displayed in a space-fill model.
 |-
 | Ball&amp;Stick
 | The selected atoms are displayed in a ball &amp; stick model.
 |-
 | Ribbons
 | The selected atoms are displayed in a ribbon model.
 |-
 | Cartoon
 | The selected atoms are displayed in a cartoon model.
 |}

;3) Colors menu
{| class="wikitable" border="1"
 |-
 | style="background-color:gainsboro" | Component
 | style="background-color:gainsboro" | Function
 |-
 | Monochrome
 | The selected atoms are colored in white.
 |-
 | CPK
 | The selected atoms are colored by CPK color scheme.
 |-
 | Shapely
 | The selected atoms are colored by the color scheme in which each amino acid and nucleic acid is assigned a unique color according to the amino acid and nucleic acid properties.
 |-
 | Group
 | The atoms of every chain are drawn as a smooth spectrum from red (N-terminal of the molecule) to blue (C-terminal).
 |-
 | Chain
 | The selected atoms are colored by the color scheme in which each chain is assigned a unique color.
 |-
 | Temperature
 | The selected atoms are drawn as a smooth spectrum from red (high value) to blue (low value) according to the value of the temperature factor.
 |-
 | Structure
 | The secondary structures are colored by the color scheme in which each secondary structure is assigned a unique color.
 |-
 | Charge
 | The selected atoms are drawn as a smooth spectrum from blue (positive) to red (negative) according to the charge.
 |-
 | Amino
 | The selected atoms are colored by the color scheme in which each amino acid is assigned a unique color.
 |}

;4) Options menu
{| class="wikitable" border="1"
 |-
 | style="background-color:gainsboro" | Component
 | style="background-color:gainsboro" | Function
 |-
 | Hetero || Atoms	Users can choose whether the heterogeneous atoms described by ‘HETATM’ in PDB files are selected or not.
 |-
 | Hydrogens || Users can choose whether the hydrogen atoms are selected or not.
 |-
 | Slab || Users can choose whether the z-clipping plane is located on the default position or is shifted.
 |-
 | Stereo || Users can choose whether the stereo display is enabled or not.
 |-
 | Load To Center || Users can choose whether a new image is added to the center of screen or not when a new file is opened.
 |-
 | Pick Off || The mouse-pick is disabled. 
 |-
 | Pick Ident || The atom and residue names, their serial numbers, chain identifier and file ID of the object picked by mouse-click are represented.
 |-
 | Pick Coordinates || The atom and residue names, their serial numbers, chain identifier, file ID and coordinate of the object picked by mouse-click are represented.
 |-
 | Pick Distance || The distance between the first and second clicked atoms is calculated and shown.
 |-
 | Pick Center || The center of rotation and window are transferred to the clicked position.
 |-
 | Pick Select || Only clicked files are operated.
 |- 
 | Animation || The animation control dialog is opened.
 |}

;5) Help menu
{| class="wikitable" border="1"
 |-
 | style="background-color:gainsboro" | Component
 | style="background-color:gainsboro" | Function
 |-
 | About jV || Information about this application is shown.
 |}

== Open-Remode dialog ==
;1) URL with parameters
Selecting [PDBML], [PDB], [Polygon], [Script] or [Animation] menu item in the [File] – [Open – Remote] menu opens the open-remote dialog that can handle a URL with parameters. For example, Figure 5 shows a dialog opened by the [File] – [Open – Remote] – [PDBML] menu item.

[[File:Fig5.jpg|thumb|Figure5: The open-remote dialog|center|400px]]

When ‘Add’ button is clicked, a new parameter line is appended in the table at the center of the dialog. Figure 6 shows an example of a URL with one parameter. By clicking the ‘Add’ button the necessary number of times, you can attach multiple parameters. When ‘Remove’ button is clicked, a highlighted line in the parameter table is removed. When ‘Clear’ button is clicked, all parameters are removed.

[[File:Fig6.jpg|thumb|Figure6: Example of a URL with a parameter|center|400px]]

;2)'type' column and mouse pick
The ‘type’ column in the parameter table is selected from the follows.

{| class="wikitable" border="1"
 |-
 | style="background-color:gainsboro" | type
 | style="background-color:gainsboro" | values
 | style="background-color:gainsboro" | mouse pick
 |-
 | text || arbitrary value || does not work
 |-
 | atom ID || atom ID || work
 |-
 | atom || set of chain ID, residue ID and atom ID || work
 |-
 | residue || set of chain ID and residue ID || work
 |-
 | orig_coords || atom coordinates written in the molecule file || work
 |-
 | curr_coords || atom coordinates currently displayed || work
 |}

For the case of a type to which mouse pick works, selecting an atom in the screen by mouse pick sets the corresponding value to the ‘value’ column in a highlighted line in the parameter table. The value of the ‘delimiter’ field is used to delimit atom’s x, y, and z coordinate.

;3) Saving and loading the configuration
By clicking the ‘save’ button, a file chooser dialog is appeared and the current configuration can be saved to a file. In the same way, a configuration can be loaded by clicking the ‘load’ button. The contents of a configuration file are in XML format as follows.

 &lt;?xml version="1.0"?&gt;
 &amp;nbsp;
 &amp;nbsp;
 &lt;remote_file url="http://example.com"&gt;
  &lt;params attach="true" coordinates_delimiter=","&gt;
    &lt;param name="param1" value="value1" type="text"/&gt;
  &lt;/params&gt;
 &lt;/remote_file&gt;

;4) Copy of the transform
When a file ID that currently exists is entered to the ‘fit to’ field, the transform of the newly opened file is set identical to that of the specified file.

;5) Execution
When the ‘OK’ button is clicked, a new file is loaded and the dialog is closed. When you use ‘Submit’ button, on the other hand, the dialog remains visible even after a new file is loaded.

== Animation control dialog ==
The animation control dialog is visible only if [Options] - [Animation] menu is checked. When there is no animation file loaded, the animation control dialog is as Figure 7. If some animation files are opened, the animation control dialog is altered according to the number of the files. Figure 8 indicates the dialog in the presence of two files.

[[File:Fig7.jpg|thumb|Figure7: The animation control dialog in the absence of files.|center|400px]]

[[File:Fig8.jpg|thumb|Figure8: The animation control dialog in the presence of two files.|center|400px]]

Users can select which files are controlled by their checkbox. The frame position and playback and stop of the animation can be controlled individually to each file. The playback-speed and the selection of ‘loop’ and ‘swing’ modes are common for all files.</text>
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 |Description=The open remote dialog
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  <title>Main Page</title>
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    </contributor>
    <comment>/* jV version 3 Outline */</comment>
    <model>wikitext</model>
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    <text bytes="3717" xml:space="preserve">&lt;big&gt;'''Welcome to jV wiki.'''&lt;/big&gt;
jV version3 (formerly known as PDBjViewer) is a program to display molecular graphics of protein and nucleic acids. 
jV can use as a stand-alone program and can operate on a web browser as an Java applet. jV is used by PDBj services([http://ef-site.hgc.jp/eF-site/index.jsp eF-site], [http://ef-site.hgc.jp/eF-seek/index.jsp eF-seek], the molecular structure surface database of the protein functional part).

jV supports the following features:
* jV can read and display PDBML files, the canonical XML format for the Protein Data Bank.
* Of course, jV can read and display the traditional PDB format files, too.
* RasMol-like usability.
* jV can process more than one molecules.
* jV can display polygons specified by XML. ([http://ef-site.hgc.jp/eF-site/schema/polygon12.xsd XML Schema for polygons] is available.)
* Multiple polygons can be processed simultaneously, and be superimposed onto molecular images.
* Animation can be realized.
* The graphics of jV is based on OpenGL [https://jogl.dev.java.net/ JOGL]), thereby producing fairly beautiful pictures.
* jV runs on the Java Runtime Environment ([http://java.sun.com/javase/index.jsp JRE]) so that it can work as a stand-alone application as well as an applet.

The program 'jV' has been developed by [http://www.hgc.jp/~kinosita/TOP.html Kengo Kinoshita] ([http://www.hgc.jp/english/ Human Genome Center], [http://www.ims.u-tokyo.ac.jp/imsut/en/ Insutitute for Medical Science],[http://www.u-tokyo.ac.jp/index_e.html University of Tokyo]) and [http://www.protein.osaka-u.ac.jp/rcsfp/pi/ Haruki Nakamura] ([http://www.protein.osaka-u.ac.jp/index_e.php Institute for Protein Research], [http://www.osaka-u.ac.jp/eng/index.html Osaka Univeristy]), with the support from [http://www-bird.jst.go.jp/index_e.html JST-BIRD].

-[[jV version 3]] has indicated more detailed explanation and how to use.&lt;br /&gt;
-[[Installation of jV3]] is a procedure installed in a local machine.&lt;br /&gt;

&lt;font size="1"&gt;The [[old version]](jV version1 &amp; jV version2) has not carried out use recommendation.&lt;/font&gt;

&lt;gallery&gt;
File:Spacefill.jpg
File:Cartoon.jpg
File:Surface.jpg
File:edmap.jpg
&lt;/gallery&gt;

== System requirements ==
[[File:Download.png|right|link=http://ef-site.hgc.jp/eF-site/servlet/DownloadViewerBinary|Download]] jV version 3 is now used to display molecules and their surfaces as a Java applet program.&lt;br /&gt;&lt;font size="1"&gt;Version 3.6 was released on 11, Aug, 2008.&lt;br /&gt;This version is fully compativle with [https://applet-launcher.dev.java.net/ applet-launcher].&lt;/font&gt;&lt;br /&gt;Go to [[jV version 3]].
&lt;br /&gt;
It requires the following softwares.
* [http://java.sun.com/products/plugin/index-1.4.html JRE] 1.4.2 or later  (recommend 1.4.2_12)
* [https://jogl.dev.java.net/ JOGL] 1.0, 1.1.1 or JSR-231 1.0.0  (recommend JSR-231)&lt;br /&gt;
** version 1.0 [[http://ef-site.hgc.jp/eF-site/jV/JOGL1.0_win32.zip Windows],[http://ef-site.hgc.jp/eF-site/jV/JOGL1.0_macosx.tar.gz Mac OS X],[http://ef-site.hgc.jp/eF-site/jV/JOGL1.0_linux.tar.gz Linux]]
** version 1.1.1 [[http://ef-site.hgc.jp/eF-site/jV/JOGL1.1.1_win32.zip Windows],[http://ef-site.hgc.jp/eF-site/jV/JOGL1.1.1_macosx.tar.gz Mac OS X], [http://ef-site.hgc.jp/eF-site/jV/JOGL1.1.1_linux.tar.gz Linux]]
** JSR-231 1.0.0 [[http://ef-site.hgc.jp/eF-site/jV/JOGL_JSR231_win32.zip Windows], [http://ef-site.hgc.jp/eF-site/jV/JOGL_JSR231_macosx_ppc.tar.gz Mac OS X ppc], [http://ef-site.hgc.jp/eF-site/jV/JOGL_JSR231_macosx_universal.tar.gz Mac OS X universal], [http://ef-site.hgc.jp/eF-site/jV/JOGL_JSR231_linux_i586.tar.gz Linux]]

&lt;font size="1"&gt;Note: &amp;nbsp; JOGL 1.0 and 1.1.1 are not available for Intel Mac.The latest version of JOGL, JSR-231 1.0.0, runs on Intel Mac.&lt;/font&gt;</text>
    <sha1>9cf4c26ee620975c6907259f9f0780060c1b9ac4</sha1>
  </revision>
  <revision>
    <id>233</id>
    <parentid>232</parentid>
    <timestamp>2009-03-09T10:33:51Z</timestamp>
    <contributor>
      <username>JVuser</username>
      <id>2</id>
    </contributor>
    <comment>/* System requirements */</comment>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="3711" xml:space="preserve">&lt;big&gt;'''Welcome to jV wiki.'''&lt;/big&gt;
jV version3 (formerly known as PDBjViewer) is a program to display molecular graphics of protein and nucleic acids. 
jV can use as a stand-alone program and can operate on a web browser as an Java applet. jV is used by PDBj services([http://ef-site.hgc.jp/eF-site/index.jsp eF-site], [http://ef-site.hgc.jp/eF-seek/index.jsp eF-seek], the molecular structure surface database of the protein functional part).

jV supports the following features:
* jV can read and display PDBML files, the canonical XML format for the Protein Data Bank.
* Of course, jV can read and display the traditional PDB format files, too.
* RasMol-like usability.
* jV can process more than one molecules.
* jV can display polygons specified by XML. ([http://ef-site.hgc.jp/eF-site/schema/polygon12.xsd XML Schema for polygons] is available.)
* Multiple polygons can be processed simultaneously, and be superimposed onto molecular images.
* Animation can be realized.
* The graphics of jV is based on OpenGL [https://jogl.dev.java.net/ JOGL]), thereby producing fairly beautiful pictures.
* jV runs on the Java Runtime Environment ([http://java.sun.com/javase/index.jsp JRE]) so that it can work as a stand-alone application as well as an applet.

The program 'jV' has been developed by [http://www.hgc.jp/~kinosita/TOP.html Kengo Kinoshita] ([http://www.hgc.jp/english/ Human Genome Center], [http://www.ims.u-tokyo.ac.jp/imsut/en/ Insutitute for Medical Science],[http://www.u-tokyo.ac.jp/index_e.html University of Tokyo]) and [http://www.protein.osaka-u.ac.jp/rcsfp/pi/ Haruki Nakamura] ([http://www.protein.osaka-u.ac.jp/index_e.php Institute for Protein Research], [http://www.osaka-u.ac.jp/eng/index.html Osaka Univeristy]), with the support from [http://www-bird.jst.go.jp/index_e.html JST-BIRD].

-[[jV version 3]] has indicated more detailed explanation and how to use.&lt;br /&gt;
-[[Installation of jV3]] is a procedure installed in a local machine.&lt;br /&gt;

&lt;font size="1"&gt;The [[old version]](jV version1 &amp; jV version2) has not carried out use recommendation.&lt;/font&gt;

&lt;gallery&gt;
File:Spacefill.jpg
File:Cartoon.jpg
File:Surface.jpg
File:edmap.jpg
&lt;/gallery&gt;

== System requirements ==
[[File:Download.png|right|link=http://ef-site.hgc.jp/eF-site/servlet/DownloadViewerBinary|Download]] jV version 3 is now used to display molecules and their surfaces as a Java applet program.&lt;br /&gt;&lt;font size="1"&gt;Version 3.6 was released on 11, Aug, 2008.&lt;br /&gt;This version is fully compativle with [https://applet-launcher.dev.java.net/ applet-launcher].&lt;/font&gt;&lt;br /&gt;Go to [[jV version 3]].
&lt;br /&gt;
It requires the following softwares.
* [http://java.sun.com/j2se/1.4.2/download.html JRE] 1.4.2 or later  (recommend 1.4.2_12)
* [https://jogl.dev.java.net/ JOGL] 1.0, 1.1.1 or JSR-231 1.0.0  (recommend JSR-231)&lt;br /&gt;
** version 1.0 [[http://ef-site.hgc.jp/eF-site/jV/JOGL1.0_win32.zip Windows],[http://ef-site.hgc.jp/eF-site/jV/JOGL1.0_macosx.tar.gz Mac OS X],[http://ef-site.hgc.jp/eF-site/jV/JOGL1.0_linux.tar.gz Linux]]
** version 1.1.1 [[http://ef-site.hgc.jp/eF-site/jV/JOGL1.1.1_win32.zip Windows],[http://ef-site.hgc.jp/eF-site/jV/JOGL1.1.1_macosx.tar.gz Mac OS X], [http://ef-site.hgc.jp/eF-site/jV/JOGL1.1.1_linux.tar.gz Linux]]
** JSR-231 1.0.0 [[http://ef-site.hgc.jp/eF-site/jV/JOGL_JSR231_win32.zip Windows], [http://ef-site.hgc.jp/eF-site/jV/JOGL_JSR231_macosx_ppc.tar.gz Mac OS X ppc], [http://ef-site.hgc.jp/eF-site/jV/JOGL_JSR231_macosx_universal.tar.gz Mac OS X universal], [http://ef-site.hgc.jp/eF-site/jV/JOGL_JSR231_linux_i586.tar.gz Linux]]

&lt;font size="1"&gt;Note: &amp;nbsp; JOGL 1.0 and 1.1.1 are not available for Intel Mac.The latest version of JOGL, JSR-231 1.0.0, runs on Intel Mac.&lt;/font&gt;</text>
    <sha1>f8c2799f05b831b12cc65f445759a370f7f3b5e4</sha1>
  </revision>
  <revision>
    <id>234</id>
    <parentid>233</parentid>
    <timestamp>2009-03-09T10:34:48Z</timestamp>
    <contributor>
      <username>JVuser</username>
      <id>2</id>
    </contributor>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="3740" xml:space="preserve">&lt;big&gt;'''Welcome to jV wiki.'''&lt;/big&gt;
jV version3 (formerly known as PDBjViewer) is a program to display molecular graphics of protein and nucleic acids. 
jV can use as a stand-alone program and can operate on a web browser as an Java applet. jV is used by PDBj services([http://ef-site.hgc.jp/eF-site/index.jsp eF-site], [http://ef-site.hgc.jp/eF-seek/index.jsp eF-seek], the molecular structure surface database of the protein functional part).

jV supports the following features:
* jV can read and display PDBML files, the canonical XML format for the Protein Data Bank.
* Of course, jV can read and display the traditional PDB format files, too.
* RasMol-like usability.
* jV can process more than one molecules.
* jV can display polygons specified by XML. ([http://ef-site.hgc.jp/eF-site/schema/polygon12.xsd XML Schema for polygons] is available.)
* Multiple polygons can be processed simultaneously, and be superimposed onto molecular images.
* Animation can be realized.
* The graphics of jV is based on OpenGL [https://jogl.dev.java.net/ JOGL]), thereby producing fairly beautiful pictures.
* jV runs on the Java Runtime Environment ([http://java.sun.com/javase/index.jsp JRE]) so that it can work as a stand-alone application as well as an applet.

The program 'jV' has been developed by [http://www.hgc.jp/~kinosita/TOP.html Kengo Kinoshita] ([http://www.hgc.jp/english/ Human Genome Center], [http://www.ims.u-tokyo.ac.jp/imsut/en/ Insutitute for Medical Science],[http://www.u-tokyo.ac.jp/index_e.html University of Tokyo]) and [http://www.protein.osaka-u.ac.jp/rcsfp/pi/ Haruki Nakamura] ([http://www.protein.osaka-u.ac.jp/index_e.php Institute for Protein Research], [http://www.osaka-u.ac.jp/eng/index.html Osaka Univeristy]), with the support from [http://www-bird.jst.go.jp/index_e.html JST-BIRD].

;How to use jV3
 [[jV version 3]] has indicated more detailed explanation and how to use.&lt;br /&gt;
;jV3 install
 [[Installation of jV3]] is a procedure installed in a local machine.&lt;br /&gt;

&lt;font size="1"&gt;The [[old version]](jV version1 &amp; jV version2) has not carried out use recommendation.&lt;/font&gt;

&lt;gallery&gt;
File:Spacefill.jpg
File:Cartoon.jpg
File:Surface.jpg
File:edmap.jpg
&lt;/gallery&gt;

== System requirements ==
[[File:Download.png|right|link=http://ef-site.hgc.jp/eF-site/servlet/DownloadViewerBinary|Download]] jV version 3 is now used to display molecules and their surfaces as a Java applet program.&lt;br /&gt;&lt;font size="1"&gt;Version 3.6 was released on 11, Aug, 2008.&lt;br /&gt;This version is fully compativle with [https://applet-launcher.dev.java.net/ applet-launcher].&lt;/font&gt;&lt;br /&gt;Go to [[jV version 3]].
&lt;br /&gt;
It requires the following softwares.
* [http://java.sun.com/j2se/1.4.2/download.html JRE] 1.4.2 or later  (recommend 1.4.2_12)
* [https://jogl.dev.java.net/ JOGL] 1.0, 1.1.1 or JSR-231 1.0.0  (recommend JSR-231)&lt;br /&gt;
** version 1.0 [[http://ef-site.hgc.jp/eF-site/jV/JOGL1.0_win32.zip Windows],[http://ef-site.hgc.jp/eF-site/jV/JOGL1.0_macosx.tar.gz Mac OS X],[http://ef-site.hgc.jp/eF-site/jV/JOGL1.0_linux.tar.gz Linux]]
** version 1.1.1 [[http://ef-site.hgc.jp/eF-site/jV/JOGL1.1.1_win32.zip Windows],[http://ef-site.hgc.jp/eF-site/jV/JOGL1.1.1_macosx.tar.gz Mac OS X], [http://ef-site.hgc.jp/eF-site/jV/JOGL1.1.1_linux.tar.gz Linux]]
** JSR-231 1.0.0 [[http://ef-site.hgc.jp/eF-site/jV/JOGL_JSR231_win32.zip Windows], [http://ef-site.hgc.jp/eF-site/jV/JOGL_JSR231_macosx_ppc.tar.gz Mac OS X ppc], [http://ef-site.hgc.jp/eF-site/jV/JOGL_JSR231_macosx_universal.tar.gz Mac OS X universal], [http://ef-site.hgc.jp/eF-site/jV/JOGL_JSR231_linux_i586.tar.gz Linux]]

&lt;font size="1"&gt;Note: &amp;nbsp; JOGL 1.0 and 1.1.1 are not available for Intel Mac.The latest version of JOGL, JSR-231 1.0.0, runs on Intel Mac.&lt;/font&gt;</text>
    <sha1>26e8955bb830a5e85ed2ca16b11d0fc290856ff6</sha1>
  </revision>
  <revision>
    <id>235</id>
    <parentid>234</parentid>
    <timestamp>2009-03-09T10:35:07Z</timestamp>
    <contributor>
      <username>JVuser</username>
      <id>2</id>
    </contributor>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="3738" xml:space="preserve">&lt;big&gt;'''Welcome to jV wiki.'''&lt;/big&gt;
jV version3 (formerly known as PDBjViewer) is a program to display molecular graphics of protein and nucleic acids. 
jV can use as a stand-alone program and can operate on a web browser as an Java applet. jV is used by PDBj services([http://ef-site.hgc.jp/eF-site/index.jsp eF-site], [http://ef-site.hgc.jp/eF-seek/index.jsp eF-seek], the molecular structure surface database of the protein functional part).

jV supports the following features:
* jV can read and display PDBML files, the canonical XML format for the Protein Data Bank.
* Of course, jV can read and display the traditional PDB format files, too.
* RasMol-like usability.
* jV can process more than one molecules.
* jV can display polygons specified by XML. ([http://ef-site.hgc.jp/eF-site/schema/polygon12.xsd XML Schema for polygons] is available.)
* Multiple polygons can be processed simultaneously, and be superimposed onto molecular images.
* Animation can be realized.
* The graphics of jV is based on OpenGL [https://jogl.dev.java.net/ JOGL]), thereby producing fairly beautiful pictures.
* jV runs on the Java Runtime Environment ([http://java.sun.com/javase/index.jsp JRE]) so that it can work as a stand-alone application as well as an applet.

The program 'jV' has been developed by [http://www.hgc.jp/~kinosita/TOP.html Kengo Kinoshita] ([http://www.hgc.jp/english/ Human Genome Center], [http://www.ims.u-tokyo.ac.jp/imsut/en/ Insutitute for Medical Science],[http://www.u-tokyo.ac.jp/index_e.html University of Tokyo]) and [http://www.protein.osaka-u.ac.jp/rcsfp/pi/ Haruki Nakamura] ([http://www.protein.osaka-u.ac.jp/index_e.php Institute for Protein Research], [http://www.osaka-u.ac.jp/eng/index.html Osaka Univeristy]), with the support from [http://www-bird.jst.go.jp/index_e.html JST-BIRD].

;How to use jV3
[[jV version 3]] has indicated more detailed explanation and how to use.&lt;br /&gt;
;jV3 install
[[Installation of jV3]] is a procedure installed in a local machine.&lt;br /&gt;

&lt;font size="1"&gt;The [[old version]](jV version1 &amp; jV version2) has not carried out use recommendation.&lt;/font&gt;

&lt;gallery&gt;
File:Spacefill.jpg
File:Cartoon.jpg
File:Surface.jpg
File:edmap.jpg
&lt;/gallery&gt;

== System requirements ==
[[File:Download.png|right|link=http://ef-site.hgc.jp/eF-site/servlet/DownloadViewerBinary|Download]] jV version 3 is now used to display molecules and their surfaces as a Java applet program.&lt;br /&gt;&lt;font size="1"&gt;Version 3.6 was released on 11, Aug, 2008.&lt;br /&gt;This version is fully compativle with [https://applet-launcher.dev.java.net/ applet-launcher].&lt;/font&gt;&lt;br /&gt;Go to [[jV version 3]].
&lt;br /&gt;
It requires the following softwares.
* [http://java.sun.com/j2se/1.4.2/download.html JRE] 1.4.2 or later  (recommend 1.4.2_12)
* [https://jogl.dev.java.net/ JOGL] 1.0, 1.1.1 or JSR-231 1.0.0  (recommend JSR-231)&lt;br /&gt;
** version 1.0 [[http://ef-site.hgc.jp/eF-site/jV/JOGL1.0_win32.zip Windows],[http://ef-site.hgc.jp/eF-site/jV/JOGL1.0_macosx.tar.gz Mac OS X],[http://ef-site.hgc.jp/eF-site/jV/JOGL1.0_linux.tar.gz Linux]]
** version 1.1.1 [[http://ef-site.hgc.jp/eF-site/jV/JOGL1.1.1_win32.zip Windows],[http://ef-site.hgc.jp/eF-site/jV/JOGL1.1.1_macosx.tar.gz Mac OS X], [http://ef-site.hgc.jp/eF-site/jV/JOGL1.1.1_linux.tar.gz Linux]]
** JSR-231 1.0.0 [[http://ef-site.hgc.jp/eF-site/jV/JOGL_JSR231_win32.zip Windows], [http://ef-site.hgc.jp/eF-site/jV/JOGL_JSR231_macosx_ppc.tar.gz Mac OS X ppc], [http://ef-site.hgc.jp/eF-site/jV/JOGL_JSR231_macosx_universal.tar.gz Mac OS X universal], [http://ef-site.hgc.jp/eF-site/jV/JOGL_JSR231_linux_i586.tar.gz Linux]]

&lt;font size="1"&gt;Note: &amp;nbsp; JOGL 1.0 and 1.1.1 are not available for Intel Mac.The latest version of JOGL, JSR-231 1.0.0, runs on Intel Mac.&lt;/font&gt;</text>
    <sha1>5753068cda2a4ac8197836ae10626f51c17805c0</sha1>
  </revision>
  <revision>
    <id>236</id>
    <parentid>235</parentid>
    <timestamp>2009-03-09T10:35:57Z</timestamp>
    <contributor>
      <username>JVuser</username>
      <id>2</id>
    </contributor>
    <comment>/* System requirements */</comment>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="3745" xml:space="preserve">&lt;big&gt;'''Welcome to jV wiki.'''&lt;/big&gt;
jV version3 (formerly known as PDBjViewer) is a program to display molecular graphics of protein and nucleic acids. 
jV can use as a stand-alone program and can operate on a web browser as an Java applet. jV is used by PDBj services([http://ef-site.hgc.jp/eF-site/index.jsp eF-site], [http://ef-site.hgc.jp/eF-seek/index.jsp eF-seek], the molecular structure surface database of the protein functional part).

jV supports the following features:
* jV can read and display PDBML files, the canonical XML format for the Protein Data Bank.
* Of course, jV can read and display the traditional PDB format files, too.
* RasMol-like usability.
* jV can process more than one molecules.
* jV can display polygons specified by XML. ([http://ef-site.hgc.jp/eF-site/schema/polygon12.xsd XML Schema for polygons] is available.)
* Multiple polygons can be processed simultaneously, and be superimposed onto molecular images.
* Animation can be realized.
* The graphics of jV is based on OpenGL [https://jogl.dev.java.net/ JOGL]), thereby producing fairly beautiful pictures.
* jV runs on the Java Runtime Environment ([http://java.sun.com/javase/index.jsp JRE]) so that it can work as a stand-alone application as well as an applet.

The program 'jV' has been developed by [http://www.hgc.jp/~kinosita/TOP.html Kengo Kinoshita] ([http://www.hgc.jp/english/ Human Genome Center], [http://www.ims.u-tokyo.ac.jp/imsut/en/ Insutitute for Medical Science],[http://www.u-tokyo.ac.jp/index_e.html University of Tokyo]) and [http://www.protein.osaka-u.ac.jp/rcsfp/pi/ Haruki Nakamura] ([http://www.protein.osaka-u.ac.jp/index_e.php Institute for Protein Research], [http://www.osaka-u.ac.jp/eng/index.html Osaka Univeristy]), with the support from [http://www-bird.jst.go.jp/index_e.html JST-BIRD].

;How to use jV3
[[jV version 3]] has indicated more detailed explanation and how to use.&lt;br /&gt;
;jV3 install
[[Installation of jV3]] is a procedure installed in a local machine.&lt;br /&gt;

&lt;font size="1"&gt;The [[old version]](jV version1 &amp; jV version2) has not carried out use recommendation.&lt;/font&gt;

&lt;gallery&gt;
File:Spacefill.jpg
File:Cartoon.jpg
File:Surface.jpg
File:edmap.jpg
&lt;/gallery&gt;

== System requirements ==
[[File:Download.png|right|link=http://ef-site.hgc.jp/eF-site/servlet/DownloadViewerBinary|Download]] jV version 3 is now used to display molecules and their surfaces as a Java applet program.&lt;br /&gt;&lt;font size="1"&gt;Version 3.6 was released on 11, Aug, 2008.&lt;br /&gt;This version is fully compativle with [https://applet-launcher.dev.java.net/ applet-launcher].&lt;/font&gt;&lt;br /&gt;Go to [[Installation of jV3]].
&lt;br /&gt;
It requires the following softwares.
* [http://java.sun.com/j2se/1.4.2/download.html JRE] 1.4.2 or later  (recommend 1.4.2_12)
* [https://jogl.dev.java.net/ JOGL] 1.0, 1.1.1 or JSR-231 1.0.0  (recommend JSR-231)&lt;br /&gt;
** version 1.0 [[http://ef-site.hgc.jp/eF-site/jV/JOGL1.0_win32.zip Windows],[http://ef-site.hgc.jp/eF-site/jV/JOGL1.0_macosx.tar.gz Mac OS X],[http://ef-site.hgc.jp/eF-site/jV/JOGL1.0_linux.tar.gz Linux]]
** version 1.1.1 [[http://ef-site.hgc.jp/eF-site/jV/JOGL1.1.1_win32.zip Windows],[http://ef-site.hgc.jp/eF-site/jV/JOGL1.1.1_macosx.tar.gz Mac OS X], [http://ef-site.hgc.jp/eF-site/jV/JOGL1.1.1_linux.tar.gz Linux]]
** JSR-231 1.0.0 [[http://ef-site.hgc.jp/eF-site/jV/JOGL_JSR231_win32.zip Windows], [http://ef-site.hgc.jp/eF-site/jV/JOGL_JSR231_macosx_ppc.tar.gz Mac OS X ppc], [http://ef-site.hgc.jp/eF-site/jV/JOGL_JSR231_macosx_universal.tar.gz Mac OS X universal], [http://ef-site.hgc.jp/eF-site/jV/JOGL_JSR231_linux_i586.tar.gz Linux]]

&lt;font size="1"&gt;Note: &amp;nbsp; JOGL 1.0 and 1.1.1 are not available for Intel Mac.The latest version of JOGL, JSR-231 1.0.0, runs on Intel Mac.&lt;/font&gt;</text>
    <sha1>7227a2442c6b067fb0942a9ee4c8dba4e980cffb</sha1>
  </revision>
  <revision>
    <id>241</id>
    <parentid>236</parentid>
    <timestamp>2009-03-09T11:14:23Z</timestamp>
    <contributor>
      <username>JVuser</username>
      <id>2</id>
    </contributor>
    <comment>/* System requirements */</comment>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="3753" xml:space="preserve">&lt;big&gt;'''Welcome to jV wiki.'''&lt;/big&gt;
jV version3 (formerly known as PDBjViewer) is a program to display molecular graphics of protein and nucleic acids. 
jV can use as a stand-alone program and can operate on a web browser as an Java applet. jV is used by PDBj services([http://ef-site.hgc.jp/eF-site/index.jsp eF-site], [http://ef-site.hgc.jp/eF-seek/index.jsp eF-seek], the molecular structure surface database of the protein functional part).

jV supports the following features:
* jV can read and display PDBML files, the canonical XML format for the Protein Data Bank.
* Of course, jV can read and display the traditional PDB format files, too.
* RasMol-like usability.
* jV can process more than one molecules.
* jV can display polygons specified by XML. ([http://ef-site.hgc.jp/eF-site/schema/polygon12.xsd XML Schema for polygons] is available.)
* Multiple polygons can be processed simultaneously, and be superimposed onto molecular images.
* Animation can be realized.
* The graphics of jV is based on OpenGL [https://jogl.dev.java.net/ JOGL]), thereby producing fairly beautiful pictures.
* jV runs on the Java Runtime Environment ([http://java.sun.com/javase/index.jsp JRE]) so that it can work as a stand-alone application as well as an applet.

The program 'jV' has been developed by [http://www.hgc.jp/~kinosita/TOP.html Kengo Kinoshita] ([http://www.hgc.jp/english/ Human Genome Center], [http://www.ims.u-tokyo.ac.jp/imsut/en/ Insutitute for Medical Science],[http://www.u-tokyo.ac.jp/index_e.html University of Tokyo]) and [http://www.protein.osaka-u.ac.jp/rcsfp/pi/ Haruki Nakamura] ([http://www.protein.osaka-u.ac.jp/index_e.php Institute for Protein Research], [http://www.osaka-u.ac.jp/eng/index.html Osaka Univeristy]), with the support from [http://www-bird.jst.go.jp/index_e.html JST-BIRD].

;How to use jV3
[[jV version 3]] has indicated more detailed explanation and how to use.&lt;br /&gt;
;jV3 install
[[Installation of jV3]] is a procedure installed in a local machine.&lt;br /&gt;

&lt;font size="1"&gt;The [[old version]](jV version1 &amp; jV version2) has not carried out use recommendation.&lt;/font&gt;

&lt;gallery&gt;
File:Spacefill.jpg
File:Cartoon.jpg
File:Surface.jpg
File:edmap.jpg
&lt;/gallery&gt;

== System requirements ==
[[File:Download.png|right|link=http://ef-site.hgc.jp/eF-site/servlet/DownloadViewerBinary|Download]] jV version 3 is now used to display molecules and their surfaces as a Java applet program.&lt;br /&gt;&lt;font size="1"&gt;Version 3.6 was released on 11, Aug, 2008.&lt;br /&gt;This version is fully compativle with [https://applet-launcher.dev.java.net/ applet-launcher].&lt;/font&gt;&lt;br /&gt;More details  [[Installation of jV3]].
&lt;br /&gt;
It requires the following softwares.
* [http://java.sun.com/j2se/1.4.2/download.html JRE] 1.4.2 or later  (recommend 1.4.2_12)
* [https://jogl.dev.java.net/ JOGL] 1.0, 1.1.1 or JSR-231 1.0.0  (recommend JSR-231)&lt;br /&gt;
** version 1.0 [[http://ef-site.hgc.jp/eF-site/jV/JOGL1.0_win32.zip Windows],[http://ef-site.hgc.jp/eF-site/jV/JOGL1.0_macosx.tar.gz Mac OS X],[http://ef-site.hgc.jp/eF-site/jV/JOGL1.0_linux.tar.gz Linux]]
** version 1.1.1 [[http://ef-site.hgc.jp/eF-site/jV/JOGL1.1.1_win32.zip Windows],[http://ef-site.hgc.jp/eF-site/jV/JOGL1.1.1_macosx.tar.gz Mac OS X], [http://ef-site.hgc.jp/eF-site/jV/JOGL1.1.1_linux.tar.gz Linux]]
** JSR-231 1.0.0 [[http://ef-site.hgc.jp/eF-site/jV/JOGL_JSR231_win32.zip Windows], [http://ef-site.hgc.jp/eF-site/jV/JOGL_JSR231_macosx_ppc.tar.gz Mac OS X ppc], [http://ef-site.hgc.jp/eF-site/jV/JOGL_JSR231_macosx_universal.tar.gz Mac OS X universal], [http://ef-site.hgc.jp/eF-site/jV/JOGL_JSR231_linux_i586.tar.gz Linux]]

&lt;font size="1"&gt;Note: &amp;nbsp; JOGL 1.0 and 1.1.1 are not available for Intel Mac.The latest version of JOGL, JSR-231 1.0.0, runs on Intel Mac.&lt;/font&gt;</text>
    <sha1>ed8b0d27a96c1d546725c1cc439726a229e23e2f</sha1>
  </revision>
  <revision>
    <id>245</id>
    <parentid>241</parentid>
    <timestamp>2009-03-09T11:27:24Z</timestamp>
    <contributor>
      <username>JVuser</username>
      <id>2</id>
    </contributor>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="3752" xml:space="preserve">&lt;big&gt;'''Welcome to jV wiki.'''&lt;/big&gt;
jV version3 (formerly known as PDBjViewer) is a program to display molecular graphics of protein and nucleic acids. 
jV can use as a stand-alone program and can operate on a web browser as an Java applet. jV is used by PDBj services([http://ef-site.hgc.jp/eF-site/index.jsp eF-site], [http://ef-site.hgc.jp/eF-seek/index.jsp eF-seek], the molecular structure surface database of the protein functional part).

jV supports the following features:
* jV can read and display PDBML files, the canonical XML format for the Protein Data Bank.
* Of course, jV can read and display the traditional PDB format files, too.
* RasMol-like usability.
* jV can process more than one molecules.
* jV can display polygons specified by XML. ([http://ef-site.hgc.jp/eF-site/schema/polygon12.xsd XML Schema for polygons] is available.)
* Multiple polygons can be processed simultaneously, and be superimposed onto molecular images.
* Animation can be realized.
* The graphics of jV is based on OpenGL [https://jogl.dev.java.net/ JOGL]), thereby producing fairly beautiful pictures.
* jV runs on the Java Runtime Environment ([http://java.sun.com/javase/index.jsp JRE]) so that it can work as a stand-alone application as well as an applet.

The program 'jV' has been developed by [http://www.hgc.jp/~kinosita/TOP.html Kengo Kinoshita] ([http://www.hgc.jp/english/ Human Genome Center], [http://www.ims.u-tokyo.ac.jp/imsut/en/ Insutitute for Medical Science],[http://www.u-tokyo.ac.jp/index_e.html University of Tokyo]) and [http://www.protein.osaka-u.ac.jp/rcsfp/pi/ Haruki Nakamura] ([http://www.protein.osaka-u.ac.jp/index_e.php Institute for Protein Research], [http://www.osaka-u.ac.jp/eng/index.html Osaka Univeristy]), with the support from [http://www-bird.jst.go.jp/index_e.html JST-BIRD].

;How to use jV3
[[jV version 3]] has indicated more detailed explanation and how to use.&lt;br /&gt;
;jV3 install
[[Installaion of jV3]] is a procedure installed in a local machine.&lt;br /&gt;

&lt;font size="1"&gt;The [[old version]](jV version1 &amp; jV version2) has not carried out use recommendation.&lt;/font&gt;

&lt;gallery&gt;
File:Spacefill.jpg
File:Cartoon.jpg
File:Surface.jpg
File:edmap.jpg
&lt;/gallery&gt;

== System requirements ==
[[File:Download.png|right|link=http://ef-site.hgc.jp/eF-site/servlet/DownloadViewerBinary|Download]] jV version 3 is now used to display molecules and their surfaces as a Java applet program.&lt;br /&gt;&lt;font size="1"&gt;Version 3.6 was released on 11, Aug, 2008.&lt;br /&gt;This version is fully compativle with [https://applet-launcher.dev.java.net/ applet-launcher].&lt;/font&gt;&lt;br /&gt;More details  [[Installation of jV3]].
&lt;br /&gt;
It requires the following softwares.
* [http://java.sun.com/j2se/1.4.2/download.html JRE] 1.4.2 or later  (recommend 1.4.2_12)
* [https://jogl.dev.java.net/ JOGL] 1.0, 1.1.1 or JSR-231 1.0.0  (recommend JSR-231)&lt;br /&gt;
** version 1.0 [[http://ef-site.hgc.jp/eF-site/jV/JOGL1.0_win32.zip Windows],[http://ef-site.hgc.jp/eF-site/jV/JOGL1.0_macosx.tar.gz Mac OS X],[http://ef-site.hgc.jp/eF-site/jV/JOGL1.0_linux.tar.gz Linux]]
** version 1.1.1 [[http://ef-site.hgc.jp/eF-site/jV/JOGL1.1.1_win32.zip Windows],[http://ef-site.hgc.jp/eF-site/jV/JOGL1.1.1_macosx.tar.gz Mac OS X], [http://ef-site.hgc.jp/eF-site/jV/JOGL1.1.1_linux.tar.gz Linux]]
** JSR-231 1.0.0 [[http://ef-site.hgc.jp/eF-site/jV/JOGL_JSR231_win32.zip Windows], [http://ef-site.hgc.jp/eF-site/jV/JOGL_JSR231_macosx_ppc.tar.gz Mac OS X ppc], [http://ef-site.hgc.jp/eF-site/jV/JOGL_JSR231_macosx_universal.tar.gz Mac OS X universal], [http://ef-site.hgc.jp/eF-site/jV/JOGL_JSR231_linux_i586.tar.gz Linux]]

&lt;font size="1"&gt;Note: &amp;nbsp; JOGL 1.0 and 1.1.1 are not available for Intel Mac.The latest version of JOGL, JSR-231 1.0.0, runs on Intel Mac.&lt;/font&gt;</text>
    <sha1>7f62a1a9e1c3d994a5a3b714a73be25cdd0b8832</sha1>
  </revision>
  <revision>
    <id>247</id>
    <parentid>245</parentid>
    <timestamp>2009-03-09T11:28:45Z</timestamp>
    <contributor>
      <username>JVuser</username>
      <id>2</id>
    </contributor>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="3753" xml:space="preserve">&lt;big&gt;'''Welcome to jV wiki.'''&lt;/big&gt;
jV version3 (formerly known as PDBjViewer) is a program to display molecular graphics of protein and nucleic acids. 
jV can use as a stand-alone program and can operate on a web browser as an Java applet. jV is used by PDBj services([http://ef-site.hgc.jp/eF-site/index.jsp eF-site], [http://ef-site.hgc.jp/eF-seek/index.jsp eF-seek], the molecular structure surface database of the protein functional part).

jV supports the following features:
* jV can read and display PDBML files, the canonical XML format for the Protein Data Bank.
* Of course, jV can read and display the traditional PDB format files, too.
* RasMol-like usability.
* jV can process more than one molecules.
* jV can display polygons specified by XML. ([http://ef-site.hgc.jp/eF-site/schema/polygon12.xsd XML Schema for polygons] is available.)
* Multiple polygons can be processed simultaneously, and be superimposed onto molecular images.
* Animation can be realized.
* The graphics of jV is based on OpenGL [https://jogl.dev.java.net/ JOGL]), thereby producing fairly beautiful pictures.
* jV runs on the Java Runtime Environment ([http://java.sun.com/javase/index.jsp JRE]) so that it can work as a stand-alone application as well as an applet.

The program 'jV' has been developed by [http://www.hgc.jp/~kinosita/TOP.html Kengo Kinoshita] ([http://www.hgc.jp/english/ Human Genome Center], [http://www.ims.u-tokyo.ac.jp/imsut/en/ Insutitute for Medical Science],[http://www.u-tokyo.ac.jp/index_e.html University of Tokyo]) and [http://www.protein.osaka-u.ac.jp/rcsfp/pi/ Haruki Nakamura] ([http://www.protein.osaka-u.ac.jp/index_e.php Institute for Protein Research], [http://www.osaka-u.ac.jp/eng/index.html Osaka Univeristy]), with the support from [http://www-bird.jst.go.jp/index_e.html JST-BIRD].

;How to use jV3
[[jV version 3]] has indicated more detailed explanation and how to use.&lt;br /&gt;
;jV3 install
[[Installation of jV3]] is a procedure installed in a local machine.&lt;br /&gt;

&lt;font size="1"&gt;The [[old version]](jV version1 &amp; jV version2) has not carried out use recommendation.&lt;/font&gt;

&lt;gallery&gt;
File:Spacefill.jpg
File:Cartoon.jpg
File:Surface.jpg
File:edmap.jpg
&lt;/gallery&gt;

== System requirements ==
[[File:Download.png|right|link=http://ef-site.hgc.jp/eF-site/servlet/DownloadViewerBinary|Download]] jV version 3 is now used to display molecules and their surfaces as a Java applet program.&lt;br /&gt;&lt;font size="1"&gt;Version 3.6 was released on 11, Aug, 2008.&lt;br /&gt;This version is fully compativle with [https://applet-launcher.dev.java.net/ applet-launcher].&lt;/font&gt;&lt;br /&gt;More details  [[Installation of jV3]].
&lt;br /&gt;
It requires the following softwares.
* [http://java.sun.com/j2se/1.4.2/download.html JRE] 1.4.2 or later  (recommend 1.4.2_12)
* [https://jogl.dev.java.net/ JOGL] 1.0, 1.1.1 or JSR-231 1.0.0  (recommend JSR-231)&lt;br /&gt;
** version 1.0 [[http://ef-site.hgc.jp/eF-site/jV/JOGL1.0_win32.zip Windows],[http://ef-site.hgc.jp/eF-site/jV/JOGL1.0_macosx.tar.gz Mac OS X],[http://ef-site.hgc.jp/eF-site/jV/JOGL1.0_linux.tar.gz Linux]]
** version 1.1.1 [[http://ef-site.hgc.jp/eF-site/jV/JOGL1.1.1_win32.zip Windows],[http://ef-site.hgc.jp/eF-site/jV/JOGL1.1.1_macosx.tar.gz Mac OS X], [http://ef-site.hgc.jp/eF-site/jV/JOGL1.1.1_linux.tar.gz Linux]]
** JSR-231 1.0.0 [[http://ef-site.hgc.jp/eF-site/jV/JOGL_JSR231_win32.zip Windows], [http://ef-site.hgc.jp/eF-site/jV/JOGL_JSR231_macosx_ppc.tar.gz Mac OS X ppc], [http://ef-site.hgc.jp/eF-site/jV/JOGL_JSR231_macosx_universal.tar.gz Mac OS X universal], [http://ef-site.hgc.jp/eF-site/jV/JOGL_JSR231_linux_i586.tar.gz Linux]]

&lt;font size="1"&gt;Note: &amp;nbsp; JOGL 1.0 and 1.1.1 are not available for Intel Mac.The latest version of JOGL, JSR-231 1.0.0, runs on Intel Mac.&lt;/font&gt;</text>
    <sha1>ed8b0d27a96c1d546725c1cc439726a229e23e2f</sha1>
  </revision>
</page>
<page arvcontinue="20090309093027|201">
  <title>How to use</title>
  <ns>0</ns>
  <id>11</id>
  <revision>
    <id>237</id>
    <parentid>181</parentid>
    <timestamp>2009-03-09T10:38:36Z</timestamp>
    <contributor>
      <username>JVuser</username>
      <id>2</id>
    </contributor>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="2999" xml:space="preserve">jV is an interactive 3D viewer program to visualize protein and nucleic acid molecules. The program reads in a PDBML file that is an XML format for PDB. Usual PDB format files are also accepted. More than one molecule files can be opened and displayed at the same time and their display models and transforms can be operated separately. In addition to molecule files, a polygon file written in XML can be read and displayed. More than one polygon files can be opened at the same time and superposed on molecule images. The [http://ef-site.hgc.jp/eF-site/schema/polygon12.xsd XML schema] of the polygon file is available. jV can perform an animation of molecules. The animation file is a PDB format file in which each frame is separated by a MODEL line.

jV runs on Java Runtime Environment ([http://java.sun.com/j2se/1.4.2/download.html JRE]) and can be used both as a standalone program and an applet. The 3D rendering is performed with the use of [https://jogl.dev.java.net/ JOGL] API. The version requirements are as follows.

* JRE (includes Java Plug-in) 1.4.2 or later
* JOGL 1.1.1 or JSR-231

Here, [http://java.sun.com/products/plugin/ Java Plug-in] is required in order to use the program as an applet.

The program allows an interactive mouse control and command execution. The commnad syntax follows that of [http://www.rasmol.org/ Rasmol] with some modifications. In order to handle the transform of each molecule and polygon separately, every files are set to be either selected or not selected. The transform operation commands, such as rotate or translate, act only on selected files. On the other hand, every atoms in a molecule are also set to be either selected or not selected independently of whether the molecule itself is selected or not selected. Only selected atoms are the target of display model operations, such as wireframe or spacefill commands, and coloring operations.

[[Release note]]
== How to use ==
The following table shows hot to do the minimum things with jV.&lt;br /&gt;
{| class="wikitable" border="1" style="margin:0 auto" 
 ! Action !! Window, Linux !! Mac OS X 
 |-
 ! style="text-align:left" | rotate around X,Y axes
 | left drag || mouse drag
 |-
 ! style="text-align:left" | rotate around Z axis
 | Shift + right drag || Shift + command + drag
 |-
 ! style="text-align:left" | translate along X,Y axes
 | right drag || command + drag
 |-
 ! style="text-align:left" | translate along Z axis (zoom in/out)
 | Shift + left drag || Shift + drag
 |}
For the detail,&lt;br /&gt;

; The install manual 
* [[Installaion of jV3]]
; The reference manual
* User's Guide &amp;nbsp;[[Media:JV3_User'sGuide.pdf|pdf(30 October 2006)]]
# [[Tutorials]]
# [[GUI]]
# [[Document type of the polygon file]]
# [[Functional site information for molecules]]
* Manual &amp;nbsp;[[Media:JV_manual.pdf|pdf(30 Octover 2006)]]
# [[Command List]]
# [[Atom Expression]]
# [[Vertex Expression]]
# [[Color Expression]]
# [[Use as Applet]]

;Some examples
# [[Animation]]
# [[User jV with applet launcher]]</text>
    <sha1>845700b9958d1a42da3365cd072a7cacd1973739</sha1>
  </revision>
  <revision>
    <id>248</id>
    <parentid>237</parentid>
    <timestamp>2009-03-09T11:29:06Z</timestamp>
    <contributor>
      <username>JVuser</username>
      <id>2</id>
    </contributor>
    <comment>/* How to use */</comment>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="3000" xml:space="preserve">jV is an interactive 3D viewer program to visualize protein and nucleic acid molecules. The program reads in a PDBML file that is an XML format for PDB. Usual PDB format files are also accepted. More than one molecule files can be opened and displayed at the same time and their display models and transforms can be operated separately. In addition to molecule files, a polygon file written in XML can be read and displayed. More than one polygon files can be opened at the same time and superposed on molecule images. The [http://ef-site.hgc.jp/eF-site/schema/polygon12.xsd XML schema] of the polygon file is available. jV can perform an animation of molecules. The animation file is a PDB format file in which each frame is separated by a MODEL line.

jV runs on Java Runtime Environment ([http://java.sun.com/j2se/1.4.2/download.html JRE]) and can be used both as a standalone program and an applet. The 3D rendering is performed with the use of [https://jogl.dev.java.net/ JOGL] API. The version requirements are as follows.

* JRE (includes Java Plug-in) 1.4.2 or later
* JOGL 1.1.1 or JSR-231

Here, [http://java.sun.com/products/plugin/ Java Plug-in] is required in order to use the program as an applet.

The program allows an interactive mouse control and command execution. The commnad syntax follows that of [http://www.rasmol.org/ Rasmol] with some modifications. In order to handle the transform of each molecule and polygon separately, every files are set to be either selected or not selected. The transform operation commands, such as rotate or translate, act only on selected files. On the other hand, every atoms in a molecule are also set to be either selected or not selected independently of whether the molecule itself is selected or not selected. Only selected atoms are the target of display model operations, such as wireframe or spacefill commands, and coloring operations.

[[Release note]]
== How to use ==
The following table shows hot to do the minimum things with jV.&lt;br /&gt;
{| class="wikitable" border="1" style="margin:0 auto" 
 ! Action !! Window, Linux !! Mac OS X 
 |-
 ! style="text-align:left" | rotate around X,Y axes
 | left drag || mouse drag
 |-
 ! style="text-align:left" | rotate around Z axis
 | Shift + right drag || Shift + command + drag
 |-
 ! style="text-align:left" | translate along X,Y axes
 | right drag || command + drag
 |-
 ! style="text-align:left" | translate along Z axis (zoom in/out)
 | Shift + left drag || Shift + drag
 |}
For the detail,&lt;br /&gt;

; The install manual 
* [[Installation of jV3]]
; The reference manual
* User's Guide &amp;nbsp;[[Media:JV3_User'sGuide.pdf|pdf(30 October 2006)]]
# [[Tutorials]]
# [[GUI]]
# [[Document type of the polygon file]]
# [[Functional site information for molecules]]
* Manual &amp;nbsp;[[Media:JV_manual.pdf|pdf(30 Octover 2006)]]
# [[Command List]]
# [[Atom Expression]]
# [[Vertex Expression]]
# [[Color Expression]]
# [[Use as Applet]]

;Some examples
# [[Animation]]
# [[User jV with applet launcher]]</text>
    <sha1>4c694a08a97fa79700e4758b36eb53e40d09b045</sha1>
  </revision>
</page>
<page arvcontinue="20090309093027|201">
  <title>Document type of the polygon file</title>
  <ns>0</ns>
  <id>35</id>
  <revision>
    <id>238</id>
    <timestamp>2009-03-09T10:40:59Z</timestamp>
    <contributor>
      <username>JVuser</username>
      <id>2</id>
    </contributor>
    <comment>Created page with 'The contents of a polygon file are organized as follows.   &lt;?xml version="1.0"?&gt;  &amp;nbsp;  &lt;polygon&gt;   &lt;vertices count="100" id_numbers=”use”&gt;            ←impossible to omit...'</comment>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="5002" xml:space="preserve">The contents of a polygon file are organized as follows.

 &lt;?xml version="1.0"?&gt;
 &amp;nbsp;
 &lt;polygon&gt;
  &lt;vertices count="100" id_numbers=”use”&gt;            ←impossible to omit
    &lt;vertex id="1" image="x y z nx ny nz R G B"/&gt;
    &lt;vertex id="2" image="x y z nx ny nz R G B"/&gt;
    ・・・
  &lt;/vertices&gt;
 &amp;nbsp;
  &lt;point_array count="2" size=”3”&gt;                   ←possible to omit
    &lt;point id="1" vertex="v1"/&gt;
    &lt;point id="2" vertex="v1"/&gt;
  &lt;/point_array&gt;
 &amp;nbsp;
  &lt;line_array count="2" width=”2”&gt;                   ←possible to omit
    &lt;line id="1" vertex="v1 v2"/&gt;
    &lt;line id="2" vertex="v1 v2"/&gt;
  &lt;/line_array&gt;
 &amp;nbsp;
  &lt;triangle_array count="2" transparency=”0.5”&gt;      ←possible to omit
    &lt;triangle id="1" vertex="v1 v2 v3"/&gt;
    &lt;triangle id="2" vertex="v1 v2 v3"/&gt;
  &lt;/triangle_array&gt;
 &amp;nbsp;
  &lt;quad_array count="2"&gt;                               ←possible to omit
    &lt;quad id="1" vertex="v1 v2 v3 v4"/&gt;
    &lt;quad id="2" vertex="v1 v2 v3 v4"/&gt;
  &lt;/quad_array&gt;
 &amp;nbsp;
  &lt;polyline_array count="2" width=”1”&gt;               ←possible to omit
    &lt;polyline id="1" vertex="v1 v2 v3 v4 v5 ・・・"/&gt;
    &lt;polyline id="2" vertex="v1 v2 v3 v4 v5 ・・・"/&gt;
  &lt;/quad_array&gt;
 &amp;nbsp;
&lt;/polygon&gt;

The ‘vertices’ element contains the sequence of vertices and the number of vertices is specified by the ‘count’ attribute. If the value of the ‘id_numbers’ attribute is ‘ignore’, the vertex id is automatically numbered starting from 1. If the ‘id_numbers’ attribute is set to be ‘use’, users can assign arbitrary numbers to each vertex id. In the ‘vertex’ element, x, y and z represent the x, y and z coordinates of the vertex, respectively, and nx, ny and nz represent the x, y and z components of the normal vector at the vertex, respectively. They are assigned real numbers. The color of each vertex is defined according to the RGB color scheme; R, G and B take the real numbers from 0 to 255. The ‘point_array’, ‘line_array’, ‘traiangle_array’, ‘quad_array’ and ‘polyline_array’ elements contain the sequence of polygons such as dots, lines, triangles, quadrangles and polylines, respectively. They can be omitted. The v1, v2, v3, v4 and v5 describe id of the vertices constructing the polygon. For these elements, the ‘transparency’ attribute that is omissible can be used to set the transparency of the image. To specify the size of dots and the width of lines, the ‘point_array’ element has the omissible ‘size’ attribute and ‘line_array’ and ‘polyline_array’ elements have the omissible ‘width’ attribute, respectively. The XML schema file that describes the type definitions and element declarations is published at http://ef-site.hgc.jp/eF-site/schema/polygon12.xsd. A simple example of a polygon is shown below. It represents a colored cube. The file is published at http://ef-site.hgc.jp/eF-site/jV/cube.xml. Before you open this polygon, you should close all files currently loaded to the application to get an appropriate viewpoint for the cube. To do this, you can use [File] – [Close] menu, or execute ‘zap’ in the command line.

 &lt;?xml version="1.0"?&gt;
 &amp;nbsp;
  &lt;polygon&gt;
   &lt;vertices count="24" id_numbers="use"&gt;
    &lt;vertex id="1"  image=" 1  1  1  0  0  1 255   0   0"/&gt;
    &lt;vertex id="2"  image="-1  1  1  0  0  1 255   0   0"/&gt;
    &lt;vertex id="3"  image="-1 -1  1  0  0  1 255   0   0"/&gt;
    &lt;vertex id="4"  image=" 1 -1  1  0  0  1 255   0   0"/&gt;
    &lt;vertex id="5"  image="-1  1 -1  0  0 -1   0 255 255"/&gt;
    &lt;vertex id="6"  image=" 1  1 -1  0  0 -1   0 255 255"/&gt;
    &lt;vertex id="7"  image=" 1 -1 -1  0  0 -1   0 255 255"/&gt;
    &lt;vertex id="8"  image="-1 -1 -1  0  0 -1   0 255 255"/&gt;
    &lt;vertex id="9"  image=" 1  1  1  1  0  0   0 255   0"/&gt;
    &lt;vertex id="10" image=" 1 -1  1  1  0  0   0 255   0"/&gt;
    &lt;vertex id="11" image=" 1 -1 -1  1  0  0   0 255   0"/&gt;
    &lt;vertex id="12" image=" 1  1 -1  1  0  0   0 255   0"/&gt;
    &lt;vertex id="13" image="-1  1 -1 -1  0  0 255   0 255"/&gt;
    &lt;vertex id="14" image="-1 -1 -1 -1  0  0 255   0 255"/&gt;
    &lt;vertex id="15" image="-1 -1  1 -1  0  0 255   0 255"/&gt;
    &lt;vertex id="16" image="-1  1  1 -1  0  0 255   0 255"/&gt;
    &lt;vertex id="17" image=" 1  1  1  0  1  0   0   0 255"/&gt;
    &lt;vertex id="18" image=" 1  1 -1  0  1  0   0   0 255"/&gt;
    &lt;vertex id="19" image="-1  1 -1  0  1  0   0   0 255"/&gt;
    &lt;vertex id="20" image="-1  1  1  0  1  0   0   0 255"/&gt;
    &lt;vertex id="21" image=" 1 -1 -1  0 -1  0 255 255   0"/&gt;
    &lt;vertex id="22" image=" 1 -1  1  0 -1  0 255 255   0"/&gt;
    &lt;vertex id="23" image="-1 -1  1  0 -1  0 255 255   0"/&gt;
    &lt;vertex id="24" image="-1 -1 -1  0 -1  0 255 255   0"/&gt;
   &lt;/vertices&gt;
   &lt;quad_array count="6"&gt;
    &lt;quad id="1" vertex=" 1  2  3  4"/&gt;
    &lt;quad id="2" vertex=" 5  6  7  8"/&gt;
    &lt;quad id="3" vertex=" 9 10 11 12"/&gt;
    &lt;quad id="4" vertex="13 14 15 16"/&gt;
    &lt;quad id="5" vertex="17 18 19 20"/&gt;
    &lt;quad id="6" vertex="21 22 23 24"/&gt;
   &lt;/quad_array&gt;
  &lt;/polygon&gt;</text>
    <sha1>825fb9fec2e3505dadc429711fd8f4f526b775bf</sha1>
  </revision>
  <revision>
    <id>239</id>
    <parentid>238</parentid>
    <timestamp>2009-03-09T10:41:22Z</timestamp>
    <contributor>
      <username>JVuser</username>
      <id>2</id>
    </contributor>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="5003" xml:space="preserve">The contents of a polygon file are organized as follows.

 &lt;?xml version="1.0"?&gt;
 &amp;nbsp;
 &lt;polygon&gt;
  &lt;vertices count="100" id_numbers=”use”&gt;            ←impossible to omit
    &lt;vertex id="1" image="x y z nx ny nz R G B"/&gt;
    &lt;vertex id="2" image="x y z nx ny nz R G B"/&gt;
    ・・・
  &lt;/vertices&gt;
 &amp;nbsp;
  &lt;point_array count="2" size=”3”&gt;                   ←possible to omit
    &lt;point id="1" vertex="v1"/&gt;
    &lt;point id="2" vertex="v1"/&gt;
  &lt;/point_array&gt;
 &amp;nbsp;
  &lt;line_array count="2" width=”2”&gt;                   ←possible to omit
    &lt;line id="1" vertex="v1 v2"/&gt;
    &lt;line id="2" vertex="v1 v2"/&gt;
  &lt;/line_array&gt;
 &amp;nbsp;
  &lt;triangle_array count="2" transparency=”0.5”&gt;      ←possible to omit
    &lt;triangle id="1" vertex="v1 v2 v3"/&gt;
    &lt;triangle id="2" vertex="v1 v2 v3"/&gt;
  &lt;/triangle_array&gt;
 &amp;nbsp;
  &lt;quad_array count="2"&gt;                               ←possible to omit
    &lt;quad id="1" vertex="v1 v2 v3 v4"/&gt;
    &lt;quad id="2" vertex="v1 v2 v3 v4"/&gt;
  &lt;/quad_array&gt;
 &amp;nbsp;
  &lt;polyline_array count="2" width=”1”&gt;               ←possible to omit
    &lt;polyline id="1" vertex="v1 v2 v3 v4 v5 ・・・"/&gt;
    &lt;polyline id="2" vertex="v1 v2 v3 v4 v5 ・・・"/&gt;
  &lt;/quad_array&gt;
 &amp;nbsp;
 &lt;/polygon&gt;

The ‘vertices’ element contains the sequence of vertices and the number of vertices is specified by the ‘count’ attribute. If the value of the ‘id_numbers’ attribute is ‘ignore’, the vertex id is automatically numbered starting from 1. If the ‘id_numbers’ attribute is set to be ‘use’, users can assign arbitrary numbers to each vertex id. In the ‘vertex’ element, x, y and z represent the x, y and z coordinates of the vertex, respectively, and nx, ny and nz represent the x, y and z components of the normal vector at the vertex, respectively. They are assigned real numbers. The color of each vertex is defined according to the RGB color scheme; R, G and B take the real numbers from 0 to 255. The ‘point_array’, ‘line_array’, ‘traiangle_array’, ‘quad_array’ and ‘polyline_array’ elements contain the sequence of polygons such as dots, lines, triangles, quadrangles and polylines, respectively. They can be omitted. The v1, v2, v3, v4 and v5 describe id of the vertices constructing the polygon. For these elements, the ‘transparency’ attribute that is omissible can be used to set the transparency of the image. To specify the size of dots and the width of lines, the ‘point_array’ element has the omissible ‘size’ attribute and ‘line_array’ and ‘polyline_array’ elements have the omissible ‘width’ attribute, respectively. The XML schema file that describes the type definitions and element declarations is published at http://ef-site.hgc.jp/eF-site/schema/polygon12.xsd. A simple example of a polygon is shown below. It represents a colored cube. The file is published at http://ef-site.hgc.jp/eF-site/jV/cube.xml. Before you open this polygon, you should close all files currently loaded to the application to get an appropriate viewpoint for the cube. To do this, you can use [File] – [Close] menu, or execute ‘zap’ in the command line.

 &lt;?xml version="1.0"?&gt;
 &amp;nbsp;
  &lt;polygon&gt;
   &lt;vertices count="24" id_numbers="use"&gt;
    &lt;vertex id="1"  image=" 1  1  1  0  0  1 255   0   0"/&gt;
    &lt;vertex id="2"  image="-1  1  1  0  0  1 255   0   0"/&gt;
    &lt;vertex id="3"  image="-1 -1  1  0  0  1 255   0   0"/&gt;
    &lt;vertex id="4"  image=" 1 -1  1  0  0  1 255   0   0"/&gt;
    &lt;vertex id="5"  image="-1  1 -1  0  0 -1   0 255 255"/&gt;
    &lt;vertex id="6"  image=" 1  1 -1  0  0 -1   0 255 255"/&gt;
    &lt;vertex id="7"  image=" 1 -1 -1  0  0 -1   0 255 255"/&gt;
    &lt;vertex id="8"  image="-1 -1 -1  0  0 -1   0 255 255"/&gt;
    &lt;vertex id="9"  image=" 1  1  1  1  0  0   0 255   0"/&gt;
    &lt;vertex id="10" image=" 1 -1  1  1  0  0   0 255   0"/&gt;
    &lt;vertex id="11" image=" 1 -1 -1  1  0  0   0 255   0"/&gt;
    &lt;vertex id="12" image=" 1  1 -1  1  0  0   0 255   0"/&gt;
    &lt;vertex id="13" image="-1  1 -1 -1  0  0 255   0 255"/&gt;
    &lt;vertex id="14" image="-1 -1 -1 -1  0  0 255   0 255"/&gt;
    &lt;vertex id="15" image="-1 -1  1 -1  0  0 255   0 255"/&gt;
    &lt;vertex id="16" image="-1  1  1 -1  0  0 255   0 255"/&gt;
    &lt;vertex id="17" image=" 1  1  1  0  1  0   0   0 255"/&gt;
    &lt;vertex id="18" image=" 1  1 -1  0  1  0   0   0 255"/&gt;
    &lt;vertex id="19" image="-1  1 -1  0  1  0   0   0 255"/&gt;
    &lt;vertex id="20" image="-1  1  1  0  1  0   0   0 255"/&gt;
    &lt;vertex id="21" image=" 1 -1 -1  0 -1  0 255 255   0"/&gt;
    &lt;vertex id="22" image=" 1 -1  1  0 -1  0 255 255   0"/&gt;
    &lt;vertex id="23" image="-1 -1  1  0 -1  0 255 255   0"/&gt;
    &lt;vertex id="24" image="-1 -1 -1  0 -1  0 255 255   0"/&gt;
   &lt;/vertices&gt;
   &lt;quad_array count="6"&gt;
    &lt;quad id="1" vertex=" 1  2  3  4"/&gt;
    &lt;quad id="2" vertex=" 5  6  7  8"/&gt;
    &lt;quad id="3" vertex=" 9 10 11 12"/&gt;
    &lt;quad id="4" vertex="13 14 15 16"/&gt;
    &lt;quad id="5" vertex="17 18 19 20"/&gt;
    &lt;quad id="6" vertex="21 22 23 24"/&gt;
   &lt;/quad_array&gt;
  &lt;/polygon&gt;</text>
    <sha1>1a1fd4c105801ce90106095bea74b58a23534252</sha1>
  </revision>
</page>
<page arvcontinue="20090309093027|201">
  <title>Functional site information for molecules</title>
  <ns>0</ns>
  <id>36</id>
  <revision>
    <id>240</id>
    <timestamp>2009-03-09T10:45:18Z</timestamp>
    <contributor>
      <username>JVuser</username>
      <id>2</id>
    </contributor>
    <comment>Created page with 'A simple XML file is defined in jV3 in order to describe functional sites of a molecule. If an external database server that returns this type of XML file is prepared, you can le...'</comment>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="5548" xml:space="preserve">A simple XML file is defined in jV3 in order to describe functional sites of a molecule. If an external database server that returns this type of XML file is prepared, you can let jV3 read the file through the network and obtain the functional site information. An example of the XML file is as follows.

 &lt;?xml version=”1.0” ?&gt;
 &amp;nbsp;
 &lt;site_list&gt;
  &lt;site id=”CATRES1” db=”CATRES” category=”catalytic”
        description=”a catalytic site defined by CATRES, Medline 98100076”&gt;
    &lt;region chain_id=”A” beg_seq_id=”100” end_seq_id=”100”/&gt;
    &lt;region chain_id=”A” beg_seq_id=”46” end_seq_id=”46”/&gt;
    &lt;region chain_id=”A” beg_seq_id=”116” end_seq_id=”116”/&gt;
  &lt;/site&gt;
  &lt;site id=”ASN” db=”pdb_hetatom” category=”binding”
        description=”ASPARAGINE binding site”&gt;
    &lt;region chain_id=”A” beg_seq_id=”48” end_seq_id=”48”/&gt;
    &lt;region chain_id=”A” beg_seq_id=”72” end_seq_id=”74”/&gt;
  &lt;/site&gt;
  &lt;site id=”0006529” db=”godata” category=”biological_process”
        description=”asparagine biosynthesis”&gt;
    &lt;region chain_id=”A”/&gt;
  &lt;/site&gt;
  &lt;site id=”0016874” db=”godata” category=”molecular_function”
        description=”ligase activity”&gt;
    &lt;region chain_id=”A”/&gt;
  &lt;/site&gt;
 &lt;/site_list&gt;

The XML schema file that defines the document type of the above XML file is published at http://ef-site.hgc.jp/eF-site/schema/sitelist10.xsd. When a text file ‘properties.txt’ exists in the same directory as the application jar file, jV3 reads the file as a configuration file for the application. The current configuration file, which is attached to the binary distribution, contains a set of URL necessary to connect to the xPSSS and eF-site system as follows.

 # PDBML files are retrieved from the following site.
 pdbml_noatom=ftp://www.pdbj.org/XML/alpha/all-noatom/
 pdbml_extatom=ftp://www.pdbj.org/XML/alpha/all-extatom/
 pdbml_plus=ftp://www.pdbj.org/XML/pdbmlplus/pdbml_xp/
 &amp;nbsp;
 # eF-site data are retrieved from the following site.
 efsite=http://ef-site.hgc.jp/eF-site/

If a database server that returns the functional site file is prepared, its URL should be appended to the configuration file. Because one functional site file is assumed to exist for one PDB ID, the URL written in the configuration file depends on the PDB ID. Therefore, the URL is represented with the use of substitute characters {0}, {1}, {2} and {3} that are substituted by each column of the PDB ID sequentially. An example is as follows.

 # works with my database.
 mydb=http://myhost.jp/mydb/jv3/{0}{1}{2}{3}_jv.xml

Here, the property name, ‘mydb’ in the above example, is arbitrary. Note that a PDB ID {0}{1}{2}{3} is substituted as lowercases and available protocols are http:, ftp: and file:. For simplicity, it is assumed that only one molecule file that corresponds to the above example XML file opens in the application. Then functional site information can be displayed by the ‘show’ command as follows.

 jV3&gt; show site mydb
 File 1:
  db           category
  -------------------------------
  CATRES       catalytic
  pdb_hetatom  binding
  godata       biological_process
  godata       molcular_function
 jV3&gt; show site mydb:CATRES
 File 1:
  id=CATRES1  category=catalytic  region=A:100-100,A:46-46,A:116-116
      description=a catalytic site defined by CATRES, Medline 98100076
 jV3&gt; show site mydb:pdb_hetatom:binding
 File 1:
  id=ASN  category=binding  region=A:48-48,A:72-74 
      description=ASPARAGINE binding site
 jV3&gt; show site mydb:godata
 File 1:
  id=0006529  category=biological_process  region=A
      description=asparagine biosynthesis
  id=0016874  category=molecular_function  region=A
      description=ligase activity
 jV3&gt; show site mydb:godata:molecular_function
 File 1:
  id=0016874  category=molecular_function  region=A
      description=ligase activity
 jV3&gt;

With a similar syntax, the ‘select’ command can be used to select the relevant set of atoms. To demonstrate the operations described in this section, let us add a following line to the configuration file ‘properties.txt’.

 ex=http://ef-site.hgc.jp/jv3site/servlet/Site?pdb={0}{1}{2}{3}

The above URL provides functional site information whose contents are equivalent to those of xPSSS for all PDB. To reload the configuration file, quit the application (if it runs) and restart it. Then open the molecule ‘1yec’ as an example. To do this, you can use [File] – [Open – Remote] – [PDB ID] menu item as in the section 4.2, or equivalently execute ‘load ftp 1yec’ in the command line. Subsequently, execute ‘show site ex’ and the following keywords will be listed (the contents may change in the future).

 jV3&gt; show site ex
 File 1:
  db           category
  ---------------------
  prosite      prosite
  pdb_hetatom  binding

Detail site information can be shown as follows.

 jV3&gt; show site ex:prosite
 File 1:
  id=PS00290  db=prosite  category=prosite  region=L:192-198
    description=Immunoglobulins and major histocompatibility complex proteins signature. [FY]-{L}-C-x-[VA]-{LC}-H

Atoms in the region ‘L:192-198’ can be selected with a similar syntax.

 jV3&gt; select ex:prosite
 56 Atoms Selected.

In the same way, the following atom selections are possible.

 jV3&gt; select ex:pdb_hetatom
 298 Atoms Selected.
 jV3&gt; select ex:
 354 Atoms Selected.

Here the last command selects both regions specified by ‘prosite’ and ‘pdb_hetatom’ keywords, respectively.</text>
    <sha1>3b1720e66f229cc796cc1cd611b844a57dfde274</sha1>
  </revision>
</page>
<page arvcontinue="20090309093027|201">
  <title>Installation of jV</title>
  <ns>0</ns>
  <id>38</id>
  <revision>
    <id>246</id>
    <timestamp>2009-03-09T11:28:20Z</timestamp>
    <contributor>
      <username>JVuser</username>
      <id>2</id>
    </contributor>
    <comment>Created page with '{| style="float:right"  |__TOC__  |} == System requirements == jV3 runs on the Java Runtime Environment (JRE) with JOGL API. The version requirements are as follows. * [http://ja...'</comment>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="2361" xml:space="preserve">{| style="float:right"
 |__TOC__
 |}
== System requirements ==
jV3 runs on the Java Runtime Environment (JRE) with JOGL API. The version requirements are as follows.
* [http://java.sun.com/j2se/1.4.2/download.html JRE] (includes Java Plug-in) 1.4.2 or later
* [https://jogl.dev.java.net/ JOGL] API JSR-231 1.0.0 or later 
These softwares are available on typical operation systems such as Windows (2000/XP/Vista), Mac OS X 10.3 or later, and Red Hat Linux 7.3 or later.

== Installing JOGL API ==
=== Automatic install ===
In this section, it is assumed that JRE 1.4.2 or later has been installed on your computer. Installing JOGL is just deploying several files to JRE. A tool that automatically performs the JOGL installation with a graphical user interface is available at [[jV version 3]].

=== Manual install ===
It is also possible to install JOGL manually. According to the kind of your operation system, you should get the following files from [https://jogl.dev.java.net/ JOGL].

{| class="wikitable" border="1"
 ! !! Windows !! Mac OS X !! Linux
 |-
 | JSR-231 1.1.1
 | jogl.jar&lt;br /&gt;jogl.dll&lt;br /&gt;jogl_cg.dll&lt;br /&gt;jogl_awt.dll&lt;br /&gt;gluegen-rt.jar&lt;br /&gt;gluegen-rt.dll
 | jogl.jar&lt;br /&gt;libjogl.jnilib&lt;br /&gt;libjogl_cg.jnilib&lt;br /&gt;libjogl_awt.jnilib&lt;br /&gt;gluegen-rt.jar&lt;br /&gt;libgluegen-rt.jnilib
 | jogl.jar&lt;br /&gt;libjogl.so&lt;br /&gt;libjogl_cg.so&lt;br /&gt;libjogl_awt.so&lt;br /&gt;gluegen-rt.jar&lt;br /&gt;libgluegen-rt.so
 |}

==== Windows ====
The folder that JRE has been installed is denoted by &lt;JRE&gt;. It depends on the environment, however it is typically as follows.
 &lt;JRE&gt;=C:\Program Files\Java\j2re1.4.2_12
The files ‘jogl.jar’ and ‘gluegen-rt.jar’ should be copied to &lt;JRE&gt;\lib\ext, and the other files should be copied to &lt;JRE&gt;\bin.

==== Mac OS X ====
When operating from the command terminal, you should copy all files to /Library/Java/Extensions. When operating through the graphical interface, the above destination folder is shown as ‘Macintosh HD/Library/Java/Extensions’. In this operation, the password for root is required.

==== Linux ====
The directory that JRE has been installed is denoted by &lt;JRE&gt;. It depends on the environment, however it is typically as follows.
 &lt;JRE&gt;=/usr/java/j2sdk1.4.2_12/jre
files ‘jogl.jar’ and ‘gluegen-rt.jar’ should be copied to &lt;JRE&gt;/lib/ext, and the other files should be copied to &lt;JRE&gt;/lib/i386.</text>
    <sha1>6bb8a7c460e535609385ce14f558d0c0b73075bf</sha1>
  </revision>
  <revision>
    <id>249</id>
    <parentid>246</parentid>
    <timestamp>2009-03-09T11:39:35Z</timestamp>
    <contributor>
      <username>JVuser</username>
      <id>2</id>
    </contributor>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="2533" xml:space="preserve">{| style="float:right"
 |__TOC__
 |}
== System requirements ==
jV3 runs on the Java Runtime Environment (JRE) with JOGL API. The version requirements are as follows.
* [http://java.sun.com/j2se/1.4.2/download.html JRE] (includes Java Plug-in) 1.4.2 or later
* [https://jogl.dev.java.net/ JOGL] API JSR-231 1.0.0 or later 
These softwares are available on typical operation systems such as Windows (2000/XP/Vista), Mac OS X 10.3 or later, and Red Hat Linux 7.3 or later.

== Installing JOGL API ==
=== Automatic install ===
In this section, it is assumed that JRE 1.4.2 or later has been installed on your computer. Installing JOGL is just deploying several files to JRE. A tool that automatically performs the JOGL installation with a graphical user interface is available at [[jV version 3]].

=== Manual install ===
It is also possible to install JOGL manually. According to the kind of your operation system, you should get the following files from [https://jogl.dev.java.net/ JOGL].

{| class="wikitable" border="1"
 ! !! Windows !! Mac OS X !! Linux
 |-
 | JSR-231 1.1.1
 | jogl.jar&lt;br /&gt;jogl.dll&lt;br /&gt;jogl_cg.dll&lt;br /&gt;jogl_awt.dll&lt;br /&gt;gluegen-rt.jar&lt;br /&gt;gluegen-rt.dll
 | jogl.jar&lt;br /&gt;libjogl.jnilib&lt;br /&gt;libjogl_cg.jnilib&lt;br /&gt;libjogl_awt.jnilib&lt;br /&gt;gluegen-rt.jar&lt;br /&gt;libgluegen-rt.jnilib
 | jogl.jar&lt;br /&gt;libjogl.so&lt;br /&gt;libjogl_cg.so&lt;br /&gt;libjogl_awt.so&lt;br /&gt;gluegen-rt.jar&lt;br /&gt;libgluegen-rt.so
 |}

==== Windows ====
The folder that JRE has been installed is denoted by &lt;JRE&gt;. It depends on the environment, however it is typically as follows.
 &lt;JRE&gt;=C:\Program Files\Java\j2re1.4.2_12
The files ‘jogl.jar’ and ‘gluegen-rt.jar’ should be copied to &lt;JRE&gt;\lib\ext, and the other files should be copied to &lt;JRE&gt;\bin.

==== Mac OS X ====
When operating from the command terminal, you should copy all files to /Library/Java/Extensions. When operating through the graphical interface, the above destination folder is shown as ‘Macintosh HD/Library/Java/Extensions’. In this operation, the password for root is required.

==== Linux ====
The directory that JRE has been installed is denoted by &lt;JRE&gt;. It depends on the environment, however it is typically as follows.
 &lt;JRE&gt;=/usr/java/j2sdk1.4.2_12/jre
files ‘jogl.jar’ and ‘gluegen-rt.jar’ should be copied to &lt;JRE&gt;/lib/ext, and the other files should be copied to &lt;JRE&gt;/lib/i386.

== Download jV ==
* Download jV
** [http://ef-site.hgc.jp/eF-site/servlet/DownloadViewerBinary binary]
** [http://ef-site.hgc.jp/eF-site/servlet/Registration sourcecode]}</text>
    <sha1>2bdcd6615d27648aa97669dc3eb7324893d60faa</sha1>
  </revision>
  <revision>
    <id>250</id>
    <parentid>249</parentid>
    <timestamp>2009-03-09T11:42:17Z</timestamp>
    <contributor>
      <username>JVuser</username>
      <id>2</id>
    </contributor>
    <comment>/* Download jV */</comment>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="2799" xml:space="preserve">{| style="float:right"
 |__TOC__
 |}
== System requirements ==
jV3 runs on the Java Runtime Environment (JRE) with JOGL API. The version requirements are as follows.
* [http://java.sun.com/j2se/1.4.2/download.html JRE] (includes Java Plug-in) 1.4.2 or later
* [https://jogl.dev.java.net/ JOGL] API JSR-231 1.0.0 or later 
These softwares are available on typical operation systems such as Windows (2000/XP/Vista), Mac OS X 10.3 or later, and Red Hat Linux 7.3 or later.

== Installing JOGL API ==
=== Automatic install ===
In this section, it is assumed that JRE 1.4.2 or later has been installed on your computer. Installing JOGL is just deploying several files to JRE. A tool that automatically performs the JOGL installation with a graphical user interface is available at [[jV version 3]].

=== Manual install ===
It is also possible to install JOGL manually. According to the kind of your operation system, you should get the following files from [https://jogl.dev.java.net/ JOGL].

{| class="wikitable" border="1"
 ! !! Windows !! Mac OS X !! Linux
 |-
 | JSR-231 1.1.1
 | jogl.jar&lt;br /&gt;jogl.dll&lt;br /&gt;jogl_cg.dll&lt;br /&gt;jogl_awt.dll&lt;br /&gt;gluegen-rt.jar&lt;br /&gt;gluegen-rt.dll
 | jogl.jar&lt;br /&gt;libjogl.jnilib&lt;br /&gt;libjogl_cg.jnilib&lt;br /&gt;libjogl_awt.jnilib&lt;br /&gt;gluegen-rt.jar&lt;br /&gt;libgluegen-rt.jnilib
 | jogl.jar&lt;br /&gt;libjogl.so&lt;br /&gt;libjogl_cg.so&lt;br /&gt;libjogl_awt.so&lt;br /&gt;gluegen-rt.jar&lt;br /&gt;libgluegen-rt.so
 |}

==== Windows ====
The folder that JRE has been installed is denoted by &lt;JRE&gt;. It depends on the environment, however it is typically as follows.
 &lt;JRE&gt;=C:\Program Files\Java\j2re1.4.2_12
The files ‘jogl.jar’ and ‘gluegen-rt.jar’ should be copied to &lt;JRE&gt;\lib\ext, and the other files should be copied to &lt;JRE&gt;\bin.

==== Mac OS X ====
When operating from the command terminal, you should copy all files to /Library/Java/Extensions. When operating through the graphical interface, the above destination folder is shown as ‘Macintosh HD/Library/Java/Extensions’. In this operation, the password for root is required.

==== Linux ====
The directory that JRE has been installed is denoted by &lt;JRE&gt;. It depends on the environment, however it is typically as follows.
 &lt;JRE&gt;=/usr/java/j2sdk1.4.2_12/jre
files ‘jogl.jar’ and ‘gluegen-rt.jar’ should be copied to &lt;JRE&gt;/lib/ext, and the other files should be copied to &lt;JRE&gt;/lib/i386.

== Download jV ==
* Download jV&lt;br /&gt;
 In order to obtain jV and PDBjViewer you must agree to the software license. 
** [http://ef-site.hgc.jp/eF-site/servlet/DownloadViewerBinary binary]
** [http://ef-site.hgc.jp/eF-site/servlet/Registration sourcecode] &lt;br /&gt;Registration is required.When the registration is completed, a URL for downloading the source code of jV and PDBjViewer is sent to you by email. The URL is valid for 24 hours.</text>
    <sha1>4d2f257cd954cf8204ee46902f0707aae5e957cb</sha1>
  </revision>
  <revision>
    <id>251</id>
    <parentid>250</parentid>
    <timestamp>2009-03-09T11:42:39Z</timestamp>
    <contributor>
      <username>JVuser</username>
      <id>2</id>
    </contributor>
    <comment>/* Download jV */</comment>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="2797" xml:space="preserve">{| style="float:right"
 |__TOC__
 |}
== System requirements ==
jV3 runs on the Java Runtime Environment (JRE) with JOGL API. The version requirements are as follows.
* [http://java.sun.com/j2se/1.4.2/download.html JRE] (includes Java Plug-in) 1.4.2 or later
* [https://jogl.dev.java.net/ JOGL] API JSR-231 1.0.0 or later 
These softwares are available on typical operation systems such as Windows (2000/XP/Vista), Mac OS X 10.3 or later, and Red Hat Linux 7.3 or later.

== Installing JOGL API ==
=== Automatic install ===
In this section, it is assumed that JRE 1.4.2 or later has been installed on your computer. Installing JOGL is just deploying several files to JRE. A tool that automatically performs the JOGL installation with a graphical user interface is available at [[jV version 3]].

=== Manual install ===
It is also possible to install JOGL manually. According to the kind of your operation system, you should get the following files from [https://jogl.dev.java.net/ JOGL].

{| class="wikitable" border="1"
 ! !! Windows !! Mac OS X !! Linux
 |-
 | JSR-231 1.1.1
 | jogl.jar&lt;br /&gt;jogl.dll&lt;br /&gt;jogl_cg.dll&lt;br /&gt;jogl_awt.dll&lt;br /&gt;gluegen-rt.jar&lt;br /&gt;gluegen-rt.dll
 | jogl.jar&lt;br /&gt;libjogl.jnilib&lt;br /&gt;libjogl_cg.jnilib&lt;br /&gt;libjogl_awt.jnilib&lt;br /&gt;gluegen-rt.jar&lt;br /&gt;libgluegen-rt.jnilib
 | jogl.jar&lt;br /&gt;libjogl.so&lt;br /&gt;libjogl_cg.so&lt;br /&gt;libjogl_awt.so&lt;br /&gt;gluegen-rt.jar&lt;br /&gt;libgluegen-rt.so
 |}

==== Windows ====
The folder that JRE has been installed is denoted by &lt;JRE&gt;. It depends on the environment, however it is typically as follows.
 &lt;JRE&gt;=C:\Program Files\Java\j2re1.4.2_12
The files ‘jogl.jar’ and ‘gluegen-rt.jar’ should be copied to &lt;JRE&gt;\lib\ext, and the other files should be copied to &lt;JRE&gt;\bin.

==== Mac OS X ====
When operating from the command terminal, you should copy all files to /Library/Java/Extensions. When operating through the graphical interface, the above destination folder is shown as ‘Macintosh HD/Library/Java/Extensions’. In this operation, the password for root is required.

==== Linux ====
The directory that JRE has been installed is denoted by &lt;JRE&gt;. It depends on the environment, however it is typically as follows.
 &lt;JRE&gt;=/usr/java/j2sdk1.4.2_12/jre
files ‘jogl.jar’ and ‘gluegen-rt.jar’ should be copied to &lt;JRE&gt;/lib/ext, and the other files should be copied to &lt;JRE&gt;/lib/i386.

== Download jV ==
* Download jV&lt;br /&gt;In order to obtain jV and PDBjViewer you must agree to the software license. 
** [http://ef-site.hgc.jp/eF-site/servlet/DownloadViewerBinary binary]
** [http://ef-site.hgc.jp/eF-site/servlet/Registration sourcecode] &lt;br /&gt;Registration is required.When the registration is completed, a URL for downloading the source code of jV and PDBjViewer is sent to you by email. The URL is valid for 24 hours.</text>
    <sha1>abbd58eb4482579bca2d0f4183de18c3a3f2e042</sha1>
  </revision>
  <revision>
    <id>252</id>
    <parentid>251</parentid>
    <timestamp>2009-03-09T11:43:11Z</timestamp>
    <contributor>
      <username>JVuser</username>
      <id>2</id>
    </contributor>
    <comment>/* Download jV */</comment>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="2798" xml:space="preserve">{| style="float:right"
 |__TOC__
 |}
== System requirements ==
jV3 runs on the Java Runtime Environment (JRE) with JOGL API. The version requirements are as follows.
* [http://java.sun.com/j2se/1.4.2/download.html JRE] (includes Java Plug-in) 1.4.2 or later
* [https://jogl.dev.java.net/ JOGL] API JSR-231 1.0.0 or later 
These softwares are available on typical operation systems such as Windows (2000/XP/Vista), Mac OS X 10.3 or later, and Red Hat Linux 7.3 or later.

== Installing JOGL API ==
=== Automatic install ===
In this section, it is assumed that JRE 1.4.2 or later has been installed on your computer. Installing JOGL is just deploying several files to JRE. A tool that automatically performs the JOGL installation with a graphical user interface is available at [[jV version 3]].

=== Manual install ===
It is also possible to install JOGL manually. According to the kind of your operation system, you should get the following files from [https://jogl.dev.java.net/ JOGL].

{| class="wikitable" border="1"
 ! !! Windows !! Mac OS X !! Linux
 |-
 | JSR-231 1.1.1
 | jogl.jar&lt;br /&gt;jogl.dll&lt;br /&gt;jogl_cg.dll&lt;br /&gt;jogl_awt.dll&lt;br /&gt;gluegen-rt.jar&lt;br /&gt;gluegen-rt.dll
 | jogl.jar&lt;br /&gt;libjogl.jnilib&lt;br /&gt;libjogl_cg.jnilib&lt;br /&gt;libjogl_awt.jnilib&lt;br /&gt;gluegen-rt.jar&lt;br /&gt;libgluegen-rt.jnilib
 | jogl.jar&lt;br /&gt;libjogl.so&lt;br /&gt;libjogl_cg.so&lt;br /&gt;libjogl_awt.so&lt;br /&gt;gluegen-rt.jar&lt;br /&gt;libgluegen-rt.so
 |}

==== Windows ====
The folder that JRE has been installed is denoted by &lt;JRE&gt;. It depends on the environment, however it is typically as follows.
 &lt;JRE&gt;=C:\Program Files\Java\j2re1.4.2_12
The files ‘jogl.jar’ and ‘gluegen-rt.jar’ should be copied to &lt;JRE&gt;\lib\ext, and the other files should be copied to &lt;JRE&gt;\bin.

==== Mac OS X ====
When operating from the command terminal, you should copy all files to /Library/Java/Extensions. When operating through the graphical interface, the above destination folder is shown as ‘Macintosh HD/Library/Java/Extensions’. In this operation, the password for root is required.

==== Linux ====
The directory that JRE has been installed is denoted by &lt;JRE&gt;. It depends on the environment, however it is typically as follows.
 &lt;JRE&gt;=/usr/java/j2sdk1.4.2_12/jre
files ‘jogl.jar’ and ‘gluegen-rt.jar’ should be copied to &lt;JRE&gt;/lib/ext, and the other files should be copied to &lt;JRE&gt;/lib/i386.

== Download jV ==
* Download jV&lt;br /&gt;In order to obtain jV and PDBjViewer you must agree to the software license. 
** [http://ef-site.hgc.jp/eF-site/servlet/DownloadViewerBinary binary]
** [http://ef-site.hgc.jp/eF-site/servlet/Registration sourcecode] &lt;br /&gt;Registration is required. When the registration is completed, a URL for downloading the source code of jV and PDBjViewer is sent to you by email. The URL is valid for 24 hours.</text>
    <sha1>9a83866036a5abc7d1f0091126ad50dd3718446b</sha1>
  </revision>
  <revision>
    <id>253</id>
    <parentid>252</parentid>
    <timestamp>2009-03-09T11:44:46Z</timestamp>
    <contributor>
      <username>JVuser</username>
      <id>2</id>
    </contributor>
    <comment>/* Download jV */</comment>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="3785" xml:space="preserve">{| style="float:right"
 |__TOC__
 |}
== System requirements ==
jV3 runs on the Java Runtime Environment (JRE) with JOGL API. The version requirements are as follows.
* [http://java.sun.com/j2se/1.4.2/download.html JRE] (includes Java Plug-in) 1.4.2 or later
* [https://jogl.dev.java.net/ JOGL] API JSR-231 1.0.0 or later 
These softwares are available on typical operation systems such as Windows (2000/XP/Vista), Mac OS X 10.3 or later, and Red Hat Linux 7.3 or later.

== Installing JOGL API ==
=== Automatic install ===
In this section, it is assumed that JRE 1.4.2 or later has been installed on your computer. Installing JOGL is just deploying several files to JRE. A tool that automatically performs the JOGL installation with a graphical user interface is available at [[jV version 3]].

=== Manual install ===
It is also possible to install JOGL manually. According to the kind of your operation system, you should get the following files from [https://jogl.dev.java.net/ JOGL].

{| class="wikitable" border="1"
 ! !! Windows !! Mac OS X !! Linux
 |-
 | JSR-231 1.1.1
 | jogl.jar&lt;br /&gt;jogl.dll&lt;br /&gt;jogl_cg.dll&lt;br /&gt;jogl_awt.dll&lt;br /&gt;gluegen-rt.jar&lt;br /&gt;gluegen-rt.dll
 | jogl.jar&lt;br /&gt;libjogl.jnilib&lt;br /&gt;libjogl_cg.jnilib&lt;br /&gt;libjogl_awt.jnilib&lt;br /&gt;gluegen-rt.jar&lt;br /&gt;libgluegen-rt.jnilib
 | jogl.jar&lt;br /&gt;libjogl.so&lt;br /&gt;libjogl_cg.so&lt;br /&gt;libjogl_awt.so&lt;br /&gt;gluegen-rt.jar&lt;br /&gt;libgluegen-rt.so
 |}

==== Windows ====
The folder that JRE has been installed is denoted by &lt;JRE&gt;. It depends on the environment, however it is typically as follows.
 &lt;JRE&gt;=C:\Program Files\Java\j2re1.4.2_12
The files ‘jogl.jar’ and ‘gluegen-rt.jar’ should be copied to &lt;JRE&gt;\lib\ext, and the other files should be copied to &lt;JRE&gt;\bin.

==== Mac OS X ====
When operating from the command terminal, you should copy all files to /Library/Java/Extensions. When operating through the graphical interface, the above destination folder is shown as ‘Macintosh HD/Library/Java/Extensions’. In this operation, the password for root is required.

==== Linux ====
The directory that JRE has been installed is denoted by &lt;JRE&gt;. It depends on the environment, however it is typically as follows.
 &lt;JRE&gt;=/usr/java/j2sdk1.4.2_12/jre
files ‘jogl.jar’ and ‘gluegen-rt.jar’ should be copied to &lt;JRE&gt;/lib/ext, and the other files should be copied to &lt;JRE&gt;/lib/i386.

== Download jV ==
* Download jV&lt;br /&gt;In order to obtain jV and PDBjViewer you must agree to the software license. 
** [http://ef-site.hgc.jp/eF-site/servlet/DownloadViewerBinary binary]
** [http://ef-site.hgc.jp/eF-site/servlet/Registration sourcecode] &lt;br /&gt;Registration is required. When the registration is completed, a URL for downloading the source code of jV and PDBjViewer is sent to you by email. The URL is valid for 24 hours.
* [https://jogl.dev.java.net/ JOGL] 1.0, 1.1.1 or JSR-231 1.0.0  (recommend JSR-231)&lt;br /&gt;
** version 1.0 [[http://ef-site.hgc.jp/eF-site/jV/JOGL1.0_win32.zip Windows],[http://ef-site.hgc.jp/eF-site/jV/JOGL1.0_macosx.tar.gz Mac OS X],[http://ef-site.hgc.jp/eF-site/jV/JOGL1.0_linux.tar.gz Linux]]
** version 1.1.1 [[http://ef-site.hgc.jp/eF-site/jV/JOGL1.1.1_win32.zip Windows],[http://ef-site.hgc.jp/eF-site/jV/JOGL1.1.1_macosx.tar.gz Mac OS X], [http://ef-site.hgc.jp/eF-site/jV/JOGL1.1.1_linux.tar.gz Linux]]
** JSR-231 1.0.0 [[http://ef-site.hgc.jp/eF-site/jV/JOGL_JSR231_win32.zip Windows], [http://ef-site.hgc.jp/eF-site/jV/JOGL_JSR231_macosx_ppc.tar.gz Mac OS X ppc], [http://ef-site.hgc.jp/eF-site/jV/JOGL_JSR231_macosx_universal.tar.gz Mac OS X universal], [http://ef-site.hgc.jp/eF-site/jV/JOGL_JSR231_linux_i586.tar.gz Linux]]

&lt;font size="1"&gt;Note: &amp;nbsp; JOGL 1.0 and 1.1.1 are not available for Intel Mac.The latest version of JOGL, JSR-231 1.0.0, runs on Intel Mac.&lt;/font&gt;</text>
    <sha1>29ab419858fc6a3c83a86c22b454179347cd1b86</sha1>
  </revision>
</page>
<page arvcontinue="20090309114529|254">
  <title>Installation of jV</title>
  <ns>0</ns>
  <id>38</id>
  <revision>
    <id>254</id>
    <parentid>253</parentid>
    <timestamp>2009-03-09T11:45:29Z</timestamp>
    <contributor>
      <username>JVuser</username>
      <id>2</id>
    </contributor>
    <comment>/* Download jV */</comment>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="3792" xml:space="preserve">{| style="float:right"
 |__TOC__
 |}
== System requirements ==
jV3 runs on the Java Runtime Environment (JRE) with JOGL API. The version requirements are as follows.
* [http://java.sun.com/j2se/1.4.2/download.html JRE] (includes Java Plug-in) 1.4.2 or later
* [https://jogl.dev.java.net/ JOGL] API JSR-231 1.0.0 or later 
These softwares are available on typical operation systems such as Windows (2000/XP/Vista), Mac OS X 10.3 or later, and Red Hat Linux 7.3 or later.

== Installing JOGL API ==
=== Automatic install ===
In this section, it is assumed that JRE 1.4.2 or later has been installed on your computer. Installing JOGL is just deploying several files to JRE. A tool that automatically performs the JOGL installation with a graphical user interface is available at [[jV version 3]].

=== Manual install ===
It is also possible to install JOGL manually. According to the kind of your operation system, you should get the following files from [https://jogl.dev.java.net/ JOGL].

{| class="wikitable" border="1"
 ! !! Windows !! Mac OS X !! Linux
 |-
 | JSR-231 1.1.1
 | jogl.jar&lt;br /&gt;jogl.dll&lt;br /&gt;jogl_cg.dll&lt;br /&gt;jogl_awt.dll&lt;br /&gt;gluegen-rt.jar&lt;br /&gt;gluegen-rt.dll
 | jogl.jar&lt;br /&gt;libjogl.jnilib&lt;br /&gt;libjogl_cg.jnilib&lt;br /&gt;libjogl_awt.jnilib&lt;br /&gt;gluegen-rt.jar&lt;br /&gt;libgluegen-rt.jnilib
 | jogl.jar&lt;br /&gt;libjogl.so&lt;br /&gt;libjogl_cg.so&lt;br /&gt;libjogl_awt.so&lt;br /&gt;gluegen-rt.jar&lt;br /&gt;libgluegen-rt.so
 |}

==== Windows ====
The folder that JRE has been installed is denoted by &lt;JRE&gt;. It depends on the environment, however it is typically as follows.
 &lt;JRE&gt;=C:\Program Files\Java\j2re1.4.2_12
The files ‘jogl.jar’ and ‘gluegen-rt.jar’ should be copied to &lt;JRE&gt;\lib\ext, and the other files should be copied to &lt;JRE&gt;\bin.

==== Mac OS X ====
When operating from the command terminal, you should copy all files to /Library/Java/Extensions. When operating through the graphical interface, the above destination folder is shown as ‘Macintosh HD/Library/Java/Extensions’. In this operation, the password for root is required.

==== Linux ====
The directory that JRE has been installed is denoted by &lt;JRE&gt;. It depends on the environment, however it is typically as follows.
 &lt;JRE&gt;=/usr/java/j2sdk1.4.2_12/jre
files ‘jogl.jar’ and ‘gluegen-rt.jar’ should be copied to &lt;JRE&gt;/lib/ext, and the other files should be copied to &lt;JRE&gt;/lib/i386.

== Download jV &amp; JOGL ==
* Download jV&lt;br /&gt;In order to obtain jV and PDBjViewer you must agree to the software license. 
** [http://ef-site.hgc.jp/eF-site/servlet/DownloadViewerBinary binary]
** [http://ef-site.hgc.jp/eF-site/servlet/Registration sourcecode] &lt;br /&gt;Registration is required. When the registration is completed, a URL for downloading the source code of jV and PDBjViewer is sent to you by email. The URL is valid for 24 hours.
* [https://jogl.dev.java.net/ JOGL] 1.0, 1.1.1 or JSR-231 1.0.0  (recommend JSR-231)&lt;br /&gt;
** version 1.0 [[http://ef-site.hgc.jp/eF-site/jV/JOGL1.0_win32.zip Windows],[http://ef-site.hgc.jp/eF-site/jV/JOGL1.0_macosx.tar.gz Mac OS X],[http://ef-site.hgc.jp/eF-site/jV/JOGL1.0_linux.tar.gz Linux]]
** version 1.1.1 [[http://ef-site.hgc.jp/eF-site/jV/JOGL1.1.1_win32.zip Windows],[http://ef-site.hgc.jp/eF-site/jV/JOGL1.1.1_macosx.tar.gz Mac OS X], [http://ef-site.hgc.jp/eF-site/jV/JOGL1.1.1_linux.tar.gz Linux]]
** JSR-231 1.0.0 [[http://ef-site.hgc.jp/eF-site/jV/JOGL_JSR231_win32.zip Windows], [http://ef-site.hgc.jp/eF-site/jV/JOGL_JSR231_macosx_ppc.tar.gz Mac OS X ppc], [http://ef-site.hgc.jp/eF-site/jV/JOGL_JSR231_macosx_universal.tar.gz Mac OS X universal], [http://ef-site.hgc.jp/eF-site/jV/JOGL_JSR231_linux_i586.tar.gz Linux]]

&lt;font size="1"&gt;Note: &amp;nbsp; JOGL 1.0 and 1.1.1 are not available for Intel Mac.The latest version of JOGL, JSR-231 1.0.0, runs on Intel Mac.&lt;/font&gt;</text>
    <sha1>0ae10db3c15f8999d6807581e4339482c3acf63d</sha1>
  </revision>
  <revision>
    <id>259</id>
    <parentid>254</parentid>
    <timestamp>2009-03-09T11:55:35Z</timestamp>
    <contributor>
      <username>JVuser</username>
      <id>2</id>
    </contributor>
    <comment>/* Download jV &amp; JOGL */</comment>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="3927" xml:space="preserve">{| style="float:right"
 |__TOC__
 |}
== System requirements ==
jV3 runs on the Java Runtime Environment (JRE) with JOGL API. The version requirements are as follows.
* [http://java.sun.com/j2se/1.4.2/download.html JRE] (includes Java Plug-in) 1.4.2 or later
* [https://jogl.dev.java.net/ JOGL] API JSR-231 1.0.0 or later 
These softwares are available on typical operation systems such as Windows (2000/XP/Vista), Mac OS X 10.3 or later, and Red Hat Linux 7.3 or later.

== Installing JOGL API ==
=== Automatic install ===
In this section, it is assumed that JRE 1.4.2 or later has been installed on your computer. Installing JOGL is just deploying several files to JRE. A tool that automatically performs the JOGL installation with a graphical user interface is available at [[jV version 3]].

=== Manual install ===
It is also possible to install JOGL manually. According to the kind of your operation system, you should get the following files from [https://jogl.dev.java.net/ JOGL].

{| class="wikitable" border="1"
 ! !! Windows !! Mac OS X !! Linux
 |-
 | JSR-231 1.1.1
 | jogl.jar&lt;br /&gt;jogl.dll&lt;br /&gt;jogl_cg.dll&lt;br /&gt;jogl_awt.dll&lt;br /&gt;gluegen-rt.jar&lt;br /&gt;gluegen-rt.dll
 | jogl.jar&lt;br /&gt;libjogl.jnilib&lt;br /&gt;libjogl_cg.jnilib&lt;br /&gt;libjogl_awt.jnilib&lt;br /&gt;gluegen-rt.jar&lt;br /&gt;libgluegen-rt.jnilib
 | jogl.jar&lt;br /&gt;libjogl.so&lt;br /&gt;libjogl_cg.so&lt;br /&gt;libjogl_awt.so&lt;br /&gt;gluegen-rt.jar&lt;br /&gt;libgluegen-rt.so
 |}

==== Windows ====
The folder that JRE has been installed is denoted by &lt;JRE&gt;. It depends on the environment, however it is typically as follows.
 &lt;JRE&gt;=C:\Program Files\Java\j2re1.4.2_12
The files ‘jogl.jar’ and ‘gluegen-rt.jar’ should be copied to &lt;JRE&gt;\lib\ext, and the other files should be copied to &lt;JRE&gt;\bin.

==== Mac OS X ====
When operating from the command terminal, you should copy all files to /Library/Java/Extensions. When operating through the graphical interface, the above destination folder is shown as ‘Macintosh HD/Library/Java/Extensions’. In this operation, the password for root is required.

==== Linux ====
The directory that JRE has been installed is denoted by &lt;JRE&gt;. It depends on the environment, however it is typically as follows.
 &lt;JRE&gt;=/usr/java/j2sdk1.4.2_12/jre
files ‘jogl.jar’ and ‘gluegen-rt.jar’ should be copied to &lt;JRE&gt;/lib/ext, and the other files should be copied to &lt;JRE&gt;/lib/i386.

== Download jV &amp; JOGL ==
[[File:Download.png|right|link=http://ef-site.hgc.jp/eF-site/servlet/DownloadViewerBinary|Download]] 
* Download jV&lt;br /&gt;In order to obtain jV and PDBjViewer you must agree to the software license. 
** [http://ef-site.hgc.jp/eF-site/servlet/DownloadViewerBinary binary]&lt;br /&gt;Click right Download image.
** [http://ef-site.hgc.jp/eF-site/servlet/Registration sourcecode] &lt;br /&gt;Registration is required. When the registration is completed, a URL for downloading the source code of jV and PDBjViewer is sent to you by email. The URL is valid for 24 hours.
* [https://jogl.dev.java.net/ JOGL] 1.0, 1.1.1 or JSR-231 1.0.0  (recommend JSR-231)&lt;br /&gt;
** version 1.0 [[http://ef-site.hgc.jp/eF-site/jV/JOGL1.0_win32.zip Windows],[http://ef-site.hgc.jp/eF-site/jV/JOGL1.0_macosx.tar.gz Mac OS X],[http://ef-site.hgc.jp/eF-site/jV/JOGL1.0_linux.tar.gz Linux]]
** version 1.1.1 [[http://ef-site.hgc.jp/eF-site/jV/JOGL1.1.1_win32.zip Windows],[http://ef-site.hgc.jp/eF-site/jV/JOGL1.1.1_macosx.tar.gz Mac OS X], [http://ef-site.hgc.jp/eF-site/jV/JOGL1.1.1_linux.tar.gz Linux]]
** JSR-231 1.0.0 [[http://ef-site.hgc.jp/eF-site/jV/JOGL_JSR231_win32.zip Windows], [http://ef-site.hgc.jp/eF-site/jV/JOGL_JSR231_macosx_ppc.tar.gz Mac OS X ppc], [http://ef-site.hgc.jp/eF-site/jV/JOGL_JSR231_macosx_universal.tar.gz Mac OS X universal], [http://ef-site.hgc.jp/eF-site/jV/JOGL_JSR231_linux_i586.tar.gz Linux]]

&lt;font size="1"&gt;Note: &amp;nbsp; JOGL 1.0 and 1.1.1 are not available for Intel Mac.The latest version of JOGL, JSR-231 1.0.0, runs on Intel Mac.&lt;/font&gt;</text>
    <sha1>cb31c72c515fc56579ede27a7688013da964af00</sha1>
  </revision>
  <revision>
    <id>260</id>
    <parentid>259</parentid>
    <timestamp>2009-03-09T12:01:52Z</timestamp>
    <contributor>
      <username>JVuser</username>
      <id>2</id>
    </contributor>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="4013" xml:space="preserve">{| style="float:right"
 |__TOC__
 |}
== System requirements ==
jV3 runs on the Java Runtime Environment (JRE) with JOGL API. The version requirements are as follows.
* [http://java.sun.com/j2se/1.4.2/download.html JRE] (includes Java Plug-in) 1.4.2 or later
* [https://jogl.dev.java.net/ JOGL] API JSR-231 1.0.0 or later 
These softwares are available on typical operation systems such as Windows (2000/XP/Vista), Mac OS X 10.3 or later, and Red Hat Linux 7.3 or later.

== Installing JOGL API ==
=== Automatic install ===
In this section, it is assumed that JRE 1.4.2 or later has been installed on your computer. Installing JOGL is just deploying several files to JRE. A tool that automatically performs the JOGL installation with a graphical user interface is available at [[jV version 3]].

=== Manual install ===
It is also possible to install JOGL manually. According to the kind of your operation system, you should get the following files from [https://jogl.dev.java.net/ JOGL].

{| class="wikitable" border="1"
 ! !! Windows !! Mac OS X !! Linux
 |-
 | JSR-231 1.1.1
 | jogl.jar&lt;br /&gt;jogl.dll&lt;br /&gt;jogl_cg.dll&lt;br /&gt;jogl_awt.dll&lt;br /&gt;gluegen-rt.jar&lt;br /&gt;gluegen-rt.dll
 | jogl.jar&lt;br /&gt;libjogl.jnilib&lt;br /&gt;libjogl_cg.jnilib&lt;br /&gt;libjogl_awt.jnilib&lt;br /&gt;gluegen-rt.jar&lt;br /&gt;libgluegen-rt.jnilib
 | jogl.jar&lt;br /&gt;libjogl.so&lt;br /&gt;libjogl_cg.so&lt;br /&gt;libjogl_awt.so&lt;br /&gt;gluegen-rt.jar&lt;br /&gt;libgluegen-rt.so
 |}

==== Windows ====
The folder that JRE has been installed is denoted by &lt;JRE&gt;. It depends on the environment, however it is typically as follows.
 &lt;JRE&gt;=C:\Program Files\Java\j2re1.4.2_12
The files ‘jogl.jar’ and ‘gluegen-rt.jar’ should be copied to &lt;JRE&gt;\lib\ext, and the other files should be copied to &lt;JRE&gt;\bin.

==== Mac OS X ====
When operating from the command terminal, you should copy all files to /Library/Java/Extensions. When operating through the graphical interface, the above destination folder is shown as ‘Macintosh HD/Library/Java/Extensions’. In this operation, the password for root is required.

==== Linux ====
The directory that JRE has been installed is denoted by &lt;JRE&gt;. It depends on the environment, however it is typically as follows.
 &lt;JRE&gt;=/usr/java/j2sdk1.4.2_12/jre
files ‘jogl.jar’ and ‘gluegen-rt.jar’ should be copied to &lt;JRE&gt;/lib/ext, and the other files should be copied to &lt;JRE&gt;/lib/i386.

== Download jV ==
[[File:Download.png|right|link=http://ef-site.hgc.jp/eF-site/servlet/DownloadViewerBinary|Download]] 
* Download jV&lt;br /&gt;In order to obtain jV and PDBjViewer you must agree to the software license. 
** [http://ef-site.hgc.jp/eF-site/servlet/DownloadViewerBinary binary]&lt;br /&gt;Click right Download image.
** [http://ef-site.hgc.jp/eF-site/servlet/Registration sourcecode] &lt;br /&gt;Registration is required. When the registration is completed, a URL for downloading the source code of jV and PDBjViewer is sent to you by email. The URL is valid for 24 hours.

== Download JOGL ==
* [https://jogl.dev.java.net/ JOGL] 1.0, 1.1.1 or JSR-231 1.0.0  (recommend JSR-231)&lt;br /&gt;
** version 1.0 [[http://ef-site.hgc.jp/eF-site/jV/JOGL1.0_win32.zip Windows],[http://ef-site.hgc.jp/eF-site/jV/JOGL1.0_macosx.tar.gz Mac OS X],[http://ef-site.hgc.jp/eF-site/jV/JOGL1.0_linux.tar.gz Linux]]
** version 1.1.1 [[http://ef-site.hgc.jp/eF-site/jV/JOGL1.1.1_win32.zip Windows],[http://ef-site.hgc.jp/eF-site/jV/JOGL1.1.1_macosx.tar.gz Mac OS X], [http://ef-site.hgc.jp/eF-site/jV/JOGL1.1.1_linux.tar.gz Linux]]
** JSR-231 1.0.0 [[http://ef-site.hgc.jp/eF-site/jV/JOGL_JSR231_win32.zip Windows], [http://ef-site.hgc.jp/eF-site/jV/JOGL_JSR231_macosx_ppc.tar.gz Mac OS X ppc], [http://ef-site.hgc.jp/eF-site/jV/JOGL_JSR231_macosx_universal.tar.gz Mac OS X universal], [http://ef-site.hgc.jp/eF-site/jV/JOGL_JSR231_linux_i586.tar.gz Linux]]

&lt;font size="1"&gt;Note: &amp;nbsp; JOGL 1.0 and 1.1.1 are not available for Intel Mac.The latest version of JOGL, JSR-231 1.0.0, runs on Intel Mac.&lt;/font&gt;

== Download Manual &amp; User's Guide ==
PDF file.
* User's Guide
* Manual</text>
    <sha1>4a45b03f5375e1bf4bd1384d01a0203c8ac2d454</sha1>
  </revision>
  <revision>
    <id>264</id>
    <parentid>260</parentid>
    <timestamp>2009-03-09T12:06:49Z</timestamp>
    <contributor>
      <username>JVuser</username>
      <id>2</id>
    </contributor>
    <comment>/* Download Manual &amp; User's Guide */</comment>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="4101" xml:space="preserve">{| style="float:right"
 |__TOC__
 |}
== System requirements ==
jV3 runs on the Java Runtime Environment (JRE) with JOGL API. The version requirements are as follows.
* [http://java.sun.com/j2se/1.4.2/download.html JRE] (includes Java Plug-in) 1.4.2 or later
* [https://jogl.dev.java.net/ JOGL] API JSR-231 1.0.0 or later 
These softwares are available on typical operation systems such as Windows (2000/XP/Vista), Mac OS X 10.3 or later, and Red Hat Linux 7.3 or later.

== Installing JOGL API ==
=== Automatic install ===
In this section, it is assumed that JRE 1.4.2 or later has been installed on your computer. Installing JOGL is just deploying several files to JRE. A tool that automatically performs the JOGL installation with a graphical user interface is available at [[jV version 3]].

=== Manual install ===
It is also possible to install JOGL manually. According to the kind of your operation system, you should get the following files from [https://jogl.dev.java.net/ JOGL].

{| class="wikitable" border="1"
 ! !! Windows !! Mac OS X !! Linux
 |-
 | JSR-231 1.1.1
 | jogl.jar&lt;br /&gt;jogl.dll&lt;br /&gt;jogl_cg.dll&lt;br /&gt;jogl_awt.dll&lt;br /&gt;gluegen-rt.jar&lt;br /&gt;gluegen-rt.dll
 | jogl.jar&lt;br /&gt;libjogl.jnilib&lt;br /&gt;libjogl_cg.jnilib&lt;br /&gt;libjogl_awt.jnilib&lt;br /&gt;gluegen-rt.jar&lt;br /&gt;libgluegen-rt.jnilib
 | jogl.jar&lt;br /&gt;libjogl.so&lt;br /&gt;libjogl_cg.so&lt;br /&gt;libjogl_awt.so&lt;br /&gt;gluegen-rt.jar&lt;br /&gt;libgluegen-rt.so
 |}

==== Windows ====
The folder that JRE has been installed is denoted by &lt;JRE&gt;. It depends on the environment, however it is typically as follows.
 &lt;JRE&gt;=C:\Program Files\Java\j2re1.4.2_12
The files ‘jogl.jar’ and ‘gluegen-rt.jar’ should be copied to &lt;JRE&gt;\lib\ext, and the other files should be copied to &lt;JRE&gt;\bin.

==== Mac OS X ====
When operating from the command terminal, you should copy all files to /Library/Java/Extensions. When operating through the graphical interface, the above destination folder is shown as ‘Macintosh HD/Library/Java/Extensions’. In this operation, the password for root is required.

==== Linux ====
The directory that JRE has been installed is denoted by &lt;JRE&gt;. It depends on the environment, however it is typically as follows.
 &lt;JRE&gt;=/usr/java/j2sdk1.4.2_12/jre
files ‘jogl.jar’ and ‘gluegen-rt.jar’ should be copied to &lt;JRE&gt;/lib/ext, and the other files should be copied to &lt;JRE&gt;/lib/i386.

== Download jV ==
[[File:Download.png|right|link=http://ef-site.hgc.jp/eF-site/servlet/DownloadViewerBinary|Download]] 
* Download jV&lt;br /&gt;In order to obtain jV and PDBjViewer you must agree to the software license. 
** [http://ef-site.hgc.jp/eF-site/servlet/DownloadViewerBinary binary]&lt;br /&gt;Click right Download image.
** [http://ef-site.hgc.jp/eF-site/servlet/Registration sourcecode] &lt;br /&gt;Registration is required. When the registration is completed, a URL for downloading the source code of jV and PDBjViewer is sent to you by email. The URL is valid for 24 hours.

== Download JOGL ==
* [https://jogl.dev.java.net/ JOGL] 1.0, 1.1.1 or JSR-231 1.0.0  (recommend JSR-231)&lt;br /&gt;
** version 1.0 [[http://ef-site.hgc.jp/eF-site/jV/JOGL1.0_win32.zip Windows],[http://ef-site.hgc.jp/eF-site/jV/JOGL1.0_macosx.tar.gz Mac OS X],[http://ef-site.hgc.jp/eF-site/jV/JOGL1.0_linux.tar.gz Linux]]
** version 1.1.1 [[http://ef-site.hgc.jp/eF-site/jV/JOGL1.1.1_win32.zip Windows],[http://ef-site.hgc.jp/eF-site/jV/JOGL1.1.1_macosx.tar.gz Mac OS X], [http://ef-site.hgc.jp/eF-site/jV/JOGL1.1.1_linux.tar.gz Linux]]
** JSR-231 1.0.0 [[http://ef-site.hgc.jp/eF-site/jV/JOGL_JSR231_win32.zip Windows], [http://ef-site.hgc.jp/eF-site/jV/JOGL_JSR231_macosx_ppc.tar.gz Mac OS X ppc], [http://ef-site.hgc.jp/eF-site/jV/JOGL_JSR231_macosx_universal.tar.gz Mac OS X universal], [http://ef-site.hgc.jp/eF-site/jV/JOGL_JSR231_linux_i586.tar.gz Linux]]

&lt;font size="1"&gt;Note: &amp;nbsp; JOGL 1.0 and 1.1.1 are not available for Intel Mac.The latest version of JOGL, JSR-231 1.0.0, runs on Intel Mac.&lt;/font&gt;

== Download Manual &amp; User's Guide ==
PDF file.
* [[Media:JV3_User'sGuide.pdf|User's Guide]](30 October 2006)
* [[Media:JV_manual.pdf|Manual]](30 Octover 2006)</text>
    <sha1>8f1c6507b6c3bb532cb55fdeae6d2acba1b2406c</sha1>
  </revision>
  <revision>
    <id>265</id>
    <parentid>264</parentid>
    <timestamp>2009-03-09T12:09:56Z</timestamp>
    <contributor>
      <username>JVuser</username>
      <id>2</id>
    </contributor>
    <comment>/* Download jV */</comment>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="4161" xml:space="preserve">{| style="float:right"
 |__TOC__
 |}
== System requirements ==
jV3 runs on the Java Runtime Environment (JRE) with JOGL API. The version requirements are as follows.
* [http://java.sun.com/j2se/1.4.2/download.html JRE] (includes Java Plug-in) 1.4.2 or later
* [https://jogl.dev.java.net/ JOGL] API JSR-231 1.0.0 or later 
These softwares are available on typical operation systems such as Windows (2000/XP/Vista), Mac OS X 10.3 or later, and Red Hat Linux 7.3 or later.

== Installing JOGL API ==
=== Automatic install ===
In this section, it is assumed that JRE 1.4.2 or later has been installed on your computer. Installing JOGL is just deploying several files to JRE. A tool that automatically performs the JOGL installation with a graphical user interface is available at [[jV version 3]].

=== Manual install ===
It is also possible to install JOGL manually. According to the kind of your operation system, you should get the following files from [https://jogl.dev.java.net/ JOGL].

{| class="wikitable" border="1"
 ! !! Windows !! Mac OS X !! Linux
 |-
 | JSR-231 1.1.1
 | jogl.jar&lt;br /&gt;jogl.dll&lt;br /&gt;jogl_cg.dll&lt;br /&gt;jogl_awt.dll&lt;br /&gt;gluegen-rt.jar&lt;br /&gt;gluegen-rt.dll
 | jogl.jar&lt;br /&gt;libjogl.jnilib&lt;br /&gt;libjogl_cg.jnilib&lt;br /&gt;libjogl_awt.jnilib&lt;br /&gt;gluegen-rt.jar&lt;br /&gt;libgluegen-rt.jnilib
 | jogl.jar&lt;br /&gt;libjogl.so&lt;br /&gt;libjogl_cg.so&lt;br /&gt;libjogl_awt.so&lt;br /&gt;gluegen-rt.jar&lt;br /&gt;libgluegen-rt.so
 |}

==== Windows ====
The folder that JRE has been installed is denoted by &lt;JRE&gt;. It depends on the environment, however it is typically as follows.
 &lt;JRE&gt;=C:\Program Files\Java\j2re1.4.2_12
The files ‘jogl.jar’ and ‘gluegen-rt.jar’ should be copied to &lt;JRE&gt;\lib\ext, and the other files should be copied to &lt;JRE&gt;\bin.

==== Mac OS X ====
When operating from the command terminal, you should copy all files to /Library/Java/Extensions. When operating through the graphical interface, the above destination folder is shown as ‘Macintosh HD/Library/Java/Extensions’. In this operation, the password for root is required.

==== Linux ====
The directory that JRE has been installed is denoted by &lt;JRE&gt;. It depends on the environment, however it is typically as follows.
 &lt;JRE&gt;=/usr/java/j2sdk1.4.2_12/jre
files ‘jogl.jar’ and ‘gluegen-rt.jar’ should be copied to &lt;JRE&gt;/lib/ext, and the other files should be copied to &lt;JRE&gt;/lib/i386.

== Download jV ==
[[File:Download.png|right|link=http://ef-site.hgc.jp/eF-site/servlet/DownloadViewerBinary|Download]]
* Download jV&lt;br /&gt;In order to obtain jV and PDBjViewer you must agree to the software license. 
** [http://ef-site.hgc.jp/eF-site/servlet/DownloadViewerBinary binary]&lt;br /&gt;Click right Download image.
** [http://ef-site.hgc.jp/eF-site/servlet/Registration sourcecode] &lt;br /&gt;Registration is required. When the registration is completed, a URL for downloading the source code of jV and PDBjViewer is sent to you by email. The URL is valid for 24 hours.
** [Media:jV.jnlp Java WebStart version] for stable version.

== Download JOGL ==
* [https://jogl.dev.java.net/ JOGL] 1.0, 1.1.1 or JSR-231 1.0.0  (recommend JSR-231)&lt;br /&gt;
** version 1.0 [[http://ef-site.hgc.jp/eF-site/jV/JOGL1.0_win32.zip Windows],[http://ef-site.hgc.jp/eF-site/jV/JOGL1.0_macosx.tar.gz Mac OS X],[http://ef-site.hgc.jp/eF-site/jV/JOGL1.0_linux.tar.gz Linux]]
** version 1.1.1 [[http://ef-site.hgc.jp/eF-site/jV/JOGL1.1.1_win32.zip Windows],[http://ef-site.hgc.jp/eF-site/jV/JOGL1.1.1_macosx.tar.gz Mac OS X], [http://ef-site.hgc.jp/eF-site/jV/JOGL1.1.1_linux.tar.gz Linux]]
** JSR-231 1.0.0 [[http://ef-site.hgc.jp/eF-site/jV/JOGL_JSR231_win32.zip Windows], [http://ef-site.hgc.jp/eF-site/jV/JOGL_JSR231_macosx_ppc.tar.gz Mac OS X ppc], [http://ef-site.hgc.jp/eF-site/jV/JOGL_JSR231_macosx_universal.tar.gz Mac OS X universal], [http://ef-site.hgc.jp/eF-site/jV/JOGL_JSR231_linux_i586.tar.gz Linux]]

&lt;font size="1"&gt;Note: &amp;nbsp; JOGL 1.0 and 1.1.1 are not available for Intel Mac.The latest version of JOGL, JSR-231 1.0.0, runs on Intel Mac.&lt;/font&gt;

== Download Manual &amp; User's Guide ==
PDF file.
* [[Media:JV3_User'sGuide.pdf|User's Guide]](30 October 2006)
* [[Media:JV_manual.pdf|Manual]](30 Octover 2006)</text>
    <sha1>19bde5aa98795a351095c428e092674772da44c4</sha1>
  </revision>
  <revision>
    <id>266</id>
    <parentid>265</parentid>
    <timestamp>2009-03-09T12:10:37Z</timestamp>
    <contributor>
      <username>JVuser</username>
      <id>2</id>
    </contributor>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="4163" xml:space="preserve">{| style="float:right"
 |__TOC__
 |}
== System requirements ==
jV3 runs on the Java Runtime Environment (JRE) with JOGL API. The version requirements are as follows.
* [http://java.sun.com/j2se/1.4.2/download.html JRE] (includes Java Plug-in) 1.4.2 or later
* [https://jogl.dev.java.net/ JOGL] API JSR-231 1.0.0 or later 
These softwares are available on typical operation systems such as Windows (2000/XP/Vista), Mac OS X 10.3 or later, and Red Hat Linux 7.3 or later.

== Installing JOGL API ==
=== Automatic install ===
In this section, it is assumed that JRE 1.4.2 or later has been installed on your computer. Installing JOGL is just deploying several files to JRE. A tool that automatically performs the JOGL installation with a graphical user interface is available at [[jV version 3]].

=== Manual install ===
It is also possible to install JOGL manually. According to the kind of your operation system, you should get the following files from [https://jogl.dev.java.net/ JOGL].

{| class="wikitable" border="1"
 ! !! Windows !! Mac OS X !! Linux
 |-
 | JSR-231 1.1.1
 | jogl.jar&lt;br /&gt;jogl.dll&lt;br /&gt;jogl_cg.dll&lt;br /&gt;jogl_awt.dll&lt;br /&gt;gluegen-rt.jar&lt;br /&gt;gluegen-rt.dll
 | jogl.jar&lt;br /&gt;libjogl.jnilib&lt;br /&gt;libjogl_cg.jnilib&lt;br /&gt;libjogl_awt.jnilib&lt;br /&gt;gluegen-rt.jar&lt;br /&gt;libgluegen-rt.jnilib
 | jogl.jar&lt;br /&gt;libjogl.so&lt;br /&gt;libjogl_cg.so&lt;br /&gt;libjogl_awt.so&lt;br /&gt;gluegen-rt.jar&lt;br /&gt;libgluegen-rt.so
 |}

==== Windows ====
The folder that JRE has been installed is denoted by &lt;JRE&gt;. It depends on the environment, however it is typically as follows.
 &lt;JRE&gt;=C:\Program Files\Java\j2re1.4.2_12
The files ‘jogl.jar’ and ‘gluegen-rt.jar’ should be copied to &lt;JRE&gt;\lib\ext, and the other files should be copied to &lt;JRE&gt;\bin.

==== Mac OS X ====
When operating from the command terminal, you should copy all files to /Library/Java/Extensions. When operating through the graphical interface, the above destination folder is shown as ‘Macintosh HD/Library/Java/Extensions’. In this operation, the password for root is required.

==== Linux ====
The directory that JRE has been installed is denoted by &lt;JRE&gt;. It depends on the environment, however it is typically as follows.
 &lt;JRE&gt;=/usr/java/j2sdk1.4.2_12/jre
files ‘jogl.jar’ and ‘gluegen-rt.jar’ should be copied to &lt;JRE&gt;/lib/ext, and the other files should be copied to &lt;JRE&gt;/lib/i386.

== Download jV ==
[[File:Download.png|right|link=http://ef-site.hgc.jp/eF-site/servlet/DownloadViewerBinary|Download]]
* Download jV&lt;br /&gt;In order to obtain jV and PDBjViewer you must agree to the software license. 
** [http://ef-site.hgc.jp/eF-site/servlet/DownloadViewerBinary binary]&lt;br /&gt;Click right Download image.
** [http://ef-site.hgc.jp/eF-site/servlet/Registration sourcecode] &lt;br /&gt;Registration is required. When the registration is completed, a URL for downloading the source code of jV and PDBjViewer is sent to you by email. The URL is valid for 24 hours.
** [[Media:jV.jnlp|Java WebStart version]] for stable version.

== Download JOGL ==
* [https://jogl.dev.java.net/ JOGL] 1.0, 1.1.1 or JSR-231 1.0.0  (recommend JSR-231)&lt;br /&gt;
** version 1.0 [[http://ef-site.hgc.jp/eF-site/jV/JOGL1.0_win32.zip Windows],[http://ef-site.hgc.jp/eF-site/jV/JOGL1.0_macosx.tar.gz Mac OS X],[http://ef-site.hgc.jp/eF-site/jV/JOGL1.0_linux.tar.gz Linux]]
** version 1.1.1 [[http://ef-site.hgc.jp/eF-site/jV/JOGL1.1.1_win32.zip Windows],[http://ef-site.hgc.jp/eF-site/jV/JOGL1.1.1_macosx.tar.gz Mac OS X], [http://ef-site.hgc.jp/eF-site/jV/JOGL1.1.1_linux.tar.gz Linux]]
** JSR-231 1.0.0 [[http://ef-site.hgc.jp/eF-site/jV/JOGL_JSR231_win32.zip Windows], [http://ef-site.hgc.jp/eF-site/jV/JOGL_JSR231_macosx_ppc.tar.gz Mac OS X ppc], [http://ef-site.hgc.jp/eF-site/jV/JOGL_JSR231_macosx_universal.tar.gz Mac OS X universal], [http://ef-site.hgc.jp/eF-site/jV/JOGL_JSR231_linux_i586.tar.gz Linux]]

&lt;font size="1"&gt;Note: &amp;nbsp; JOGL 1.0 and 1.1.1 are not available for Intel Mac.The latest version of JOGL, JSR-231 1.0.0, runs on Intel Mac.&lt;/font&gt;

== Download Manual &amp; User's Guide ==
PDF file.
* [[Media:JV3_User'sGuide.pdf|User's Guide]](30 October 2006)
* [[Media:JV_manual.pdf|Manual]](30 Octover 2006)</text>
    <sha1>b1c1d023374e88ec0c23df697d54c0c7de11a6e6</sha1>
  </revision>
  <revision>
    <id>267</id>
    <parentid>266</parentid>
    <timestamp>2009-03-09T12:12:33Z</timestamp>
    <contributor>
      <username>JVuser</username>
      <id>2</id>
    </contributor>
    <comment>/* Download jV */</comment>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="4176" xml:space="preserve">{| style="float:right"
 |__TOC__
 |}
== System requirements ==
jV3 runs on the Java Runtime Environment (JRE) with JOGL API. The version requirements are as follows.
* [http://java.sun.com/j2se/1.4.2/download.html JRE] (includes Java Plug-in) 1.4.2 or later
* [https://jogl.dev.java.net/ JOGL] API JSR-231 1.0.0 or later 
These softwares are available on typical operation systems such as Windows (2000/XP/Vista), Mac OS X 10.3 or later, and Red Hat Linux 7.3 or later.

== Installing JOGL API ==
=== Automatic install ===
In this section, it is assumed that JRE 1.4.2 or later has been installed on your computer. Installing JOGL is just deploying several files to JRE. A tool that automatically performs the JOGL installation with a graphical user interface is available at [[jV version 3]].

=== Manual install ===
It is also possible to install JOGL manually. According to the kind of your operation system, you should get the following files from [https://jogl.dev.java.net/ JOGL].

{| class="wikitable" border="1"
 ! !! Windows !! Mac OS X !! Linux
 |-
 | JSR-231 1.1.1
 | jogl.jar&lt;br /&gt;jogl.dll&lt;br /&gt;jogl_cg.dll&lt;br /&gt;jogl_awt.dll&lt;br /&gt;gluegen-rt.jar&lt;br /&gt;gluegen-rt.dll
 | jogl.jar&lt;br /&gt;libjogl.jnilib&lt;br /&gt;libjogl_cg.jnilib&lt;br /&gt;libjogl_awt.jnilib&lt;br /&gt;gluegen-rt.jar&lt;br /&gt;libgluegen-rt.jnilib
 | jogl.jar&lt;br /&gt;libjogl.so&lt;br /&gt;libjogl_cg.so&lt;br /&gt;libjogl_awt.so&lt;br /&gt;gluegen-rt.jar&lt;br /&gt;libgluegen-rt.so
 |}

==== Windows ====
The folder that JRE has been installed is denoted by &lt;JRE&gt;. It depends on the environment, however it is typically as follows.
 &lt;JRE&gt;=C:\Program Files\Java\j2re1.4.2_12
The files ‘jogl.jar’ and ‘gluegen-rt.jar’ should be copied to &lt;JRE&gt;\lib\ext, and the other files should be copied to &lt;JRE&gt;\bin.

==== Mac OS X ====
When operating from the command terminal, you should copy all files to /Library/Java/Extensions. When operating through the graphical interface, the above destination folder is shown as ‘Macintosh HD/Library/Java/Extensions’. In this operation, the password for root is required.

==== Linux ====
The directory that JRE has been installed is denoted by &lt;JRE&gt;. It depends on the environment, however it is typically as follows.
 &lt;JRE&gt;=/usr/java/j2sdk1.4.2_12/jre
files ‘jogl.jar’ and ‘gluegen-rt.jar’ should be copied to &lt;JRE&gt;/lib/ext, and the other files should be copied to &lt;JRE&gt;/lib/i386.

== Download jV ==
[[File:Download.png|right|link=http://ef-site.hgc.jp/eF-site/servlet/DownloadViewerBinary|Download]]
* Download jV&lt;br /&gt;In order to obtain jV and PDBjViewer you must agree to the software license. 
** [http://ef-site.hgc.jp/eF-site/servlet/DownloadViewerBinary binary]&lt;br /&gt;Click right Download image.
** [http://ef-site.hgc.jp/eF-site/servlet/Registration sourcecode] &lt;br /&gt;Registration is required. When the registration is completed, a URL for downloading the source code of jV and PDBjViewer is sent to you by email. The URL is valid for 24 hours.
** [[Media:jV.jnlp|Java WebStart version]] for stable version.(recommended)

== Download JOGL ==
* [https://jogl.dev.java.net/ JOGL] 1.0, 1.1.1 or JSR-231 1.0.0  (recommend JSR-231)&lt;br /&gt;
** version 1.0 [[http://ef-site.hgc.jp/eF-site/jV/JOGL1.0_win32.zip Windows],[http://ef-site.hgc.jp/eF-site/jV/JOGL1.0_macosx.tar.gz Mac OS X],[http://ef-site.hgc.jp/eF-site/jV/JOGL1.0_linux.tar.gz Linux]]
** version 1.1.1 [[http://ef-site.hgc.jp/eF-site/jV/JOGL1.1.1_win32.zip Windows],[http://ef-site.hgc.jp/eF-site/jV/JOGL1.1.1_macosx.tar.gz Mac OS X], [http://ef-site.hgc.jp/eF-site/jV/JOGL1.1.1_linux.tar.gz Linux]]
** JSR-231 1.0.0 [[http://ef-site.hgc.jp/eF-site/jV/JOGL_JSR231_win32.zip Windows], [http://ef-site.hgc.jp/eF-site/jV/JOGL_JSR231_macosx_ppc.tar.gz Mac OS X ppc], [http://ef-site.hgc.jp/eF-site/jV/JOGL_JSR231_macosx_universal.tar.gz Mac OS X universal], [http://ef-site.hgc.jp/eF-site/jV/JOGL_JSR231_linux_i586.tar.gz Linux]]

&lt;font size="1"&gt;Note: &amp;nbsp; JOGL 1.0 and 1.1.1 are not available for Intel Mac.The latest version of JOGL, JSR-231 1.0.0, runs on Intel Mac.&lt;/font&gt;

== Download Manual &amp; User's Guide ==
PDF file.
* [[Media:JV3_User'sGuide.pdf|User's Guide]](30 October 2006)
* [[Media:JV_manual.pdf|Manual]](30 Octover 2006)</text>
    <sha1>b4cc3880398a0ebf15bec085202ff7aad649fd72</sha1>
  </revision>
  <revision>
    <id>268</id>
    <parentid>267</parentid>
    <timestamp>2009-03-09T12:19:27Z</timestamp>
    <contributor>
      <username>JVuser</username>
      <id>2</id>
    </contributor>
    <comment>/* Download jV */</comment>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="4202" xml:space="preserve">{| style="float:right"
 |__TOC__
 |}
== System requirements ==
jV3 runs on the Java Runtime Environment (JRE) with JOGL API. The version requirements are as follows.
* [http://java.sun.com/j2se/1.4.2/download.html JRE] (includes Java Plug-in) 1.4.2 or later
* [https://jogl.dev.java.net/ JOGL] API JSR-231 1.0.0 or later 
These softwares are available on typical operation systems such as Windows (2000/XP/Vista), Mac OS X 10.3 or later, and Red Hat Linux 7.3 or later.

== Installing JOGL API ==
=== Automatic install ===
In this section, it is assumed that JRE 1.4.2 or later has been installed on your computer. Installing JOGL is just deploying several files to JRE. A tool that automatically performs the JOGL installation with a graphical user interface is available at [[jV version 3]].

=== Manual install ===
It is also possible to install JOGL manually. According to the kind of your operation system, you should get the following files from [https://jogl.dev.java.net/ JOGL].

{| class="wikitable" border="1"
 ! !! Windows !! Mac OS X !! Linux
 |-
 | JSR-231 1.1.1
 | jogl.jar&lt;br /&gt;jogl.dll&lt;br /&gt;jogl_cg.dll&lt;br /&gt;jogl_awt.dll&lt;br /&gt;gluegen-rt.jar&lt;br /&gt;gluegen-rt.dll
 | jogl.jar&lt;br /&gt;libjogl.jnilib&lt;br /&gt;libjogl_cg.jnilib&lt;br /&gt;libjogl_awt.jnilib&lt;br /&gt;gluegen-rt.jar&lt;br /&gt;libgluegen-rt.jnilib
 | jogl.jar&lt;br /&gt;libjogl.so&lt;br /&gt;libjogl_cg.so&lt;br /&gt;libjogl_awt.so&lt;br /&gt;gluegen-rt.jar&lt;br /&gt;libgluegen-rt.so
 |}

==== Windows ====
The folder that JRE has been installed is denoted by &lt;JRE&gt;. It depends on the environment, however it is typically as follows.
 &lt;JRE&gt;=C:\Program Files\Java\j2re1.4.2_12
The files ‘jogl.jar’ and ‘gluegen-rt.jar’ should be copied to &lt;JRE&gt;\lib\ext, and the other files should be copied to &lt;JRE&gt;\bin.

==== Mac OS X ====
When operating from the command terminal, you should copy all files to /Library/Java/Extensions. When operating through the graphical interface, the above destination folder is shown as ‘Macintosh HD/Library/Java/Extensions’. In this operation, the password for root is required.

==== Linux ====
The directory that JRE has been installed is denoted by &lt;JRE&gt;. It depends on the environment, however it is typically as follows.
 &lt;JRE&gt;=/usr/java/j2sdk1.4.2_12/jre
files ‘jogl.jar’ and ‘gluegen-rt.jar’ should be copied to &lt;JRE&gt;/lib/ext, and the other files should be copied to &lt;JRE&gt;/lib/i386.

== Download jV ==
[[File:Download.png|right|link=http://ef-site.hgc.jp/eF-site/servlet/DownloadViewerBinary|Download]]
* Download jV&lt;br /&gt;In order to obtain jV and PDBjViewer you must agree to the software license. 
** [http://ef-site.hgc.jp/eF-site/servlet/DownloadViewerBinary binary]&lt;br /&gt;Click right Download image.
** [http://ef-site.hgc.jp/eF-site/servlet/Registration sourcecode] &lt;br /&gt;Registration is required. When the registration is completed, a URL for downloading the source code of jV and PDBjViewer is sent to you by email. The URL is valid for 24 hours.
** [[http://ef-site.hgc.jp/jV/stable/jV.jnlp Java WebStart version]] for stable version.(recommended)

== Download JOGL ==
* [https://jogl.dev.java.net/ JOGL] 1.0, 1.1.1 or JSR-231 1.0.0  (recommend JSR-231)&lt;br /&gt;
** version 1.0 [[http://ef-site.hgc.jp/eF-site/jV/JOGL1.0_win32.zip Windows],[http://ef-site.hgc.jp/eF-site/jV/JOGL1.0_macosx.tar.gz Mac OS X],[http://ef-site.hgc.jp/eF-site/jV/JOGL1.0_linux.tar.gz Linux]]
** version 1.1.1 [[http://ef-site.hgc.jp/eF-site/jV/JOGL1.1.1_win32.zip Windows],[http://ef-site.hgc.jp/eF-site/jV/JOGL1.1.1_macosx.tar.gz Mac OS X], [http://ef-site.hgc.jp/eF-site/jV/JOGL1.1.1_linux.tar.gz Linux]]
** JSR-231 1.0.0 [[http://ef-site.hgc.jp/eF-site/jV/JOGL_JSR231_win32.zip Windows], [http://ef-site.hgc.jp/eF-site/jV/JOGL_JSR231_macosx_ppc.tar.gz Mac OS X ppc], [http://ef-site.hgc.jp/eF-site/jV/JOGL_JSR231_macosx_universal.tar.gz Mac OS X universal], [http://ef-site.hgc.jp/eF-site/jV/JOGL_JSR231_linux_i586.tar.gz Linux]]

&lt;font size="1"&gt;Note: &amp;nbsp; JOGL 1.0 and 1.1.1 are not available for Intel Mac.The latest version of JOGL, JSR-231 1.0.0, runs on Intel Mac.&lt;/font&gt;

== Download Manual &amp; User's Guide ==
PDF file.
* [[Media:JV3_User'sGuide.pdf|User's Guide]](30 October 2006)
* [[Media:JV_manual.pdf|Manual]](30 Octover 2006)</text>
    <sha1>1be891cf0d1f8897f4bbdcc36e97d79e46fa32a4</sha1>
  </revision>
  <revision>
    <id>269</id>
    <parentid>268</parentid>
    <timestamp>2009-03-09T12:19:46Z</timestamp>
    <contributor>
      <username>JVuser</username>
      <id>2</id>
    </contributor>
    <comment>/* Download jV */</comment>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="4200" xml:space="preserve">{| style="float:right"
 |__TOC__
 |}
== System requirements ==
jV3 runs on the Java Runtime Environment (JRE) with JOGL API. The version requirements are as follows.
* [http://java.sun.com/j2se/1.4.2/download.html JRE] (includes Java Plug-in) 1.4.2 or later
* [https://jogl.dev.java.net/ JOGL] API JSR-231 1.0.0 or later 
These softwares are available on typical operation systems such as Windows (2000/XP/Vista), Mac OS X 10.3 or later, and Red Hat Linux 7.3 or later.

== Installing JOGL API ==
=== Automatic install ===
In this section, it is assumed that JRE 1.4.2 or later has been installed on your computer. Installing JOGL is just deploying several files to JRE. A tool that automatically performs the JOGL installation with a graphical user interface is available at [[jV version 3]].

=== Manual install ===
It is also possible to install JOGL manually. According to the kind of your operation system, you should get the following files from [https://jogl.dev.java.net/ JOGL].

{| class="wikitable" border="1"
 ! !! Windows !! Mac OS X !! Linux
 |-
 | JSR-231 1.1.1
 | jogl.jar&lt;br /&gt;jogl.dll&lt;br /&gt;jogl_cg.dll&lt;br /&gt;jogl_awt.dll&lt;br /&gt;gluegen-rt.jar&lt;br /&gt;gluegen-rt.dll
 | jogl.jar&lt;br /&gt;libjogl.jnilib&lt;br /&gt;libjogl_cg.jnilib&lt;br /&gt;libjogl_awt.jnilib&lt;br /&gt;gluegen-rt.jar&lt;br /&gt;libgluegen-rt.jnilib
 | jogl.jar&lt;br /&gt;libjogl.so&lt;br /&gt;libjogl_cg.so&lt;br /&gt;libjogl_awt.so&lt;br /&gt;gluegen-rt.jar&lt;br /&gt;libgluegen-rt.so
 |}

==== Windows ====
The folder that JRE has been installed is denoted by &lt;JRE&gt;. It depends on the environment, however it is typically as follows.
 &lt;JRE&gt;=C:\Program Files\Java\j2re1.4.2_12
The files ‘jogl.jar’ and ‘gluegen-rt.jar’ should be copied to &lt;JRE&gt;\lib\ext, and the other files should be copied to &lt;JRE&gt;\bin.

==== Mac OS X ====
When operating from the command terminal, you should copy all files to /Library/Java/Extensions. When operating through the graphical interface, the above destination folder is shown as ‘Macintosh HD/Library/Java/Extensions’. In this operation, the password for root is required.

==== Linux ====
The directory that JRE has been installed is denoted by &lt;JRE&gt;. It depends on the environment, however it is typically as follows.
 &lt;JRE&gt;=/usr/java/j2sdk1.4.2_12/jre
files ‘jogl.jar’ and ‘gluegen-rt.jar’ should be copied to &lt;JRE&gt;/lib/ext, and the other files should be copied to &lt;JRE&gt;/lib/i386.

== Download jV ==
[[File:Download.png|right|link=http://ef-site.hgc.jp/eF-site/servlet/DownloadViewerBinary|Download]]
* Download jV&lt;br /&gt;In order to obtain jV and PDBjViewer you must agree to the software license. 
** [http://ef-site.hgc.jp/eF-site/servlet/DownloadViewerBinary binary]&lt;br /&gt;Click right Download image.
** [http://ef-site.hgc.jp/eF-site/servlet/Registration sourcecode] &lt;br /&gt;Registration is required. When the registration is completed, a URL for downloading the source code of jV and PDBjViewer is sent to you by email. The URL is valid for 24 hours.
** [http://ef-site.hgc.jp/jV/stable/jV.jnlp Java WebStart version] for stable version.(recommended)

== Download JOGL ==
* [https://jogl.dev.java.net/ JOGL] 1.0, 1.1.1 or JSR-231 1.0.0  (recommend JSR-231)&lt;br /&gt;
** version 1.0 [[http://ef-site.hgc.jp/eF-site/jV/JOGL1.0_win32.zip Windows],[http://ef-site.hgc.jp/eF-site/jV/JOGL1.0_macosx.tar.gz Mac OS X],[http://ef-site.hgc.jp/eF-site/jV/JOGL1.0_linux.tar.gz Linux]]
** version 1.1.1 [[http://ef-site.hgc.jp/eF-site/jV/JOGL1.1.1_win32.zip Windows],[http://ef-site.hgc.jp/eF-site/jV/JOGL1.1.1_macosx.tar.gz Mac OS X], [http://ef-site.hgc.jp/eF-site/jV/JOGL1.1.1_linux.tar.gz Linux]]
** JSR-231 1.0.0 [[http://ef-site.hgc.jp/eF-site/jV/JOGL_JSR231_win32.zip Windows], [http://ef-site.hgc.jp/eF-site/jV/JOGL_JSR231_macosx_ppc.tar.gz Mac OS X ppc], [http://ef-site.hgc.jp/eF-site/jV/JOGL_JSR231_macosx_universal.tar.gz Mac OS X universal], [http://ef-site.hgc.jp/eF-site/jV/JOGL_JSR231_linux_i586.tar.gz Linux]]

&lt;font size="1"&gt;Note: &amp;nbsp; JOGL 1.0 and 1.1.1 are not available for Intel Mac.The latest version of JOGL, JSR-231 1.0.0, runs on Intel Mac.&lt;/font&gt;

== Download Manual &amp; User's Guide ==
PDF file.
* [[Media:JV3_User'sGuide.pdf|User's Guide]](30 October 2006)
* [[Media:JV_manual.pdf|Manual]](30 Octover 2006)</text>
    <sha1>74928aef4bb1f3fcd1ca5f35cca03701eaf5094d</sha1>
  </revision>
</page>
<page arvcontinue="20090309114529|254">
  <title>Main Page</title>
  <ns>0</ns>
  <id>1</id>
  <revision>
    <id>255</id>
    <parentid>247</parentid>
    <timestamp>2009-03-09T11:46:05Z</timestamp>
    <contributor>
      <username>JVuser</username>
      <id>2</id>
    </contributor>
    <comment>/* System requirements */</comment>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="2632" xml:space="preserve">&lt;big&gt;'''Welcome to jV wiki.'''&lt;/big&gt;
jV version3 (formerly known as PDBjViewer) is a program to display molecular graphics of protein and nucleic acids. 
jV can use as a stand-alone program and can operate on a web browser as an Java applet. jV is used by PDBj services([http://ef-site.hgc.jp/eF-site/index.jsp eF-site], [http://ef-site.hgc.jp/eF-seek/index.jsp eF-seek], the molecular structure surface database of the protein functional part).

jV supports the following features:
* jV can read and display PDBML files, the canonical XML format for the Protein Data Bank.
* Of course, jV can read and display the traditional PDB format files, too.
* RasMol-like usability.
* jV can process more than one molecules.
* jV can display polygons specified by XML. ([http://ef-site.hgc.jp/eF-site/schema/polygon12.xsd XML Schema for polygons] is available.)
* Multiple polygons can be processed simultaneously, and be superimposed onto molecular images.
* Animation can be realized.
* The graphics of jV is based on OpenGL [https://jogl.dev.java.net/ JOGL]), thereby producing fairly beautiful pictures.
* jV runs on the Java Runtime Environment ([http://java.sun.com/javase/index.jsp JRE]) so that it can work as a stand-alone application as well as an applet.

The program 'jV' has been developed by [http://www.hgc.jp/~kinosita/TOP.html Kengo Kinoshita] ([http://www.hgc.jp/english/ Human Genome Center], [http://www.ims.u-tokyo.ac.jp/imsut/en/ Insutitute for Medical Science],[http://www.u-tokyo.ac.jp/index_e.html University of Tokyo]) and [http://www.protein.osaka-u.ac.jp/rcsfp/pi/ Haruki Nakamura] ([http://www.protein.osaka-u.ac.jp/index_e.php Institute for Protein Research], [http://www.osaka-u.ac.jp/eng/index.html Osaka Univeristy]), with the support from [http://www-bird.jst.go.jp/index_e.html JST-BIRD].

;How to use jV3
[[jV version 3]] has indicated more detailed explanation and how to use.&lt;br /&gt;
;jV3 install
[[Installation of jV3]] is a procedure installed in a local machine.&lt;br /&gt;

&lt;font size="1"&gt;The [[old version]](jV version1 &amp; jV version2) has not carried out use recommendation.&lt;/font&gt;

&lt;gallery&gt;
File:Spacefill.jpg
File:Cartoon.jpg
File:Surface.jpg
File:edmap.jpg
&lt;/gallery&gt;

== System requirements ==
[[File:Download.png|right|link=http://ef-site.hgc.jp/eF-site/servlet/DownloadViewerBinary|Download]] jV version 3 is now used to display molecules and their surfaces as a Java applet program.&lt;br /&gt;&lt;font size="1"&gt;Version 3.6 was released on 11, Aug, 2008.&lt;br /&gt;This version is fully compativle with [https://applet-launcher.dev.java.net/ applet-launcher].&lt;/font&gt;&lt;br /&gt;More details  [[Installation of jV3]].</text>
    <sha1>bee4ee377b3868bc6683f9a98d3daa75398f9743</sha1>
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  <revision>
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    <parentid>255</parentid>
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    <contributor>
      <username>JVuser</username>
      <id>2</id>
    </contributor>
    <comment>/* System requirements */</comment>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="2531" xml:space="preserve">&lt;big&gt;'''Welcome to jV wiki.'''&lt;/big&gt;
jV version3 (formerly known as PDBjViewer) is a program to display molecular graphics of protein and nucleic acids. 
jV can use as a stand-alone program and can operate on a web browser as an Java applet. jV is used by PDBj services([http://ef-site.hgc.jp/eF-site/index.jsp eF-site], [http://ef-site.hgc.jp/eF-seek/index.jsp eF-seek], the molecular structure surface database of the protein functional part).

jV supports the following features:
* jV can read and display PDBML files, the canonical XML format for the Protein Data Bank.
* Of course, jV can read and display the traditional PDB format files, too.
* RasMol-like usability.
* jV can process more than one molecules.
* jV can display polygons specified by XML. ([http://ef-site.hgc.jp/eF-site/schema/polygon12.xsd XML Schema for polygons] is available.)
* Multiple polygons can be processed simultaneously, and be superimposed onto molecular images.
* Animation can be realized.
* The graphics of jV is based on OpenGL [https://jogl.dev.java.net/ JOGL]), thereby producing fairly beautiful pictures.
* jV runs on the Java Runtime Environment ([http://java.sun.com/javase/index.jsp JRE]) so that it can work as a stand-alone application as well as an applet.

The program 'jV' has been developed by [http://www.hgc.jp/~kinosita/TOP.html Kengo Kinoshita] ([http://www.hgc.jp/english/ Human Genome Center], [http://www.ims.u-tokyo.ac.jp/imsut/en/ Insutitute for Medical Science],[http://www.u-tokyo.ac.jp/index_e.html University of Tokyo]) and [http://www.protein.osaka-u.ac.jp/rcsfp/pi/ Haruki Nakamura] ([http://www.protein.osaka-u.ac.jp/index_e.php Institute for Protein Research], [http://www.osaka-u.ac.jp/eng/index.html Osaka Univeristy]), with the support from [http://www-bird.jst.go.jp/index_e.html JST-BIRD].

;How to use jV3
[[jV version 3]] has indicated more detailed explanation and how to use.&lt;br /&gt;
;jV3 install
[[Installation of jV3]] is a procedure installed in a local machine.&lt;br /&gt;

&lt;font size="1"&gt;The [[old version]](jV version1 &amp; jV version2) has not carried out use recommendation.&lt;/font&gt;

&lt;gallery&gt;
File:Spacefill.jpg
File:Cartoon.jpg
File:Surface.jpg
File:edmap.jpg
&lt;/gallery&gt;

== System requirements ==
jV version 3 is now used to display molecules and their surfaces as a Java applet program.&lt;br /&gt;&lt;font size="1"&gt;Version 3.6 was released on 11, Aug, 2008.&lt;br /&gt;This version is fully compativle with [https://applet-launcher.dev.java.net/ applet-launcher].&lt;/font&gt;&lt;br /&gt;More details  [[Installation of jV3]].</text>
    <sha1>dcc6c9840b433b6368a4b3dcce2c2e5161f671b4</sha1>
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  <revision>
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    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="2239" xml:space="preserve">&lt;big&gt;'''Welcome to jV wiki.'''&lt;/big&gt;

jV version3 (formerly known as PDBjViewer) is a program to display molecular graphics of protein and nucleic acids. 
jV supports the following features:
* jV can read and display PDBML files, the canonical XML format for the Protein Data Bank.
* Of course, jV can read and display the traditional PDB format files, too.
* RasMol-like usability.
* jV can process more than one molecules.
* jV can display polygons specified by XML. ([http://ef-site.hgc.jp/eF-site/schema/polygon12.xsd XML Schema for polygons] is available.)
* Multiple polygons can be processed simultaneously, and be superimposed onto molecular images.
* Animation can be realized.
* The graphics of jV is based on OpenGL [https://jogl.dev.java.net/ JOGL]), thereby producing fairly beautiful pictures.
* jV runs on the Java Runtime Environment ([http://java.sun.com/javase/index.jsp JRE]) so that it can work as a stand-alone application as well as an applet.

The program 'jV' has been developed by [http://www.hgc.jp/~kinosita/TOP.html Kengo Kinoshita] ([http://www.hgc.jp/english/ Human Genome Center], [http://www.ims.u-tokyo.ac.jp/imsut/en/ Insutitute for Medical Science],[http://www.u-tokyo.ac.jp/index_e.html University of Tokyo]) and [http://www.protein.osaka-u.ac.jp/rcsfp/pi/ Haruki Nakamura] ([http://www.protein.osaka-u.ac.jp/index_e.php Institute for Protein Research], [http://www.osaka-u.ac.jp/eng/index.html Osaka Univeristy]), with the support from [http://www-bird.jst.go.jp/index_e.html JST-BIRD].

;How to use jV3
[[jV version 3]] has indicated more detailed explanation and how to use.&lt;br /&gt;
;jV3 install
[[Installation of jV3]] is a procedure installed in a local machine.&lt;br /&gt;

&lt;font size="1"&gt;The [[old version]](jV version1 &amp; jV version2) has not carried out use recommendation.&lt;/font&gt;

&lt;gallery&gt;
File:Spacefill.jpg
File:Cartoon.jpg
File:Surface.jpg
File:edmap.jpg
&lt;/gallery&gt;

== System requirements ==
jV version 3 is now used to display molecules and their surfaces as a Java applet program.&lt;br /&gt;&lt;font size="1"&gt;Version 3.6 was released on 11, Aug, 2008.&lt;br /&gt;This version is fully compativle with [https://applet-launcher.dev.java.net/ applet-launcher].&lt;/font&gt;&lt;br /&gt;More details  [[Installation of jV3]].</text>
    <sha1>bc00413842fdacc0f4ccd294e8c80589d376e98a</sha1>
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  <revision>
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    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="1692" xml:space="preserve">&lt;big&gt;'''Welcome to jV wiki.'''&lt;/big&gt;

jV version3 (formerly known as PDBjViewer) is a program to display molecular graphics of protein and nucleic acids. 
jV supports the following features:
* jV can read and display PDBML files, the canonical XML format for the Protein Data Bank.
* Of course, jV can read and display the traditional PDB format files, too.
* RasMol-like usability.
* jV can process more than one molecules.
* jV can display polygons specified by XML. ([http://ef-site.hgc.jp/eF-site/schema/polygon12.xsd XML Schema for polygons] is available.)
* Multiple polygons can be processed simultaneously, and be superimposed onto molecular images.
* Animation can be realized.
* jV runs on the Java Runtime Environment ([http://java.sun.com/javase/index.jsp JRE]) so that it can work as a stand-alone application as well as an applet.
* The graphics of jV is based on OpenGL [https://jogl.dev.java.net/ JOGL]), thereby producing fairly beautiful pictures.


The program 'jV' has been developed by [http://www.hgc.jp/~kinosita/TOP.html Kengo Kinoshita] ([http://www.hgc.jp/english/ Human Genome Center], [http://www.ims.u-tokyo.ac.jp/imsut/en/ Insutitute for Medical Science],[http://www.u-tokyo.ac.jp/index_e.html University of Tokyo]) and [http://www.protein.osaka-u.ac.jp/rcsfp/pi/ Haruki Nakamura] ([http://www.protein.osaka-u.ac.jp/index_e.php Institute for Protein Research], [http://www.osaka-u.ac.jp/eng/index.html Osaka Univeristy]), with the support from [http://www-bird.jst.go.jp/index_e.html JST-BIRD].


&lt;gallery&gt;
File:Spacefill.jpg
File:Cartoon.jpg
File:Surface.jpg
File:edmap.jpg
&lt;/gallery&gt;


[[jV version 3]] -&lt;br /&gt;
[[Installation of jV3]] -&lt;br /&gt;
[[old version]] -</text>
    <sha1>c1e413b86b5b6758e61605df595b556c0c0c47ea</sha1>
  </revision>
  <revision>
    <id>292</id>
    <parentid>291</parentid>
    <timestamp>2009-04-22T08:26:04Z</timestamp>
    <contributor>
      <username>WikiSysop</username>
      <id>1</id>
    </contributor>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="1680" xml:space="preserve">&lt;big&gt;'''Welcome to jV wiki.'''&lt;/big&gt;

jV version3 (formerly known as PDBjViewer) is a program to display molecular graphics of protein and nucleic acids. 
jV supports the following features:
* jV can read and display PDBML files, the canonical XML format for the Protein Data Bank.
* Of course, jV can read and display the traditional PDB format files, too.
* RasMol-like usability.
* jV can process more than one molecules.
* jV can display polygons specified by XML. ([http://ef-site.hgc.jp/eF-site/schema/polygon12.xsd XML Schema for polygons] is available.)
* Multiple polygons can be processed simultaneously, and be superimposed onto molecular images.
* Animation can be realized.
* jV runs on the Java Runtime Environment ([http://java.sun.com/javase/index.jsp JRE]) so that it can work as a stand-alone application as well as an applet.
* The graphics of jV is based on OpenGL [https://jogl.dev.java.net/ JOGL]), thereby producing fairly beautiful pictures.


The program 'jV' has been developed by [http://www.hgc.jp/~kinosita/TOP.html Kengo Kinoshita] ([http://www.hgc.jp/english/ Human Genome Center], [http://www.ims.u-tokyo.ac.jp/imsut/en/ Insutitute for Medical Science],[http://www.u-tokyo.ac.jp/index_e.html University of Tokyo]) and [http://www.protein.osaka-u.ac.jp/rcsfp/pi/ Haruki Nakamura] ([http://www.protein.osaka-u.ac.jp/index_e.php Institute for Protein Research], [http://www.osaka-u.ac.jp/eng/index.html Osaka Univeristy]), with the support from [http://www-bird.jst.go.jp/index_e.html JST-BIRD].


&lt;gallery&gt;
File:Spacefill.jpg
File:Cartoon.jpg
File:Surface.jpg
File:edmap.jpg
&lt;/gallery&gt;


*[[old version|Older versions]]
*[[release note|Release note]]</text>
    <sha1>1126983308d358ddf91941112bc880cd806f08d4</sha1>
  </revision>
</page>
<page arvcontinue="20090309114529|254">
  <title>Animation</title>
  <ns>0</ns>
  <id>12</id>
  <revision>
    <id>256</id>
    <parentid>117</parentid>
    <timestamp>2009-03-09T11:51:12Z</timestamp>
    <contributor>
      <username>JVuser</username>
      <id>2</id>
    </contributor>
    <comment>/* Step-1: Minimum Example */</comment>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="3070" xml:space="preserve">{| style="float:right"
 |__TOC__
 |}
A brief introduction to user animation in jV.

== Step-1: Minimum Example ==
To display the animation on the web using jV, you should prepare an animation file and a html file.

[[File:step-1.jpg|left|step-1]]The format of the animation file is the same one as the PDB format of the NMR structure with multiple models. In other words, each frame is separated with MODEL recored. An example animation file can be obtained from [[here]].

The html file, shown below, should contain the applet tag to activate jV and it requires code parameter, codebase parameter and archive parameter. The parameter “code” is a kind of magic word to use jV. The codebase points the relative path to the jV jar file existing from the html file is stored, and archive parameter indicates the name of jar file. The jar file can be obtained from [[Installation of jV3]].

 &lt;html&gt;&lt;body&gt;
 &lt;applet code="org.pdbj.viewer.gui.ViewerApplet"
    codebase="."
    archive="jv3_3.jar"
    width=400 height=400
    &lt;param name="animURL"
        value="http://ef-site.hgc.jp/jV/example/1byi_1-anm.pdg"&gt;
    &lt;param name="commands"
        value="select all;wireframe on;anim forward"&gt;
 &lt;/applet&gt;
 &lt;/body&gt;&lt;/html&gt;

== Step-2:Make more fancy ==
[[File:step-2.jpg|right|step-2]]To display cartoon and color from N-terminal to C-terminal in white background,change “wireframe on” to “cartoon on” &amp; add “color group;”&lt;br /&gt;
&lt;font size="1"&gt;NOTE: As in this example, any jV code (similar to Rasmol script) can be used in the commands parameter. And each jV command should be separated by “;”.&lt;/font&gt;&lt;br /&gt;
Complete Code until here.

 &lt;html&gt;&lt;body&gt;
 &lt;applet code="org.pdbj.viewer.gui.ViewerApplet"
    codebase="."
    archive="jv3_3.jar"
    width=400 height=400
    &lt;param name="animURL"
        value="http://ef-site.hgc.jp/jV/example/1byi_1-anm.pdb"&gt;
    &lt;param name="commands"
        value="background white;select all;background white;
               cartoon on; anim forward"&gt;
 &lt;/applet&gt;
 &lt;/body&gt;&lt;/html&gt;

== Step-3: Swing &amp; move quick! ==
To control the speed of animation and the animation mode (shown once, swing, or loop), add two commands, “animmode swing; animspeed 20;” (20 is just an example).

 &lt;html&gt;&lt;body&gt;
 &lt;applet code="org.pdbj.viewer.gui.ViewerApplet"
    codebase="."
    archive="jv3_3.jar"
    width=400 height=400
    &lt;param name="animURL"
        value="http://ef-site.hgc.jp/jV/example/1byi_1-anm.pdb"&gt;
    &lt;param name="commands"
        value="background white;select all;background white;
               cartoon on;
               animmode swing;animspeed 20;
               anim forward"&gt;
 &lt;/applet&gt;
 &lt;/body&gt;&lt;/html&gt;

== Step-4: Advance usage in ProMode ==
[[File:ProMode.jpg|right|link=http://cube.socs.waseda.ac.jp/pages/jsp/index.jsp|ProMode]] ProMode is a database of normal mode analysis of proteins. In the database Animations are provided with jV. You can see the [http://cube.socs.waseda.ac.jp/pages/jsp/indexn.jsp?cont=menu-jv&amp;mode=1&amp;sec=dif&amp;protein=1byi#bar case of 1BYI], which is used as an example of this page.</text>
    <sha1>f314dc5db4baff6ffbb24973856a16bff810cec3</sha1>
  </revision>
  <revision>
    <id>257</id>
    <parentid>256</parentid>
    <timestamp>2009-03-09T11:52:48Z</timestamp>
    <contributor>
      <username>JVuser</username>
      <id>2</id>
    </contributor>
    <comment>/* Step-1: Minimum Example */</comment>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="3116" xml:space="preserve">{| style="float:right"
 |__TOC__
 |}
A brief introduction to user animation in jV.

== Step-1: Minimum Example ==
To display the animation on the web using jV, you should prepare an animation file and a html file.

[[File:step-1.jpg|left|step-1]]The format of the animation file is the same one as the PDB format of the NMR structure with multiple models. In other words, each frame is separated with MODEL recored. An example animation file can be obtained from [http://ef-site.hgc.jp/jV/example/1byi_1-amn.pdb here].

The html file, shown below, should contain the applet tag to activate jV and it requires code parameter, codebase parameter and archive parameter. The parameter “code” is a kind of magic word to use jV. The codebase points the relative path to the jV jar file existing from the html file is stored, and archive parameter indicates the name of jar file. The jar file can be obtained from [[Installation of jV3]].

 &lt;html&gt;&lt;body&gt;
 &lt;applet code="org.pdbj.viewer.gui.ViewerApplet"
    codebase="."
    archive="jv3_3.jar"
    width=400 height=400
    &lt;param name="animURL"
        value="http://ef-site.hgc.jp/jV/example/1byi_1-anm.pdg"&gt;
    &lt;param name="commands"
        value="select all;wireframe on;anim forward"&gt;
 &lt;/applet&gt;
 &lt;/body&gt;&lt;/html&gt;

== Step-2:Make more fancy ==
[[File:step-2.jpg|right|step-2]]To display cartoon and color from N-terminal to C-terminal in white background,change “wireframe on” to “cartoon on” &amp; add “color group;”&lt;br /&gt;
&lt;font size="1"&gt;NOTE: As in this example, any jV code (similar to Rasmol script) can be used in the commands parameter. And each jV command should be separated by “;”.&lt;/font&gt;&lt;br /&gt;
Complete Code until here.

 &lt;html&gt;&lt;body&gt;
 &lt;applet code="org.pdbj.viewer.gui.ViewerApplet"
    codebase="."
    archive="jv3_3.jar"
    width=400 height=400
    &lt;param name="animURL"
        value="http://ef-site.hgc.jp/jV/example/1byi_1-anm.pdb"&gt;
    &lt;param name="commands"
        value="background white;select all;background white;
               cartoon on; anim forward"&gt;
 &lt;/applet&gt;
 &lt;/body&gt;&lt;/html&gt;

== Step-3: Swing &amp; move quick! ==
To control the speed of animation and the animation mode (shown once, swing, or loop), add two commands, “animmode swing; animspeed 20;” (20 is just an example).

 &lt;html&gt;&lt;body&gt;
 &lt;applet code="org.pdbj.viewer.gui.ViewerApplet"
    codebase="."
    archive="jv3_3.jar"
    width=400 height=400
    &lt;param name="animURL"
        value="http://ef-site.hgc.jp/jV/example/1byi_1-anm.pdb"&gt;
    &lt;param name="commands"
        value="background white;select all;background white;
               cartoon on;
               animmode swing;animspeed 20;
               anim forward"&gt;
 &lt;/applet&gt;
 &lt;/body&gt;&lt;/html&gt;

== Step-4: Advance usage in ProMode ==
[[File:ProMode.jpg|right|link=http://cube.socs.waseda.ac.jp/pages/jsp/index.jsp|ProMode]] ProMode is a database of normal mode analysis of proteins. In the database Animations are provided with jV. You can see the [http://cube.socs.waseda.ac.jp/pages/jsp/indexn.jsp?cont=menu-jv&amp;mode=1&amp;sec=dif&amp;protein=1byi#bar case of 1BYI], which is used as an example of this page.</text>
    <sha1>23d17b548310af4e9d80ff8f3dd7575552b19890</sha1>
  </revision>
</page>
<page arvcontinue="20090309114529|254">
  <title>How to use</title>
  <ns>0</ns>
  <id>11</id>
  <revision>
    <id>261</id>
    <parentid>248</parentid>
    <timestamp>2009-03-09T12:05:08Z</timestamp>
    <contributor>
      <username>JVuser</username>
      <id>2</id>
    </contributor>
    <comment>/* How to use */</comment>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="2938" xml:space="preserve">jV is an interactive 3D viewer program to visualize protein and nucleic acid molecules. The program reads in a PDBML file that is an XML format for PDB. Usual PDB format files are also accepted. More than one molecule files can be opened and displayed at the same time and their display models and transforms can be operated separately. In addition to molecule files, a polygon file written in XML can be read and displayed. More than one polygon files can be opened at the same time and superposed on molecule images. The [http://ef-site.hgc.jp/eF-site/schema/polygon12.xsd XML schema] of the polygon file is available. jV can perform an animation of molecules. The animation file is a PDB format file in which each frame is separated by a MODEL line.

jV runs on Java Runtime Environment ([http://java.sun.com/j2se/1.4.2/download.html JRE]) and can be used both as a standalone program and an applet. The 3D rendering is performed with the use of [https://jogl.dev.java.net/ JOGL] API. The version requirements are as follows.

* JRE (includes Java Plug-in) 1.4.2 or later
* JOGL 1.1.1 or JSR-231

Here, [http://java.sun.com/products/plugin/ Java Plug-in] is required in order to use the program as an applet.

The program allows an interactive mouse control and command execution. The commnad syntax follows that of [http://www.rasmol.org/ Rasmol] with some modifications. In order to handle the transform of each molecule and polygon separately, every files are set to be either selected or not selected. The transform operation commands, such as rotate or translate, act only on selected files. On the other hand, every atoms in a molecule are also set to be either selected or not selected independently of whether the molecule itself is selected or not selected. Only selected atoms are the target of display model operations, such as wireframe or spacefill commands, and coloring operations.

[[Release note]]
== How to use ==
The following table shows hot to do the minimum things with jV.&lt;br /&gt;
{| class="wikitable" border="1" style="margin:0 auto" 
 ! Action !! Window, Linux !! Mac OS X 
 |-
 ! style="text-align:left" | rotate around X,Y axes
 | left drag || mouse drag
 |-
 ! style="text-align:left" | rotate around Z axis
 | Shift + right drag || Shift + command + drag
 |-
 ! style="text-align:left" | translate along X,Y axes
 | right drag || command + drag
 |-
 ! style="text-align:left" | translate along Z axis (zoom in/out)
 | Shift + left drag || Shift + drag
 |}
For the detail,&lt;br /&gt;

; The install manual (pdf[[Installation of jV3#Download Manual]])
* [[Installation of jV3]]
; The reference manual
* User's Guide 
# [[Tutorials]]
# [[GUI]]
# [[Document type of the polygon file]]
# [[Functional site information for molecules]]
* Manual 
# [[Command List]]
# [[Atom Expression]]
# [[Vertex Expression]]
# [[Color Expression]]
# [[Use as Applet]]

;Some examples
# [[Animation]]
# [[User jV with applet launcher]]</text>
    <sha1>dedf93ddf66a2a909fb7154947837fc91c5bc5de</sha1>
  </revision>
  <revision>
    <id>262</id>
    <parentid>261</parentid>
    <timestamp>2009-03-09T12:05:54Z</timestamp>
    <contributor>
      <username>JVuser</username>
      <id>2</id>
    </contributor>
    <comment>/* How to use */</comment>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="2944" xml:space="preserve">jV is an interactive 3D viewer program to visualize protein and nucleic acid molecules. The program reads in a PDBML file that is an XML format for PDB. Usual PDB format files are also accepted. More than one molecule files can be opened and displayed at the same time and their display models and transforms can be operated separately. In addition to molecule files, a polygon file written in XML can be read and displayed. More than one polygon files can be opened at the same time and superposed on molecule images. The [http://ef-site.hgc.jp/eF-site/schema/polygon12.xsd XML schema] of the polygon file is available. jV can perform an animation of molecules. The animation file is a PDB format file in which each frame is separated by a MODEL line.

jV runs on Java Runtime Environment ([http://java.sun.com/j2se/1.4.2/download.html JRE]) and can be used both as a standalone program and an applet. The 3D rendering is performed with the use of [https://jogl.dev.java.net/ JOGL] API. The version requirements are as follows.

* JRE (includes Java Plug-in) 1.4.2 or later
* JOGL 1.1.1 or JSR-231

Here, [http://java.sun.com/products/plugin/ Java Plug-in] is required in order to use the program as an applet.

The program allows an interactive mouse control and command execution. The commnad syntax follows that of [http://www.rasmol.org/ Rasmol] with some modifications. In order to handle the transform of each molecule and polygon separately, every files are set to be either selected or not selected. The transform operation commands, such as rotate or translate, act only on selected files. On the other hand, every atoms in a molecule are also set to be either selected or not selected independently of whether the molecule itself is selected or not selected. Only selected atoms are the target of display model operations, such as wireframe or spacefill commands, and coloring operations.

[[Release note]]
== How to use ==
The following table shows hot to do the minimum things with jV.&lt;br /&gt;
{| class="wikitable" border="1" style="margin:0 auto" 
 ! Action !! Window, Linux !! Mac OS X 
 |-
 ! style="text-align:left" | rotate around X,Y axes
 | left drag || mouse drag
 |-
 ! style="text-align:left" | rotate around Z axis
 | Shift + right drag || Shift + command + drag
 |-
 ! style="text-align:left" | translate along X,Y axes
 | right drag || command + drag
 |-
 ! style="text-align:left" | translate along Z axis (zoom in/out)
 | Shift + left drag || Shift + drag
 |}
For the detail,&lt;br /&gt;

; The install manual
pdf file : [[Installation of jV3#Download Manual]]
* [[Installation of jV3]]
; The reference manual
* User's Guide 
# [[Tutorials]]
# [[GUI]]
# [[Document type of the polygon file]]
# [[Functional site information for molecules]]
* Manual 
# [[Command List]]
# [[Atom Expression]]
# [[Vertex Expression]]
# [[Color Expression]]
# [[Use as Applet]]

;Some examples
# [[Animation]]
# [[User jV with applet launcher]]</text>
    <sha1>1e29557a7e99e5eb12fe7563e09abfb0cefd8737</sha1>
  </revision>
  <revision>
    <id>263</id>
    <parentid>262</parentid>
    <timestamp>2009-03-09T12:06:36Z</timestamp>
    <contributor>
      <username>JVuser</username>
      <id>2</id>
    </contributor>
    <comment>/* How to use */</comment>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="2944" xml:space="preserve">jV is an interactive 3D viewer program to visualize protein and nucleic acid molecules. The program reads in a PDBML file that is an XML format for PDB. Usual PDB format files are also accepted. More than one molecule files can be opened and displayed at the same time and their display models and transforms can be operated separately. In addition to molecule files, a polygon file written in XML can be read and displayed. More than one polygon files can be opened at the same time and superposed on molecule images. The [http://ef-site.hgc.jp/eF-site/schema/polygon12.xsd XML schema] of the polygon file is available. jV can perform an animation of molecules. The animation file is a PDB format file in which each frame is separated by a MODEL line.

jV runs on Java Runtime Environment ([http://java.sun.com/j2se/1.4.2/download.html JRE]) and can be used both as a standalone program and an applet. The 3D rendering is performed with the use of [https://jogl.dev.java.net/ JOGL] API. The version requirements are as follows.

* JRE (includes Java Plug-in) 1.4.2 or later
* JOGL 1.1.1 or JSR-231

Here, [http://java.sun.com/products/plugin/ Java Plug-in] is required in order to use the program as an applet.

The program allows an interactive mouse control and command execution. The commnad syntax follows that of [http://www.rasmol.org/ Rasmol] with some modifications. In order to handle the transform of each molecule and polygon separately, every files are set to be either selected or not selected. The transform operation commands, such as rotate or translate, act only on selected files. On the other hand, every atoms in a molecule are also set to be either selected or not selected independently of whether the molecule itself is selected or not selected. Only selected atoms are the target of display model operations, such as wireframe or spacefill commands, and coloring operations.

[[Release note]]
== How to use ==
The following table shows hot to do the minimum things with jV.&lt;br /&gt;
{| class="wikitable" border="1" style="margin:0 auto" 
 ! Action !! Window, Linux !! Mac OS X 
 |-
 ! style="text-align:left" | rotate around X,Y axes
 | left drag || mouse drag
 |-
 ! style="text-align:left" | rotate around Z axis
 | Shift + right drag || Shift + command + drag
 |-
 ! style="text-align:left" | translate along X,Y axes
 | right drag || command + drag
 |-
 ! style="text-align:left" | translate along Z axis (zoom in/out)
 | Shift + left drag || Shift + drag
 |}
For the detail,&lt;br /&gt;

; The install manual
* [[Installation of jV3]]
; The reference manual
pdf file : [[Installation of jV3#Download Manual]]
* User's Guide 
# [[Tutorials]]
# [[GUI]]
# [[Document type of the polygon file]]
# [[Functional site information for molecules]]
* Manual 
# [[Command List]]
# [[Atom Expression]]
# [[Vertex Expression]]
# [[Color Expression]]
# [[Use as Applet]]

;Some examples
# [[Animation]]
# [[User jV with applet launcher]]</text>
    <sha1>c7cb7db02cd4a2ff95bddd5c2ab640a84a7b4e2c</sha1>
  </revision>
  <revision>
    <id>293</id>
    <parentid>263</parentid>
    <timestamp>2009-04-23T00:36:07Z</timestamp>
    <contributor>
      <username>WikiSysop</username>
      <id>1</id>
    </contributor>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="1026" xml:space="preserve">== How to use ==
The following table shows hot to do the minimum things with jV.&lt;br /&gt;
{| class="wikitable" border="1" style="margin:0 auto" 
 ! Action !! Window, Linux !! Mac OS X 
 |-
 ! style="text-align:left" | rotate around X,Y axes
 | left drag || mouse drag
 |-
 ! style="text-align:left" | rotate around Z axis
 | Shift + right drag || Shift + command + drag
 |-
 ! style="text-align:left" | translate along X,Y axes
 | right drag || command + drag
 |-
 ! style="text-align:left" | translate along Z axis (zoom in/out)
 | Shift + left drag || Shift + drag
 |}
For the detail,&lt;br /&gt;

; The install manual
* [[Installation of jV3]]
; The reference manual
pdf file : [[Installation of jV3#Download Manual]]
* User's Guide 
# [[Tutorials]]
# [[GUI]]
# [[Document type of the polygon file]]
# [[Functional site information for molecules]]
* Manual 
# [[Command List]]
# [[Atom Expression]]
# [[Vertex Expression]]
# [[Color Expression]]
# [[Use as Applet]]

;Some examples
# [[Animation]]
# [[User jV with applet launcher]]</text>
    <sha1>c35fed7d48646605520f3be97ea7598a41d84d55</sha1>
  </revision>
  <revision>
    <id>294</id>
    <parentid>293</parentid>
    <timestamp>2009-04-23T00:36:37Z</timestamp>
    <contributor>
      <username>WikiSysop</username>
      <id>1</id>
    </contributor>
    <minor/>
    <comment>moved [[JV version 3]] to [[How to use]]</comment>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="1026" xml:space="preserve">== How to use ==
The following table shows hot to do the minimum things with jV.&lt;br /&gt;
{| class="wikitable" border="1" style="margin:0 auto" 
 ! Action !! Window, Linux !! Mac OS X 
 |-
 ! style="text-align:left" | rotate around X,Y axes
 | left drag || mouse drag
 |-
 ! style="text-align:left" | rotate around Z axis
 | Shift + right drag || Shift + command + drag
 |-
 ! style="text-align:left" | translate along X,Y axes
 | right drag || command + drag
 |-
 ! style="text-align:left" | translate along Z axis (zoom in/out)
 | Shift + left drag || Shift + drag
 |}
For the detail,&lt;br /&gt;

; The install manual
* [[Installation of jV3]]
; The reference manual
pdf file : [[Installation of jV3#Download Manual]]
* User's Guide 
# [[Tutorials]]
# [[GUI]]
# [[Document type of the polygon file]]
# [[Functional site information for molecules]]
* Manual 
# [[Command List]]
# [[Atom Expression]]
# [[Vertex Expression]]
# [[Color Expression]]
# [[Use as Applet]]

;Some examples
# [[Animation]]
# [[User jV with applet launcher]]</text>
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    <text bytes="1009" xml:space="preserve">The following table shows hot to do the minimum things with jV.&lt;br /&gt;
{| class="wikitable" border="1" style="margin:0 auto" 
 ! Action !! Window, Linux !! Mac OS X 
 |-
 ! style="text-align:left" | rotate around X,Y axes
 | left drag || mouse drag
 |-
 ! style="text-align:left" | rotate around Z axis
 | Shift + right drag || Shift + command + drag
 |-
 ! style="text-align:left" | translate along X,Y axes
 | right drag || command + drag
 |-
 ! style="text-align:left" | translate along Z axis (zoom in/out)
 | Shift + left drag || Shift + drag
 |}
For the detail,&lt;br /&gt;

; The install manual
* [[Installation of jV3]]
; The reference manual
pdf file : [[Installation of jV3#Download Manual]]
* User's Guide 
# [[Tutorials]]
# [[GUI]]
# [[Document type of the polygon file]]
# [[Functional site information for molecules]]
* Manual 
# [[Command List]]
# [[Atom Expression]]
# [[Vertex Expression]]
# [[Color Expression]]
# [[Use as Applet]]

;Some examples
# [[Animation]]
# [[User jV with applet launcher]]</text>
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    <text bytes="1133" xml:space="preserve">The following table shows how to do the minimum things with jV; the mouse controls.&lt;br /&gt;
{| class="wikitable" border="1" style="margin:0 auto" 
 ! Action !! Window, Linux !! Mac OS X 
 |-
 ! style="text-align:left" | rotate around X,Y axes
 | left drag || drag
 |-
 ! style="text-align:left" | rotate around Z axis
 | Shift + right drag || Shift + command + drag
 |-
 ! style="text-align:left" | translate along X,Y axes
 | right drag || command + drag
 |-
 ! style="text-align:left" | translate along Z axis (zoom in/out)
 | Shift + left drag || Shift + drag
 |-
 ! style="text-align:left" | translate slab plane along Z axis
 | (Alt or Ctrl) + left drag || Alt + drag
 |}
For the detail,&lt;br /&gt;

; The install manual
* [[Installation of jV3]]
; The reference manual
pdf file : [[Installation of jV3#Download Manual]]
* User's Guide 
# [[Tutorials]]
# [[GUI]]
# [[Document type of the polygon file]]
# [[Functional site information for molecules]]
* Manual 
# [[Command List]]
# [[Atom Expression]]
# [[Vertex Expression]]
# [[Color Expression]]
# [[Use as Applet]]

;Some examples
# [[Animation]]
# [[User jV with applet launcher]]</text>
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    <text bytes="1083" xml:space="preserve">The following table shows how to do the minimum things with jV; the mouse controls.
For the detail, see the reference manual and User's guide.&lt;br /&gt;
{| class="wikitable" border="1" style="margin:0 auto" 
 ! Action !! Window, Linux !! Mac OS X 
 |-
 ! style="text-align:left" | rotate around X,Y axes
 | left drag || drag
 |-
 ! style="text-align:left" | rotate around Z axis
 | Shift + right drag || Shift + command + drag
 |-
 ! style="text-align:left" | translate along X,Y axes
 | right drag || command + drag
 |-
 ! style="text-align:left" | translate along Z axis (zoom in/out)
 | Shift + left drag || Shift + drag
 |-
 ! style="text-align:left" | translate slab plane along Z axis
 | (Alt or Ctrl) + left drag || Alt + drag
 |}


; The reference manual
# [[Introduction]]
# [[Command List]]
# [[Atom Expression]]
# [[Vertex Expression]]
# [[Color Expression]]
# [[Use as Applet]]

; User's Guide 
# [[Tutorials]]
# [[GUI]]
# [[Document type of the polygon file]]
# [[Functional site information for molecules]]

;Some examples
# [[Animation]]
# [[User jV with applet launcher]]</text>
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    <text bytes="1802" xml:space="preserve">== jV version 1 (PDBjViewer) ==
Visualization of structure and surface of molecules is performed by a Java applet program called 'PDBjViewer'.

In order to use PDBjViewer, [http://java.sun.com/products/plugin/ Java Plug-in] and
[http://java.sun.com/products/java-media/3D/ Java 3D API] must be installed on your computer.
The version requirements are as follows.&lt;br /&gt;
* JRE (includes Java Plug-in) 1.4.1 or later (recommend 1.4.2)
* Java 3D API (OpenGL) 1.2.1 or later (recommend 1.2.1_04)
Important notes
# You can select two kinds of implementation of Java 3D, OpenGL version and DirectX version. But, PDBjViewer only work with OpenGL version at present.
# PDBjViewer does not work with JRE from 1.4.1_03 to 1.4.1_06.&lt;br /&gt;

== jV version 2 ==
jV version 2 is an advanced version of PDBjViewer, which can be used only as a stand-alone program. It enables to display more than one molecule images at the same time and their display models and transforms can be operated separately. An animation of molecules can be also performed. jV version 2 runs with .NET framework 1.1 on the Windows platform. Therefore the .NET framework must be installed on your computer.

== Download older versions ==
To get the older versions (if you want).
* Ver. 1&amp;2
** [http://ef-site.hgc.jp/eF-site/servlet/DownloadViewerBinary binary]
** [http://ef-site.hgc.jp/eF-site/servlet/Registration source code]
** JOGL1.0 [[http://ef-site.hgc.jp/eF-site/jV/JOGL1.0_win32.zip Windows], [http://ef-site.hgc.jp/eF-site/jV/JOGL1.0_macosx.tar.gz Mac OSX], [http://ef-site.hgc.jp/eF-site/jV/JOGL1.0_linux.tar.gz Linux]]
** JOGL 1.1.1 [[http://ef-site.hgc.jp/eF-site/jV/JOGL1.1.1_win32.zip Windows], [http://ef-site.hgc.jp/eF-site/jV/JOGL1.1.1_macosx.tar.gz Mac OS X], [http://ef-site.hgc.jp/eF-site/jV/JOGL1.1.1_linux.tar.gz Linux]]</text>
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** How to use|How to use
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** Release_note | Release note
** Links|Links
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    <text bytes="302" xml:space="preserve">* contents
** Installation_of_jV3 | Installation
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    <text bytes="332" xml:space="preserve">* contents
** Installation_of_jV3 | Installation
** How to use|How to use
** Links|Links
** old version|Older versions
* navigation
** mainpage|mainpage-description
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** helppage|help
* SEARCH
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    <text bytes="329" xml:space="preserve">* contents
** Installation_of_jV3 | Installation
** How to use|How to use
** Links|Links
** old version|Old version
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    <text bytes="2688" xml:space="preserve">Changes and improvements have been made as follows.

* version 3.1
** The following commands have been added; 'animrange', 'set adjustview', 'show godata', and 'show xps3'.
** The xPSSS expression has been added in order to select a group of atoms.
** Several public methods have been added to the applet so as to append molecule or polygon files after the applet started.
** The applet can send information about mouse-picked atoms to JavaScript.
* version 3.1.1
** Some problems in GUI menu [Options]-[Hetero Atoms] and [Hydrogens] have been fixed.
** Some problems in 'trace' command have been fixed.
* version 3.1.2
** eF-site ID has been changed to a new format.
* version 3.1.3
** Some problems in xps3 atom selection have been fixed.
* version 3.1.4
** Some problems in finalization process of openGL rendering have been fixed.
* version 3.1.5
** The output of 'show xps3' command has been modified.
** Some problems in 'save png/jpeg' command have been fixed.
* version 3.1.6
** Some problems in loading an empty polygon file have been fixed.
* version 3.1.7
** Some problems in initialization process of the applet have been fixed.
* version 3.2
** 'show site' command has been added.
* version 3.3 beta 1
** Availabe JOGL version is restricted to JSR-231 beta 5 only.
* version 3.3
** Both the previous JOGL (version 1.1.1) and JSR-231 are available.
** The following commands have been added; 'set viewpoint', 'show viewpoint', 'set imagesize', and 'show imagesize'.
* version 3.3.1
** Some problems in reading a pdbMLplus file have been fixed.
* version 3.4
** PDB format version 3 can be processed.
* version 3.5
** Discrimination of DNA and RNA linking nucleotides is based on [http://remediation.wwpdb.org/downloads.html Chemical Component Dictionary] for PDB format version 3.
** The default representation of the cartoon model has been changed. Commands 'set cartoon_loop_tube', 'set cartoon_round' and 'set ribbonback' have been added.
** The default parameters of lighting have been changed. Commands 'set ambient', 'set diffuse1', 'set diffuse1_direction', 'set diffuse2' and 'set diffuse1_direction' have been added.
** Commands 'set pdbml_noatom_url', 'set pdbml_extatom_url', 'set pdbml_plus_url', 'set efsite_url', 'set ext_site_url', 'show pdbml_url', 'show efsite_url' and 'show ext_site_url' have been added.
** The command-line option '-stdin' has been added to receive commands from stdin stream.
* version 3.6
** Users can specify the JavaScript function name used in Applet-to-JavaScript Communication.
** Applet parameter 'file_load_message' has been added.
* version 3.6.1
** Predefined set of residues has been modified.
** Old JOGL API is not supported.</text>
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  <title>Command List</title>
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  |__TOC__
  |}
Command usage of jV follows that of [http://www.rasmol.org/ Rasmol] with some modifications. In the following part, command arguments that can take an arbitrary value are denoted as &lt;value&gt; for example, arguments restricted to several possible values are listed with / as a delimiter, and arguments that can be omitted are put in brackets {}.
== anim ==
 anim forward {&lt;value&gt;}
Starts animation forward. If the &lt;value&gt; is given, just move frames forward by the specified amount.

 anim backward {&lt;value&gt;}
Starts animation backward. If the &lt;value&gt; is given, just move frames backward by the specified amount.

 anim stop
Stops animation.

== animframe ==
 animframe &lt;frame&gt; {&lt;file_ID&gt;}
Sets the frame of all animation files for the specified value. When &lt;file_ID&gt; is given, only the specified file is processed.

== animmode ==
 animmode once
Sets the behavior of animation for 'once'. When the frame reaches the last one, animation is stopped.

 animmode loop
Sets the behavior of animation for 'loop'. When the frame reaches the last one, animation is reset to the first frame and continues playing.

 animmode swing
Sets the behavior of animation for 'swing'. When the frame reaches the last one, the direction of animation is reversed.

== animrange ==
 animrange &lt;init_frame&gt;-&lt;term_frame&gt; {&lt;file_IDs&gt;}
Sets the range of all animation files. When is given, only the specified file is processed.

== animselect ==
 animselect {-a/-r} &lt;file_IDs&gt;
Selects the specified files and makes the others not selected. More than one file IDs can be specified by putting commas as the delimiter. When the option -a or -r is specified, only the selection status of the specified files are modified, selected or not selected, respectively, and the others remain unchanged.

== animspeed ==
 animspeed &lt;speed&gt;
Sets the animation speed. The argument should be an integer value from 1 to 20.

== animstep ==
 animstep &lt;step&gt; {&lt;file_ID&gt;}
Sets the step of all animation files for the specified value. When &lt;file_ID&gt; is given, only the specified file is processed.

== backbone ==
 backbone {on/true}
Turns on the selected backbone bonds.

 backbone off/false
Turns off the selected backbone bonds.

 backbone &lt;radius&gt;
Turns on the selected backbone bonds with the specified raidus (angstrom or Rasmol unit). The maximum parameter value is 2.0.

== background ==
 background &lt;color&gt;
Changes the background color. The color may be given as RGB values [r,g,b], or predefined color names.

== cartoon ==
 cartoon {on/true}
Turns on the thick ribbons for the selected residues.

 cartoon off/false
Turns off the thick ribbons for the selected residues.

 cartoon &lt;half_width&gt;
Turns on the thick ribbons for the selected residues with the specified half width (angstrom or Rasmol unit). The maximum parameter value is 4.0.

== center ==
 center {-r/-s} {&lt;atom_expression&gt;}
Sets the center of rotation and the center of the screen to the center of a group of atoms specified by the atom expression. When the option -r or -s is specified, only the center of rotation or the center of the screen is modified, respectively.

 center {-r} [x, y, z]
Moves the center of rotation and the center of the screen from the current position by the specified amount. When the option -r is specified, only the center of rotation is modified.

 center {-r} {x, y, z}
Sets the center of rotation and the center of the screen to the specified coordinates. When the option -r is specified, only the center of rotation is modified.

 center -s [x, y]
Moves the center of the screen from the current position by the specified amount.

 center -s {x, y}
Sets the center of the screen to the specified coordinates.

== color ==
 color {atoms} &lt;color&gt;
Sets the color of the selected atoms. The color may be given as RGB values [r,g,b], predefined color names, or predefined color schemes; amino, chain, charge, cpk, group, shapely, structure, and temperature.

 color bonds/backbone/ribbons/hbonds/ssbonds &lt;color&gt;
Sets the color of the specified object. The color may be given as RGB values [r,g,b] or predefined color names. For hydrogen bonds, color scheme 'type' can be specified.

 color bonds/backbone/ribbons/hbonds/ssbonds none
Resets the color of the specified object.

== colorvertex ==
 colorvertex &lt;color&gt;
Sets the color of the selected vertices. The color may be given as RGB values [r,g,b] or predefined color names.

 colorvertex none
Resets the color of the selected vertices.

== cpk ==
 cpk
A synonym of the spacefill command.

== define ==
 define &lt;name&gt; &lt;atom_expression&gt;
Associates an arbitrary set of atoms with a unique name.

== display ==
 display all
Displays the image of all files.

 display none
Turns off the image of all files.

 display {-a/-r} &lt;file_IDs&gt;
Displays the image of the specified files and turns off the others. More than one file IDs can be specified by putting commas as the delimiter. When the option -a or -r is specified, turns the image of the specified files on or off, respectively, and the others remain unchanged.

== displayvertex ==
 displayvertex {on/true}
Displays the selected vertices.

 displayvertex off/false
Turns off the selected vertices.

== echo ==
 echo &lt;string&gt;
Echoes the specified message back to the message area.

== exit ==
 exit
Terminates the application.

== fit ==
 fit &lt;file1_ID&gt; &lt;file2_ID&gt;
Sets the transform matrix of file1 identical to that of file2. 

== fselect ==
 fselect all
Selects all files.

 fselect none
Selects no files.

 fselect {-a/-r} &lt;file_IDs&gt;
Selects the specified files and makes the others not selected. More than one file IDs can be specified by putting commas as the delimiter. When the option -a or -r is specified, only the selection status of the specified files are modified, selected or not selected, respectively, and the others remain unchanged.

== hbonds ==
 hbonds {on/true}
Turns on the selected hydrogen bonds.

 hbonds off/false
Turns off the selected hydrogen bonds.

 hbonds &lt;radius&gt;
Turns on the selected hydrogen bonds with the specified raidus (angstrom or Rasmol unit). The maximum parameter value is 2.0. 

== load ==
 load {pdbml} &lt;filename&gt; {fit &lt;file_ID&gt;}
Opens a PDBML file. URL can be used to open a remote file. On loading, the transform matrix can be set identical to that of the specified file.

 load pdb &lt;filename&gt; {fit &lt;file_ID&gt;}
Opens a PDB file. URL can be used to open a remote file. On loading, the transform matrix can be set identical to that of the specified file.

 load polygon &lt;filename&gt; {fit &lt;file_ID&gt;}
Opens a polygon file. URL can be used to open a remote file. On loading, the transform matrix can be set identical to that of the specified file.

 load animation &lt;filename&gt; {fit &lt;file_ID&gt;}
Opens an animation file. URL can be used to open a remote file. On loading, the transform matrix can be set identical to that of the specified file.

 load ftp &lt;PDB_code&gt; {fit &lt;file_ID&gt;}
Retrieves a PDBML file from the PDBj FTP site and opens it. On loading, the transform matrix can be set identical to that of the specified file. 

== pause ==
 pause
Stops the execution of a script file until any key is pressed to restart. 

== quit ==
 quit
A synonym of the exit command. 

== refresh ==
 refresh
Redraws all images. 

== reset ==
=== default ===
 reset
Restores the original viewing transformation of all images, the center of rotation, and the view point. 

=== cartoon ===
 reset cartoon
Restores the thickness of the cartoon representation. 

=== line_width ===
 reset line_width
Restores the width of lines in polygon images. 

=== pickradius ===
 reset pickradius
Restores the mouse-pickable region of each atom. 

=== point_size ===
 reset point_size
Restores the size of points in polygon images. 

=== polyline_width ===
 reset polyline_width
Restores the width of polylines in polygon images. 

=== transparency ===
 reset transparency
Restores the transparency of polygon images.

 reset point_transparency
Restores the transparency of points in polygon images.

 reset line_transparency
Restores the transparency of lines in polygon images.

 reset triangle_transparency
Restores the transparency of triangles in polygon images.

 reset quad_transparency
Restores the transparency of quads in polygon images.

 reset polyline_transparency
Restores the transparency of polylines in polygon images. 

== ribbons ==
 ribbons {on/true}
Turns on the ribbon surfaces for the selected residues.

 ribbons off/false
Turns off the ribbon surfaces for the selected residues.

 ribbons &lt;half_width&gt;
Turns on the ribbon surfaces for the selected residues with the specified half width (angstrom or Rasmol unit). The maximum parameter value is 4.0. 

== rotate ==
 rotate x/y/z &lt;angle&gt;
Rotates images about the specified axis by the specified angle in degrees. 

== save ==
 save {pdb} &lt;filename&gt;
Saves the currently selected set of atoms in a PDB format file.

 save script &lt;filename&gt;
Creates a script file that reproduces the currently displayed image.

 save png &lt;filename&gt;
Creates a PNG image file of the currently displayed image.

 save jpeg &lt;filename&gt; {&lt;quality&gt;}
Creates a JPEG image file of the currently displayed image. The compression quality can be specified, 0 &lt; quality &lt;= 1, where 'quality = 1' means no compression. 

== script ==
 script &lt;filename&gt;
Opens and executes the specified script file. URL can be used to open a remote file. 

== select ==
 select
Selects all atoms. Whether hetero atoms and hydrogens are selected or not depends on the internal parameters, hetero and hydrogen, respectively.

 select all
Selects all atoms including hetero atoms and hydrogens.

 select none
Selects no atoms.

 select &lt;atom_expression&gt;
Selects a group of atoms specified by the atom expression. 

== selectvertex ==
 selectvertex {all}
Selects all vertices.

 selectvertex none
Selects no vertices.

 selectvertex &lt;vertex_expression&gt;
Selects a group of vertices specified by the vertex expression. 

== set ==
=== adjustview ===
 set adjustview on
The view point is automatically adjusted when a new file is loaded.

 set adjustview off
The view point is kept unchanged when a new file is loaded. 

=== background ===
 set background &lt;color&gt;
Changes the background color. The color may be given as RGB values [r,g,b], or predefined color names. 

=== bondmode ===
 set bondmode and
Specifies how to select an individual bonds. A bond is selected when both atoms connected by the bond are selected.

 set bondmode or
Specifies how to select an individual bonds. A bond is selected when either of the connected atoms is selected. 

=== cartoon ===
 set cartoon {&lt;value&gt;}
Specifies the thickness of the cartoon representation (angstrom or Rasmol unit). The maximum parameter value is 2.0. When the parameter is not specified, it is restored to the default value. 

=== center ===
 set center &lt;atom_expression&gt;
Sets the default center of the selected files to the center of the specified atoms.

 set center [x, y, z]
Sets the default center of the selected files to the specified coordinates. 

=== drawlevel ===
 set drawlevel &lt;value&gt;
Specifies precision of the rendering of spheres and cylinders. The value may be given as an integer (minimum 5) that stands for the number of straight line segments to represent an arc of 180 degrees. 

=== hbonds ===
 set hbonds backbone
Hydrogen bonds are displayed between backbones.

 set hbonds sidechain
Hydrogen bonds are displayed between sidechains. 

=== hetero ===
 set hetero on
Sets the default behavior of the select command such that hetero atoms are selected.

 set hetero off
Sets the default behavior of the select command such that hetero atoms are not selected. 

=== hydrogen ===
 set hydrogen on
Sets the default behavior of the select command such that hydrogens are selected.

 set hydrogen off
Sets the default behavior of the select command such that hydrogens are not selected. 

=== imagesize ===
 set imagesize &lt;width&gt; &lt;height&gt;
Sets the size of the 3D-rendering panel in pixels. The size will be set within the screen size with the width being an even integer. 

=== line_width ===
 set line_width &lt;value&gt;
Sets the width of lines in polygon images. The &lt;value&gt; should be larger than 0. 

=== loadcenter ===
 set loadcenter on
When a file is opened, sets the default center of that file to the center of all files that have already opened.

 set loadcenter off
When a file is opened, sets the default center of that file according to its own coordiantes. 

=== picking ===
 set picking off
Turns off the mouse picking.

 set picking ident
Sets the mouse picking behavior to show atom identification.

 set picking coord
Sets the mouse picking behavior to show atom coordinates with identification.

 set picking distance
Sets the mouse picking behavior to show the distance between atoms successively picked.

 set picking center
Sets the mouse picking behavior to specify the center of rotation and center of the screen.

 set picking select
Sets the mouse picking behavior to select the file that contains the atom picked. 

=== pickradius ===
 set pickradius &lt;value&gt;
Sets the mouse-pickable region of each atom to be the sphere centered to each atom with the specified radius (angstrom or Rasmol unit). 

=== point_size ===
 set point_size &lt;value&gt;
Sets the size of points in polygon images. The &lt;value&gt; should be larger than 0. 

=== polyline_width ===
 set polyline_width &lt;value&gt;
Sets the width of polylines in polygon images. The &lt;value&gt; should be larger than 0. 

=== projection ===
 set projection perspective
Sets the projection mode for a perspective projection.

 set projection parallel {&lt;size&gt;}
Sets the projection mode for a parallel projection. The size of image (fit to the height of the screen) can be specified (angstrom or Rasmol unit). 

=== specular ===
 set specular on/true
Enables the display of specular highlights on solid objects.

 set specular off/false
Disables the display of specular highlights on solid objects.

 set specular &lt;value&gt;
Enables the display of specular highlights on solid objects. The value between 0 and 100 specifies the specular color in gray scale with 0 and 100 being black and white, respectively. The default value is 50.0. 

=== specpower ===
 set specpower &lt;value&gt;
Sets the shininess of solid objects. The value between 0 and 100 specifies a material reflection coefficient with 0 being diffuse surfaces and 100 being shiny surfaces. 

=== ssbonds ===
 set ssbonds backbone
Disulfide bonds are displayed between backbones.

 set ssbonds sidechain
Disulfide bonds are displayed between sidechains. 

=== stereo ===
 set stereo
A synonym of the stereo command. 

=== transparency ===
 set transparency &lt;value&gt;
Sets the transparency of polygon images.

 set point_transparency &lt;value&gt;
Sets the transparency of points in polygon images.

 set line_transparency &lt;value&gt;
Sets the transparency of lines in polygon images.

 set triangle_transparency &lt;value&gt;
Sets the transparency of triangles in polygon images.

 set quad_transparency &lt;value&gt;
Sets the transparency of quads in polygon images.

 set polyline_transparency &lt;value&gt;
Sets the transparency of polylines in polygon images. 

=== viewpoint ===
 set viewpoint {x, y, z}
Sets the viewpoint to the specified coordinates. 

== show ==
 show godata
Displays gene ontology data of molecules.

 show imagesize
Displays the size of the 3D-rendering panel.

 show information
Displays a detail discription of molecules.

 show site {&lt;prefix&gt;:&lt;db&gt;:&lt;category&gt;}
Displays site information in an external database.

 show transform
Displays the transform matrix of molecules.

 show viewpoint
Displays the current viewpoint.

 show xps3
Displays keywords available in xps3 selection. 

== slab ==
 slab {on/true}
Enables the z-clipping plane of molecules and polygons.

 slab off/false
Disables the z-clipping plane of molecules and polygons.

 slab &lt;ratio&gt;
Sets the position of the z-clipping plane of molecules and polygons. The parameter may be given as a number from 0 to 100. The values 0 and 100 represent that image as a whole is completely invisible and visible, respectively.

 slab -v &lt;value&gt;
Sets the position of the z-clipping plane of molecules and polygons by specifying the z coordinate value. 

== spacefill ==
 spacefill {on/true}
Turns on the ball image of the selected atoms.

 spacefill off/false
Turns off the ball image of the selected atoms.

 spacefill &lt;radius&gt;
Turns on the ball image of the selected atoms with the specified radius (angstrom or Rasmol unit). The maximum parameter value is 3.0.

 spacefill temperature
Turns on the ball image of the selected atoms using the temperature factor as radius. 

== ssbonds ==
 ssbonds {on/true}
Turns on the selected disulfide bonds.

 ssbonds off/false
Turns off the selected disulfide bonds.

 ssbonds &lt;radius&gt;
Turns on the selected disulfide bonds with the specified raidus (angstrom or Rasmol unit). The maximum parameter value is 2.0. 

== stereo ==
 stereo {on/true}
Enables stereo display. This command without arguments cycles three state; 'stereo off', 'stereo on' in cross-eyed mode and 'stereo on' in parallel-eyed mode.

 stereo off/false
Disables stereo display.

 stereo &lt;angle&gt;
Enables stereo display with the specified separation angle. Positive and negative values represent cross-eyed and parallel-eyed viewing, respectively.


== structure ==
 structure
Estimates the secondary structure using Kabsch and Sander's DSSP algorithm. 

== trace ==
 trace {on/true}
Turns on a tube representation for the selected residues.

 trace off/false
Turns off a tube representation for the selected residues.

 trace &lt;radius&gt;
Turns on a tube representation for the selected residues with the specified radius (angstrom or Rasmol unit). The maximum parameter value is 2.0.


== translate ==
 translate x/y/z &lt;value&gt;
Moves images along the specified axis by the specified amount (angstrom). 

== wireframe ==
 wireframe {on/true}
Turns on the selected bonds.

 wireframe off/false
Turns off the selected bonds.

 wireframe &lt;radius&gt;
Turns on the selected bonds with the specified raidus (angstrom or Rasmol unit). The maximum parameter value is 2.0. 

== write ==
 write
A synonym of the save command. 

== zap ==
 zap {&lt;file_IDs&gt;}
Closes the specified files. More than one file IDs can be specified by putting commas as the delimiter. When the paraneter is absent, all files are closed. 

== zoom ==
 zoom {&lt;value&gt;}
Sets the magnification of the image as a whole. The value stands for the magnification as a percentage of the current scale. The minimum parameter value is 10.0.</text>
    <sha1>35ea954634228ea4c8fa54daf420d7f49d898f24</sha1>
  </revision>
</page>
<page arvcontinue="20090309114529|254">
  <title>JV:About</title>
  <ns>4</ns>
  <id>39</id>
  <revision>
    <id>274</id>
    <timestamp>2009-03-16T03:19:50Z</timestamp>
    <contributor>
      <username>WikiSysop</username>
      <id>1</id>
    </contributor>
    <comment>Created page with 'In jV wiki, the directions for jV and the report about installation can be referred to.   The program 'jV' has been developed by Kengo Kinoshita ([http://www.ims.u-tokyo.ac.jp/im...'</comment>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="637" xml:space="preserve">In jV wiki, the directions for jV and the report about installation can be referred to. 

The program 'jV' has been developed by Kengo Kinoshita ([http://www.ims.u-tokyo.ac.jp/imsut/en/ The Institute of Medical Science, The University of Tokyo]) and Haruki Nakamura ([http://www.protein.osaka-u.ac.jp/index_e.php Institute for Protein Research, Osaka Univeristy]), as one of the activities of Protein Data Bank Japan ([http://www.pdbj.org/index.html PDBj]), supported by grant-in-aid from Institute for Bioinformatics Research and Development, Japan Science and Technology Corporation ([http://www-bird.jst.go.jp/index_e.html BIRD-JST]).</text>
    <sha1>a28e1ee7e0b98de632f0a80533a8641ea9e26ad7</sha1>
  </revision>
</page>
<page arvcontinue="20090309114529|254">
  <title>JV:Privacy policy</title>
  <ns>4</ns>
  <id>40</id>
  <revision>
    <id>276</id>
    <timestamp>2009-03-16T05:34:02Z</timestamp>
    <contributor>
      <username>WikiSysop</username>
      <id>1</id>
    </contributor>
    <comment>Created page with 'jV is WEB service using Mediawiki which is a WIKI system. So, personal information, such as an access log, a mail address, a password, and Cookie, is dealt with. We promises to r...'</comment>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="4408" xml:space="preserve">jV is WEB service using Mediawiki which is a WIKI system. So, personal information, such as an access log, a mail address, a password, and Cookie, is dealt with. We promises to respect the privacy of everybody of use and to protect this in this handling.

== About security ==
About the information on the contents that the individual offered from users can be specified, it is striving for the loss / disclosure prevention, improper use prevention, alteration prevention, and destructive prevention using the rational security means. However, since it is impossible to secure absolute security, please understand the point.

=== About discernment of account and a writer ===
In jV, in order to perform contribution and edit of a report, it is necessary to perform a user registration. Under the present circumstances, a user will register an account name, a password, a mail address, and a real name (arbitrary). After it is checked that a mail address exists really, the contribution and edit of a report are permitted to the owner of the account.

=== About Password ===
If logged in to jV, it not only can perform contribution and edit of a report, but it will become possible the mail address of the account used for login, and to peruse and edit a real name (if registered). If contribution and edit of a report are performed, the act will remain in the edit history of jV. In order to keep the order of disclosure of personal information, and report creation, please do not make absolute public presentation and a share according to people two or more of a password. And please use the password which is hard to be used by stealth.

=== About Cookie ===
jV uses Mediawiki which is a WIKI system. If the WEB site of jV is visited, this system will publish Cookie. In order to log in to jV, it is necessary to permit Cookie. An end of a session will cancel Cookie. Since the time and effort which enters an account password is saved next time at the time of a visit, it is possible to set up the Cookie for performing this abbreviation. This Cookie is saved for 30 days. In order not to make other users use own account, please delete the cash of the Cookie and a browser.

== About User information ==
 As above-mentioned, in order to perform contribution and edit of a report, it is necessary to perform a user registration by jV. Under the present circumstances, a user will register an account name, a password, a mail address, and a real name (arbitrary). Moreover, in jV, I collect access logs as a material for providing the more substantial service.

=== About the use range of the collected information ===
About the information which can specify the individual who collected, preservation, use, and analysis are conducted within the limits of employment of jV. Moreover, what can specify an individual among the collected information shall be used according to the place which this privacy policy appoints.

# When asked based on a legal basis.
# When the consent about the indication to a third party has been especially obtained from the donor with offer of information
# When transferring the management of employment of jV to a third party, it sets in the range required for fulfillment of the business concerned. The rational measure is taken in order to prevent disclosing the collected information by chance to a third party.

== About deletion of contribution Brock and a report ==
When the act which bars smooth employment of jV occurs, deletion of contribution Brock and a report may be performed by [[Dbpwiki:administrator | administrator]] of jV. The judgment is entrusted with the task of [[Dbpwiki:administrator | administrator]] of jV. As long as the statement of principles of jV is followed, you may have it thought that deletion of contribution Brock and a report is not performed, but when a malicious act which passes it through is revealed, deletion of contribution Brock and a report may be too performed by administrator authority.

== About deletion of account ==
Warning is emitted from [[Dbpwiki:administrator | administrator]] by the writer who did the malicious act. A user registration may be erased when a still malicious act continues.

== About change of pribacy policy ==
The administrator of jV can change the contents of this privacy policy suitably. When the contents of the privacy policy are changed, it notifies on this site and users attention is urged.</text>
    <sha1>4957888f03162a4839291efc51cc25f82513f14b</sha1>
  </revision>
  <revision>
    <id>277</id>
    <parentid>276</parentid>
    <timestamp>2009-03-16T05:37:28Z</timestamp>
    <contributor>
      <username>WikiSysop</username>
      <id>1</id>
    </contributor>
    <comment>/* About User information */</comment>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="4407" xml:space="preserve">jV is WEB service using Mediawiki which is a WIKI system. So, personal information, such as an access log, a mail address, a password, and Cookie, is dealt with. We promises to respect the privacy of everybody of use and to protect this in this handling.

== About security ==
About the information on the contents that the individual offered from users can be specified, it is striving for the loss / disclosure prevention, improper use prevention, alteration prevention, and destructive prevention using the rational security means. However, since it is impossible to secure absolute security, please understand the point.

=== About discernment of account and a writer ===
In jV, in order to perform contribution and edit of a report, it is necessary to perform a user registration. Under the present circumstances, a user will register an account name, a password, a mail address, and a real name (arbitrary). After it is checked that a mail address exists really, the contribution and edit of a report are permitted to the owner of the account.

=== About Password ===
If logged in to jV, it not only can perform contribution and edit of a report, but it will become possible the mail address of the account used for login, and to peruse and edit a real name (if registered). If contribution and edit of a report are performed, the act will remain in the edit history of jV. In order to keep the order of disclosure of personal information, and report creation, please do not make absolute public presentation and a share according to people two or more of a password. And please use the password which is hard to be used by stealth.

=== About Cookie ===
jV uses Mediawiki which is a WIKI system. If the WEB site of jV is visited, this system will publish Cookie. In order to log in to jV, it is necessary to permit Cookie. An end of a session will cancel Cookie. Since the time and effort which enters an account password is saved next time at the time of a visit, it is possible to set up the Cookie for performing this abbreviation. This Cookie is saved for 30 days. In order not to make other users use own account, please delete the cash of the Cookie and a browser.

== About User information ==
As above-mentioned, in order to perform contribution and edit of a report, it is necessary to perform a user registration by jV. Under the present circumstances, a user will register an account name, a password, a mail address, and a real name (arbitrary). Moreover, in jV, I collect access logs as a material for providing the more substantial service.

=== About the use range of the collected information ===
About the information which can specify the individual who collected, preservation, use, and analysis are conducted within the limits of employment of jV. Moreover, what can specify an individual among the collected information shall be used according to the place which this privacy policy appoints.

# When asked based on a legal basis.
# When the consent about the indication to a third party has been especially obtained from the donor with offer of information
# When transferring the management of employment of jV to a third party, it sets in the range required for fulfillment of the business concerned. The rational measure is taken in order to prevent disclosing the collected information by chance to a third party.

== About deletion of contribution Brock and a report ==
When the act which bars smooth employment of jV occurs, deletion of contribution Brock and a report may be performed by [[Dbpwiki:administrator | administrator]] of jV. The judgment is entrusted with the task of [[Dbpwiki:administrator | administrator]] of jV. As long as the statement of principles of jV is followed, you may have it thought that deletion of contribution Brock and a report is not performed, but when a malicious act which passes it through is revealed, deletion of contribution Brock and a report may be too performed by administrator authority.

== About deletion of account ==
Warning is emitted from [[Dbpwiki:administrator | administrator]] by the writer who did the malicious act. A user registration may be erased when a still malicious act continues.

== About change of pribacy policy ==
The administrator of jV can change the contents of this privacy policy suitably. When the contents of the privacy policy are changed, it notifies on this site and users attention is urged.</text>
    <sha1>c94e2f5668e7749e61011ca72b588bceaf8c867d</sha1>
  </revision>
  <revision>
    <id>278</id>
    <parentid>277</parentid>
    <timestamp>2009-03-16T05:40:18Z</timestamp>
    <contributor>
      <username>WikiSysop</username>
      <id>1</id>
    </contributor>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="4323" xml:space="preserve">jV is WEB service using Mediawiki which is a WIKI system. So, personal information, such as an access log, a mail address, a password, and Cookie, is dealt with. We promises to respect the privacy of everybody of use and to protect this in this handling.

== About security ==
About the information on the contents that the individual offered from users can be specified, it is striving for the loss / disclosure prevention, improper use prevention, alteration prevention, and destructive prevention using the rational security means. However, since it is impossible to secure absolute security, please understand the point.

=== About discernment of account and a writer ===
In jV, in order to perform contribution and edit of a report, it is necessary to perform a user registration. Under the present circumstances, a user will register an account name, a password, a mail address, and a real name (arbitrary). After it is checked that a mail address exists really, the contribution and edit of a report are permitted to the owner of the account.

=== About Password ===
If logged in to jV, it not only can perform contribution and edit of a report, but it will become possible the mail address of the account used for login, and to peruse and edit a real name (if registered). If contribution and edit of a report are performed, the act will remain in the edit history of jV. In order to keep the order of disclosure of personal information, and report creation, please do not make absolute public presentation and a share according to people two or more of a password. And please use the password which is hard to be used by stealth.

=== About Cookie ===
jV uses Mediawiki which is a WIKI system. If the WEB site of jV is visited, this system will publish Cookie. In order to log in to jV, it is necessary to permit Cookie. An end of a session will cancel Cookie. Since the time and effort which enters an account password is saved next time at the time of a visit, it is possible to set up the Cookie for performing this abbreviation. This Cookie is saved for 30 days. In order not to make other users use own account, please delete the cash of the Cookie and a browser.

== About User information ==
As above-mentioned, in order to perform contribution and edit of a report, it is necessary to perform a user registration by jV. Under the present circumstances, a user will register an account name, a password, a mail address, and a real name (arbitrary). Moreover, in jV, I collect access logs as a material for providing the more substantial service.

=== About the use range of the collected information ===
About the information which can specify the individual who collected, preservation, use, and analysis are conducted within the limits of employment of jV. Moreover, what can specify an individual among the collected information shall be used according to the place which this privacy policy appoints.

# When asked based on a legal basis.
# When the consent about the indication to a third party has been especially obtained from the donor with offer of information
# When transferring the management of employment of jV to a third party, it sets in the range required for fulfillment of the business concerned. The rational measure is taken in order to prevent disclosing the collected information by chance to a third party.

== About deletion of contribution Brock and a report ==
When the act which bars smooth employment of jV occurs, deletion of contribution Brock and a report may be performed by administrator of jV. The judgment is entrusted with the task of administrator of jV. As long as the statement of principles of jV is followed, you may have it thought that deletion of contribution Brock and a report is not performed, but when a malicious act which passes it through is revealed, deletion of contribution Brock and a report may be too performed by administrator authority.

== About deletion of account ==
Warning is emitted from administrator by the writer who did the malicious act. A user registration may be erased when a still malicious act continues.

== About change of pribacy policy ==
The administrator of jV can change the contents of this privacy policy suitably. When the contents of the privacy policy are changed, it notifies on this site and users attention is urged.</text>
    <sha1>59e04f25f573a37cd9a4317f8c5dc78a3fe5dd9d</sha1>
  </revision>
  <revision>
    <id>280</id>
    <parentid>278</parentid>
    <timestamp>2009-03-16T05:55:33Z</timestamp>
    <contributor>
      <username>WikiSysop</username>
      <id>1</id>
    </contributor>
    <comment>/* About Cookie */</comment>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="4476" xml:space="preserve">jV is WEB service using Mediawiki which is a WIKI system. So, personal information, such as an access log, a mail address, a password, and Cookie, is dealt with. We promises to respect the privacy of everybody of use and to protect this in this handling.

== About security ==
About the information on the contents that the individual offered from users can be specified, it is striving for the loss / disclosure prevention, improper use prevention, alteration prevention, and destructive prevention using the rational security means. However, since it is impossible to secure absolute security, please understand the point.

=== About discernment of account and a writer ===
In jV, in order to perform contribution and edit of a report, it is necessary to perform a user registration. Under the present circumstances, a user will register an account name, a password, a mail address, and a real name (arbitrary). After it is checked that a mail address exists really, the contribution and edit of a report are permitted to the owner of the account.

=== About Password ===
If logged in to jV, it not only can perform contribution and edit of a report, but it will become possible the mail address of the account used for login, and to peruse and edit a real name (if registered). If contribution and edit of a report are performed, the act will remain in the edit history of jV. In order to keep the order of disclosure of personal information, and report creation, please do not make absolute public presentation and a share according to people two or more of a password. And please use the password which is hard to be used by stealth.

=== About Cookie ===
jV uses Mediawiki which is a WIKI system. The sites set a temporary session cookie on a visitor's computer whenever a Project page is visted. Readers who do not intend to log in or edit may deny this cookie; it will be deleted at the end of the browser's session. More cookies may be set when one logs in to maintain logged-in status. If one saves a user name or password in one's browser, that information will be saved for up to 30 days, and this information will be resent to the server on every visit to the same Project. Contributors using a public machine who do not wish to show their username to future users of the machine should clear these cookies after use.

== About User information ==
As above-mentioned, in order to perform contribution and edit of a report, it is necessary to perform a user registration by jV. Under the present circumstances, a user will register an account name, a password, a mail address, and a real name (arbitrary). Moreover, in jV, I collect access logs as a material for providing the more substantial service.

=== About the use range of the collected information ===
About the information which can specify the individual who collected, preservation, use, and analysis are conducted within the limits of employment of jV. Moreover, what can specify an individual among the collected information shall be used according to the place which this privacy policy appoints.

# When asked based on a legal basis.
# When the consent about the indication to a third party has been especially obtained from the donor with offer of information
# When transferring the management of employment of jV to a third party, it sets in the range required for fulfillment of the business concerned. The rational measure is taken in order to prevent disclosing the collected information by chance to a third party.

== About deletion of contribution Brock and a report ==
When the act which bars smooth employment of jV occurs, deletion of contribution Brock and a report may be performed by administrator of jV. The judgment is entrusted with the task of administrator of jV. As long as the statement of principles of jV is followed, you may have it thought that deletion of contribution Brock and a report is not performed, but when a malicious act which passes it through is revealed, deletion of contribution Brock and a report may be too performed by administrator authority.

== About deletion of account ==
Warning is emitted from administrator by the writer who did the malicious act. A user registration may be erased when a still malicious act continues.

== About change of pribacy policy ==
The administrator of jV can change the contents of this privacy policy suitably. When the contents of the privacy policy are changed, it notifies on this site and users attention is urged.</text>
    <sha1>116154bb38134141ab62974b1cfde836432dc5ae</sha1>
  </revision>
</page>
<page arvcontinue="20090309114529|254">
  <title>JV:General disclaimer</title>
  <ns>4</ns>
  <id>41</id>
  <revision>
    <id>279</id>
    <timestamp>2009-03-16T05:46:49Z</timestamp>
    <contributor>
      <username>WikiSysop</username>
      <id>1</id>
    </contributor>
    <comment>Created page with 'THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHA...'</comment>
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    <text bytes="754" xml:space="preserve">THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.</text>
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<page arvcontinue="20090309114529|254">
  <title>Help:Contents</title>
  <ns>12</ns>
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    <id>282</id>
    <timestamp>2009-03-16T08:19:47Z</timestamp>
    <contributor>
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      <id>1</id>
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    <comment>Created page with 'See Help: * [http://meta.wikimedia.org/wiki/Help:Contents　MediaWiki Help]'</comment>
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    <text bytes="75" xml:space="preserve">See Help:
* [http://meta.wikimedia.org/wiki/Help:Contents　MediaWiki Help]</text>
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    <id>283</id>
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    <contributor>
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    <model>wikitext</model>
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    <text bytes="70" xml:space="preserve">See:
* [http://meta.wikimedia.org/wiki/Help:Contents　MediaWiki:Help]</text>
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  <revision>
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* [http://meta.wikimedia.org/wiki/Help:Contents　| MediaWiki Help]</text>
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  <revision>
    <id>285</id>
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      <id>1</id>
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    <text bytes="72" xml:space="preserve">See:
* [[http://meta.wikimedia.org/wiki/Help:Contents　MediaWiki Help]]</text>
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  <revision>
    <id>286</id>
    <parentid>285</parentid>
    <timestamp>2009-03-16T08:21:41Z</timestamp>
    <contributor>
      <username>WikiSysop</username>
      <id>1</id>
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    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="66" xml:space="preserve">See:
* [http://meta.wikimedia.org/wiki/Help:Contents　 MediaWiki]</text>
    <sha1>41ac6d82d08ddcd53a88f67ebf84a159c33ef4ce</sha1>
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  <revision>
    <id>287</id>
    <parentid>286</parentid>
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      <username>WikiSysop</username>
      <id>1</id>
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* [http://meta.wikimedia.org/wiki/Help　MediaWiki help]</text>
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  <revision>
    <id>288</id>
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      <username>WikiSysop</username>
      <id>1</id>
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    <text bytes="44" xml:space="preserve">See:
* [http://meta.wikimedia.org/wiki/Help]</text>
    <sha1>8e7c5ac1eb685084d7bf8caaff93837500634ebb</sha1>
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  <revision>
    <id>289</id>
    <parentid>288</parentid>
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    <contributor>
      <username>WikiSysop</username>
      <id>1</id>
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    <format>text/x-wiki</format>
    <text bytes="77" xml:space="preserve">See:
* Mediawiki Help:Contents [http://meta.wikimedia.org/wiki/Help:Contents]</text>
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</page>
<page arvcontinue="20090309114529|254">
  <title>JV version 3</title>
  <ns>0</ns>
  <id>43</id>
  <revision>
    <id>295</id>
    <timestamp>2009-04-23T00:36:37Z</timestamp>
    <contributor>
      <username>WikiSysop</username>
      <id>1</id>
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    <comment>moved [[JV version 3]] to [[How to use]]</comment>
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    <text bytes="24" xml:space="preserve">#REDIRECT [[How to use]]</text>
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</page>
<page arvcontinue="20090309114529|254">
  <title>Introduction</title>
  <ns>0</ns>
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  <revision>
    <id>300</id>
    <timestamp>2009-04-23T01:00:34Z</timestamp>
    <contributor>
      <username>WikiSysop</username>
      <id>1</id>
    </contributor>
    <comment>Created page with 'jV is an interactive 3D viewer program to visualize protein and nucleic acid molecules. The program reads in a PDBML file that is an XML format for PDB. Usual PDB format files ar...'</comment>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="1908" xml:space="preserve">jV is an interactive 3D viewer program to visualize protein and nucleic acid molecules. The program reads in a PDBML file that is an XML format for PDB. Usual PDB format files are also accepted. More than one molecule files can be opened and displayed at the same time and their display models and transforms can be operated separately. In addition to molecule files, a polygon file written in XML can be read and displayed. More than one polygon files can be opened at the same time and superposed on molecule images. The [http://ef-site.hgc.jp/eF-site/schema/polygon12.xsd XML schema] of the polygon file is available. jV can perform an animation of molecules. The animation file is a PDB format file in which each frame is separated by a MODEL line.

jV runs on Java Runtime Environment ([http://java.sun.com/j2se/1.4.2/download.html JRE]) and can be used both as a standalone program and an applet. The 3D rendering is performed with the use of [https://jogl.dev.java.net/ JOGL] API. The version requirements are as follows.

* JRE (includes Java Plug-in) 1.4.2 or later
* JOGL JSR-231

Here, [http://java.sun.com/products/plugin/ Java Plug-in] is required in order to use the program as an applet.

The program allows an interactive mouse control and command execution. The commnad syntax follows that of [http://www.rasmol.org/ Rasmol] with some modifications. In order to handle the transform of each molecule and polygon separately, every files are set to be either selected or not selected. The transform operation commands, such as rotate or translate, act only on selected files. On the other hand, every atoms in a molecule are also set to be either selected or not selected independently of whether the molecule itself is selected or not selected. Only selected atoms are the target of display model operations, such as wireframe or spacefill commands, and coloring operations.

[[Release note]]</text>
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</page>
<page arvcontinue="20090423011428|304">
  <title>Installation of jV</title>
  <ns>0</ns>
  <id>38</id>
  <revision>
    <id>304</id>
    <parentid>269</parentid>
    <timestamp>2009-04-23T01:14:28Z</timestamp>
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      <username>WikiSysop</username>
      <id>1</id>
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    <text bytes="3503" xml:space="preserve">{| style="float:right"
 |__TOC__
 |}
== System requirements ==
jV3 runs on the Java Runtime Environment (JRE) with JOGL API. The version requirements are as follows.
* [http://java.sun.com/j2se/1.4.2/download.html JRE] (includes Java Plug-in) 1.4.2 or later
* [https://jogl.dev.java.net/ JOGL] API JSR-231 1.0.0 or later 
These softwares are available on typical operation systems such as Windows (2000/XP/Vista), Mac OS X 10.3 or later, and Red Hat Linux 7.3 or later.

== Installing JOGL API ==
=== Automatic install ===
In this section, it is assumed that JRE 1.4.2 or later has been installed on your computer. Installing JOGL is just deploying several files to JRE. A tool that automatically performs the JOGL installation with a graphical user interface is available here.

* JSR-231 1.0.0 [[http://ef-site.hgc.jp/eF-site/jV/JOGL_JSR231_win32.zip Windows], [http://ef-site.hgc.jp/eF-site/jV/JOGL_JSR231_macosx_ppc.tar.gz Mac OS X ppc], [http://ef-site.hgc.jp/eF-site/jV/JOGL_JSR231_macosx_universal.tar.gz Mac OS X universal], [http://ef-site.hgc.jp/eF-site/jV/JOGL_JSR231_linux_i586.tar.gz Linux]]

=== Manual install ===
It is also possible to install JOGL manually. According to the kind of your operation system, you should get the following files from [https://jogl.dev.java.net/ JOGL].

{| class="wikitable" border="1"
 ! !! Windows !! Mac OS X !! Linux
 |-
 | JSR-231 1.1.1
 | jogl.jar&lt;br /&gt;jogl.dll&lt;br /&gt;jogl_cg.dll&lt;br /&gt;jogl_awt.dll&lt;br /&gt;gluegen-rt.jar&lt;br /&gt;gluegen-rt.dll
 | jogl.jar&lt;br /&gt;libjogl.jnilib&lt;br /&gt;libjogl_cg.jnilib&lt;br /&gt;libjogl_awt.jnilib&lt;br /&gt;gluegen-rt.jar&lt;br /&gt;libgluegen-rt.jnilib
 | jogl.jar&lt;br /&gt;libjogl.so&lt;br /&gt;libjogl_cg.so&lt;br /&gt;libjogl_awt.so&lt;br /&gt;gluegen-rt.jar&lt;br /&gt;libgluegen-rt.so
 |}

==== Windows ====
The folder that JRE has been installed is denoted by &lt;JRE&gt;. It depends on the environment, however it is typically as follows.
 &lt;JRE&gt;=C:\Program Files\Java\j2re1.4.2_12
The files ‘jogl.jar’ and ‘gluegen-rt.jar’ should be copied to &lt;JRE&gt;\lib\ext, and the other files should be copied to &lt;JRE&gt;\bin.

==== Mac OS X ====
When operating from the command terminal, you should copy all files to /Library/Java/Extensions. When operating through the graphical interface, the above destination folder is shown as ‘Macintosh HD/Library/Java/Extensions’. In this operation, the password for root is required.

==== Linux ====
The directory that JRE has been installed is denoted by &lt;JRE&gt;. It depends on the environment, however it is typically as follows.
 &lt;JRE&gt;=/usr/java/j2sdk1.4.2_12/jre
files ‘jogl.jar’ and ‘gluegen-rt.jar’ should be copied to &lt;JRE&gt;/lib/ext, and the other files should be copied to &lt;JRE&gt;/lib/i386.

== Download jV ==
[[File:Download.png|right|link=http://ef-site.hgc.jp/eF-site/servlet/DownloadViewerBinary|Download]]
* Download jV&lt;br /&gt;In order to obtain jV and PDBjViewer you must agree to the software license. 
** [http://ef-site.hgc.jp/eF-site/servlet/DownloadViewerBinary binary]&lt;br /&gt;Click right Download image.
** [http://ef-site.hgc.jp/eF-site/servlet/Registration sourcecode] &lt;br /&gt;Registration is required. When the registration is completed, a URL for downloading the source code of jV and PDBjViewer is sent to you by email. The URL is valid for 24 hours.
** [http://ef-site.hgc.jp/jV/stable/jV.jnlp Java WebStart version] for stable version.(recommended)

== Download Manual &amp; User's Guide ==
PDF file.
* [[Media:JV3_User'sGuide.pdf|User's Guide]](30 October 2006)
* [[Media:JV_manual.pdf|Manual]](30 Octover 2006)</text>
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  <revision>
    <id>306</id>
    <parentid>304</parentid>
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    <text bytes="3187" xml:space="preserve">{| style="float:right"
 |__TOC__
 |}
== System requirements ==
jV3 runs on the Java Runtime Environment (JRE) with JOGL API. The version requirements are as follows.
* [http://java.sun.com/j2se/1.4.2/download.html JRE] (includes Java Plug-in) 1.4.2 or later
* [https://jogl.dev.java.net/ JOGL] API JSR-231 1.0.0 or later 
These softwares are available on typical operation systems such as Windows (2000/XP/Vista), Mac OS X 10.3 or later, and Red Hat Linux 7.3 or later.

== Installing JOGL API ==
=== Automatic install ===
In this section, it is assumed that JRE 1.4.2 or later has been installed on your computer. Installing JOGL is just deploying several files to JRE. A tool that automatically performs the JOGL installation with a graphical user interface is available here.

* JSR-231 1.0.0 [[http://ef-site.hgc.jp/eF-site/jV/JOGL_JSR231_win32.zip Windows], [http://ef-site.hgc.jp/eF-site/jV/JOGL_JSR231_macosx_ppc.tar.gz Mac OS X ppc], [http://ef-site.hgc.jp/eF-site/jV/JOGL_JSR231_macosx_universal.tar.gz Mac OS X universal], [http://ef-site.hgc.jp/eF-site/jV/JOGL_JSR231_linux_i586.tar.gz Linux]]

=== Manual install ===
It is also possible to install JOGL manually. According to the kind of your operation system, you should get the following files from [https://jogl.dev.java.net/ JOGL].

{| class="wikitable" border="1"
 ! !! Windows !! Mac OS X !! Linux
 |-
 | JSR-231 1.0.0
 | jogl.jar&lt;br /&gt;jogl.dll&lt;br /&gt;jogl_cg.dll&lt;br /&gt;jogl_awt.dll
 | jogl.jar&lt;br /&gt;libjogl.jnilib&lt;br /&gt;libjogl_cg.jnilib&lt;br /&gt;libjogl_awt.jnilib
 | jogl.jar&lt;br /&gt;libjogl.so&lt;br /&gt;libjogl_cg.so&lt;br /&gt;libjogl_awt.so&lt;br /&gt;libjogl_drihack.so
 |}

==== Windows ====
The folder that JRE has been installed is denoted by &lt;JRE&gt;. It depends on the environment, however it is typically as follows.
 &lt;JRE&gt;=C:\Program Files\Java\j2re1.4.2_12
The file ‘jogl.jar’ should be copied to &lt;JRE&gt;\lib\ext, and the other files should be copied to &lt;JRE&gt;\bin.

==== Mac OS X ====
When operating from the command terminal, you should copy all files to /Library/Java/Extensions. When operating through the graphical interface, the above destination folder is shown as ‘Macintosh HD/Library/Java/Extensions’. In this operation, the password for root is required.

==== Linux ====
The directory that JRE has been installed is denoted by &lt;JRE&gt;. It depends on the environment, however it is typically as follows.
 &lt;JRE&gt;=/usr/java/j2sdk1.4.2_12/jre
file ‘jogl.jar’ should be copied to &lt;JRE&gt;/lib/ext, and the other files should be copied to &lt;JRE&gt;/lib/i386.

== Download jV ==
[[File:Download.png|right|link=http://ef-site.hgc.jp/eF-site/servlet/DownloadViewerBinary|Download]]
* Download jV&lt;br /&gt;In order to obtain jV and PDBjViewer you must agree to the software license. 
** [http://ef-site.hgc.jp/eF-site/servlet/DownloadViewerBinary binary]&lt;br /&gt;Click right Download image.
** [http://ef-site.hgc.jp/eF-site/servlet/Registration sourcecode] &lt;br /&gt;Registration is required. When the registration is completed, a URL for downloading the source code of jV and PDBjViewer is sent to you by email. The URL is valid for 24 hours.
** [http://ef-site.hgc.jp/jV/stable/jV.jnlp Java WebStart version] for stable version.(recommended)</text>
    <sha1>1f55c13295b59bd6bff2f2b8c9b1c7e9f9425c80</sha1>
  </revision>
  <revision>
    <id>307</id>
    <parentid>306</parentid>
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      <username>WikiSysop</username>
      <id>1</id>
    </contributor>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="3150" xml:space="preserve">== System requirements ==
jV3 runs on the Java Runtime Environment (JRE) with JOGL API. The version requirements are as follows.
* [http://java.sun.com/j2se/1.4.2/download.html JRE] (includes Java Plug-in) 1.4.2 or later
* [https://jogl.dev.java.net/ JOGL] API JSR-231 1.0.0 or later 
These softwares are available on typical operation systems such as Windows (2000/XP/Vista), Mac OS X 10.3 or later, and Red Hat Linux 7.3 or later.

== Installing JOGL API ==
=== Automatic install ===
In this section, it is assumed that JRE 1.4.2 or later has been installed on your computer. Installing JOGL is just deploying several files to JRE. A tool that automatically performs the JOGL installation with a graphical user interface is available here.

* JSR-231 1.0.0 [[http://ef-site.hgc.jp/eF-site/jV/JOGL_JSR231_win32.zip Windows], [http://ef-site.hgc.jp/eF-site/jV/JOGL_JSR231_macosx_ppc.tar.gz Mac OS X ppc], [http://ef-site.hgc.jp/eF-site/jV/JOGL_JSR231_macosx_universal.tar.gz Mac OS X universal], [http://ef-site.hgc.jp/eF-site/jV/JOGL_JSR231_linux_i586.tar.gz Linux]]

=== Manual install ===
It is also possible to install JOGL manually. According to the kind of your operation system, you should get the following files from [https://jogl.dev.java.net/ JOGL].

{| class="wikitable" border="1"
 ! !! Windows !! Mac OS X !! Linux
 |-
 | JSR-231 1.0.0
 | jogl.jar&lt;br /&gt;jogl.dll&lt;br /&gt;jogl_cg.dll&lt;br /&gt;jogl_awt.dll
 | jogl.jar&lt;br /&gt;libjogl.jnilib&lt;br /&gt;libjogl_cg.jnilib&lt;br /&gt;libjogl_awt.jnilib
 | jogl.jar&lt;br /&gt;libjogl.so&lt;br /&gt;libjogl_cg.so&lt;br /&gt;libjogl_awt.so&lt;br /&gt;libjogl_drihack.so
 |}

==== Windows ====
The folder that JRE has been installed is denoted by &lt;JRE&gt;. It depends on the environment, however it is typically as follows.
 &lt;JRE&gt;=C:\Program Files\Java\j2re1.4.2_12
The file ‘jogl.jar’ should be copied to &lt;JRE&gt;\lib\ext, and the other files should be copied to &lt;JRE&gt;\bin.

==== Mac OS X ====
When operating from the command terminal, you should copy all files to /Library/Java/Extensions. When operating through the graphical interface, the above destination folder is shown as ‘Macintosh HD/Library/Java/Extensions’. In this operation, the password for root is required.

==== Linux ====
The directory that JRE has been installed is denoted by &lt;JRE&gt;. It depends on the environment, however it is typically as follows.
 &lt;JRE&gt;=/usr/java/j2sdk1.4.2_12/jre
file ‘jogl.jar’ should be copied to &lt;JRE&gt;/lib/ext, and the other files should be copied to &lt;JRE&gt;/lib/i386.

== Download jV ==
[[File:Download.png|right|link=http://ef-site.hgc.jp/eF-site/servlet/DownloadViewerBinary|Download]]
* Download jV&lt;br /&gt;In order to obtain jV and PDBjViewer you must agree to the software license. 
** [http://ef-site.hgc.jp/eF-site/servlet/DownloadViewerBinary binary]&lt;br /&gt;Click right Download image.
** [http://ef-site.hgc.jp/eF-site/servlet/Registration sourcecode] &lt;br /&gt;Registration is required. When the registration is completed, a URL for downloading the source code of jV and PDBjViewer is sent to you by email. The URL is valid for 24 hours.
** [http://ef-site.hgc.jp/jV/stable/jV.jnlp Java WebStart version] for stable version.(recommended)</text>
    <sha1>014188b89215c52f3f9f6189150f85c0c98ff312</sha1>
  </revision>
  <revision>
    <id>309</id>
    <parentid>307</parentid>
    <timestamp>2009-04-23T02:18:31Z</timestamp>
    <contributor>
      <username>WikiSysop</username>
      <id>1</id>
    </contributor>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="3133" xml:space="preserve">== System requirements ==
jV3 runs on the Java Runtime Environment (JRE) with JOGL API. The version requirements are as follows.
* [http://java.sun.com/j2se/1.4.2/download.html JRE] (includes Java Plug-in) 1.4.2 or later
* [https://jogl.dev.java.net/ JOGL] API JSR-231 1.0.0 or later 
These softwares are available on typical operation systems such as Windows (2000/XP/Vista), Mac OS X 10.3 or later, and Red Hat Linux 7.3 or later.

== Installing JOGL API ==
=== Automatic install ===
It is assumed that JRE 1.4.2 or later has been installed on your computer. Installing JOGL is just deploying several files to JRE. A tool that automatically performs the JOGL installation with a graphical user interface is available here.

* JSR-231 1.0.0 [[http://ef-site.hgc.jp/eF-site/jV/JOGL_JSR231_win32.zip Windows], [http://ef-site.hgc.jp/eF-site/jV/JOGL_JSR231_macosx_ppc.tar.gz Mac OS X ppc], [http://ef-site.hgc.jp/eF-site/jV/JOGL_JSR231_macosx_universal.tar.gz Mac OS X universal], [http://ef-site.hgc.jp/eF-site/jV/JOGL_JSR231_linux_i586.tar.gz Linux]]

=== Manual install ===
It is also possible to install JOGL manually. According to the kind of your operation system, you should get the following files from [https://jogl.dev.java.net/ JOGL].

{| class="wikitable" border="1"
 ! !! Windows !! Mac OS X !! Linux
 |-
 | JSR-231 1.0.0
 | jogl.jar&lt;br /&gt;jogl.dll&lt;br /&gt;jogl_cg.dll&lt;br /&gt;jogl_awt.dll
 | jogl.jar&lt;br /&gt;libjogl.jnilib&lt;br /&gt;libjogl_cg.jnilib&lt;br /&gt;libjogl_awt.jnilib
 | jogl.jar&lt;br /&gt;libjogl.so&lt;br /&gt;libjogl_cg.so&lt;br /&gt;libjogl_awt.so&lt;br /&gt;libjogl_drihack.so
 |}

==== Windows ====
The folder that JRE has been installed is denoted by &lt;JRE&gt;. It depends on the environment, however it is typically as follows.
 &lt;JRE&gt;=C:\Program Files\Java\j2re1.4.2_12
The file ‘jogl.jar’ should be copied to &lt;JRE&gt;\lib\ext, and the other files should be copied to &lt;JRE&gt;\bin.

==== Mac OS X ====
When operating from the command terminal, you should copy all files to /Library/Java/Extensions. When operating through the graphical interface, the above destination folder is shown as ‘Macintosh HD/Library/Java/Extensions’. In this operation, the password for root is required.

==== Linux ====
The directory that JRE has been installed is denoted by &lt;JRE&gt;. It depends on the environment, however it is typically as follows.
 &lt;JRE&gt;=/usr/java/j2sdk1.4.2_12/jre
file ‘jogl.jar’ should be copied to &lt;JRE&gt;/lib/ext, and the other files should be copied to &lt;JRE&gt;/lib/i386.

== Download jV ==
[[File:Download.png|right|link=http://ef-site.hgc.jp/eF-site/servlet/DownloadViewerBinary|Download]]
* Download jV&lt;br /&gt;In order to obtain jV and PDBjViewer you must agree to the software license. 
** [http://ef-site.hgc.jp/eF-site/servlet/DownloadViewerBinary binary]&lt;br /&gt;Click right Download image.
** [http://ef-site.hgc.jp/eF-site/servlet/Registration sourcecode] &lt;br /&gt;Registration is required. When the registration is completed, a URL for downloading the source code of jV and PDBjViewer is sent to you by email. The URL is valid for 24 hours.
** [http://ef-site.hgc.jp/jV/stable/jV.jnlp Java WebStart version] for stable version.(recommended)</text>
    <sha1>af4aed1199da6ab49e136338e9ce66aa82d29155</sha1>
  </revision>
  <revision>
    <id>312</id>
    <parentid>309</parentid>
    <timestamp>2009-04-23T02:58:07Z</timestamp>
    <contributor>
      <username>WikiSysop</username>
      <id>1</id>
    </contributor>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="2462" xml:space="preserve">== System requirements ==
jV3 runs on the Java Runtime Environment (JRE) with JOGL API. The version requirements are as follows.
* [http://java.sun.com/j2se/1.4.2/download.html JRE] (includes Java Plug-in) 1.4.2 or later
* [https://jogl.dev.java.net/ JOGL] API JSR-231 1.0.0 or later 
These softwares are available on typical operation systems such as Windows (2000/XP/Vista), Mac OS X 10.3 or later, and Red Hat Linux 7.3 or later.

== Installing JOGL API ==
=== Automatic install ===
It is assumed that JRE 1.4.2 or later has been installed on your computer. Installing JOGL is just deploying several files to JRE. A tool that automatically performs the JOGL installation with a graphical user interface is available here.

* JSR-231 1.0.0 [[http://ef-site.hgc.jp/eF-site/jV/JOGL_JSR231_win32.zip Windows], [http://ef-site.hgc.jp/eF-site/jV/JOGL_JSR231_macosx_ppc.tar.gz Mac OS X ppc], [http://ef-site.hgc.jp/eF-site/jV/JOGL_JSR231_macosx_universal.tar.gz Mac OS X universal], [http://ef-site.hgc.jp/eF-site/jV/JOGL_JSR231_linux_i586.tar.gz Linux]]

=== Manual install ===
It is also possible to install JOGL manually. According to the kind of your operation system, you should get the following files from [https://jogl.dev.java.net/ JOGL].

{| class="wikitable" border="1"
 ! !! Windows !! Mac OS X !! Linux
 |-
 | JSR-231 1.0.0
 | jogl.jar&lt;br /&gt;jogl.dll&lt;br /&gt;jogl_cg.dll&lt;br /&gt;jogl_awt.dll
 | jogl.jar&lt;br /&gt;libjogl.jnilib&lt;br /&gt;libjogl_cg.jnilib&lt;br /&gt;libjogl_awt.jnilib
 | jogl.jar&lt;br /&gt;libjogl.so&lt;br /&gt;libjogl_cg.so&lt;br /&gt;libjogl_awt.so&lt;br /&gt;libjogl_drihack.so
 |}

==== Windows ====
The folder that JRE has been installed is denoted by &lt;JRE&gt;. It depends on the environment, however it is typically as follows.
 &lt;JRE&gt;=C:\Program Files\Java\j2re1.4.2_12
The file ‘jogl.jar’ should be copied to &lt;JRE&gt;\lib\ext, and the other files should be copied to &lt;JRE&gt;\bin.

==== Mac OS X ====
When operating from the command terminal, you should copy all files to /Library/Java/Extensions. When operating through the graphical interface, the above destination folder is shown as ‘Macintosh HD/Library/Java/Extensions’. In this operation, the password for root is required.

==== Linux ====
The directory that JRE has been installed is denoted by &lt;JRE&gt;. It depends on the environment, however it is typically as follows.
 &lt;JRE&gt;=/usr/java/j2sdk1.4.2_12/jre
file ‘jogl.jar’ should be copied to &lt;JRE&gt;/lib/ext, and the other files should be copied to &lt;JRE&gt;/lib/i386.</text>
    <sha1>8a931f1c45eaaae2c87d78dc71de4c77f6ad1dae</sha1>
  </revision>
  <revision>
    <id>313</id>
    <parentid>312</parentid>
    <timestamp>2009-04-23T02:59:00Z</timestamp>
    <contributor>
      <username>WikiSysop</username>
      <id>1</id>
    </contributor>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="2499" xml:space="preserve">{| style="float:right"
 |__TOC__
 |}
== System requirements ==
jV3 runs on the Java Runtime Environment (JRE) with JOGL API. The version requirements are as follows.
* [http://java.sun.com/j2se/1.4.2/download.html JRE] (includes Java Plug-in) 1.4.2 or later
* [https://jogl.dev.java.net/ JOGL] API JSR-231 1.0.0 or later 
These softwares are available on typical operation systems such as Windows (2000/XP/Vista), Mac OS X 10.3 or later, and Red Hat Linux 7.3 or later.

== Installing JOGL API ==
=== Automatic install ===
It is assumed that JRE 1.4.2 or later has been installed on your computer. Installing JOGL is just deploying several files to JRE. A tool that automatically performs the JOGL installation with a graphical user interface is available here.

* JSR-231 1.0.0 [[http://ef-site.hgc.jp/eF-site/jV/JOGL_JSR231_win32.zip Windows], [http://ef-site.hgc.jp/eF-site/jV/JOGL_JSR231_macosx_ppc.tar.gz Mac OS X ppc], [http://ef-site.hgc.jp/eF-site/jV/JOGL_JSR231_macosx_universal.tar.gz Mac OS X universal], [http://ef-site.hgc.jp/eF-site/jV/JOGL_JSR231_linux_i586.tar.gz Linux]]

=== Manual install ===
It is also possible to install JOGL manually. According to the kind of your operation system, you should get the following files from [https://jogl.dev.java.net/ JOGL].

{| class="wikitable" border="1"
 ! !! Windows !! Mac OS X !! Linux
 |-
 | JSR-231 1.0.0
 | jogl.jar&lt;br /&gt;jogl.dll&lt;br /&gt;jogl_cg.dll&lt;br /&gt;jogl_awt.dll
 | jogl.jar&lt;br /&gt;libjogl.jnilib&lt;br /&gt;libjogl_cg.jnilib&lt;br /&gt;libjogl_awt.jnilib
 | jogl.jar&lt;br /&gt;libjogl.so&lt;br /&gt;libjogl_cg.so&lt;br /&gt;libjogl_awt.so&lt;br /&gt;libjogl_drihack.so
 |}

==== Windows ====
The folder that JRE has been installed is denoted by &lt;JRE&gt;. It depends on the environment, however it is typically as follows.
 &lt;JRE&gt;=C:\Program Files\Java\j2re1.4.2_12
The file ‘jogl.jar’ should be copied to &lt;JRE&gt;\lib\ext, and the other files should be copied to &lt;JRE&gt;\bin.

==== Mac OS X ====
When operating from the command terminal, you should copy all files to /Library/Java/Extensions. When operating through the graphical interface, the above destination folder is shown as ‘Macintosh HD/Library/Java/Extensions’. In this operation, the password for root is required.

==== Linux ====
The directory that JRE has been installed is denoted by &lt;JRE&gt;. It depends on the environment, however it is typically as follows.
 &lt;JRE&gt;=/usr/java/j2sdk1.4.2_12/jre
file ‘jogl.jar’ should be copied to &lt;JRE&gt;/lib/ext, and the other files should be copied to &lt;JRE&gt;/lib/i386.</text>
    <sha1>04a36454a8ad940f2f339ec21d2e7145dfb7033e</sha1>
  </revision>
  <revision>
    <id>316</id>
    <parentid>313</parentid>
    <timestamp>2009-04-23T03:04:34Z</timestamp>
    <contributor>
      <username>WikiSysop</username>
      <id>1</id>
    </contributor>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="2472" xml:space="preserve">__NOTOC__
== System requirements ==
jV3 runs on the Java Runtime Environment (JRE) with JOGL API. The version requirements are as follows.
* [http://java.sun.com/j2se/1.4.2/download.html JRE] (includes Java Plug-in) 1.4.2 or later
* [https://jogl.dev.java.net/ JOGL] API JSR-231 1.0.0 or later 
These softwares are available on typical operation systems such as Windows (2000/XP/Vista), Mac OS X 10.3 or later, and Red Hat Linux 7.3 or later.

== Installing JOGL API ==
=== Automatic install ===
It is assumed that JRE 1.4.2 or later has been installed on your computer. Installing JOGL is just deploying several files to JRE. A tool that automatically performs the JOGL installation with a graphical user interface is available here.

* JSR-231 1.0.0 [[http://ef-site.hgc.jp/eF-site/jV/JOGL_JSR231_win32.zip Windows], [http://ef-site.hgc.jp/eF-site/jV/JOGL_JSR231_macosx_ppc.tar.gz Mac OS X ppc], [http://ef-site.hgc.jp/eF-site/jV/JOGL_JSR231_macosx_universal.tar.gz Mac OS X universal], [http://ef-site.hgc.jp/eF-site/jV/JOGL_JSR231_linux_i586.tar.gz Linux]]

=== Manual install ===
It is also possible to install JOGL manually. According to the kind of your operation system, you should get the following files from [https://jogl.dev.java.net/ JOGL].

{| class="wikitable" border="1"
 ! !! Windows !! Mac OS X !! Linux
 |-
 | JSR-231 1.0.0
 | jogl.jar&lt;br /&gt;jogl.dll&lt;br /&gt;jogl_cg.dll&lt;br /&gt;jogl_awt.dll
 | jogl.jar&lt;br /&gt;libjogl.jnilib&lt;br /&gt;libjogl_cg.jnilib&lt;br /&gt;libjogl_awt.jnilib
 | jogl.jar&lt;br /&gt;libjogl.so&lt;br /&gt;libjogl_cg.so&lt;br /&gt;libjogl_awt.so&lt;br /&gt;libjogl_drihack.so
 |}

==== Windows ====
The folder that JRE has been installed is denoted by &lt;JRE&gt;. It depends on the environment, however it is typically as follows.
 &lt;JRE&gt;=C:\Program Files\Java\j2re1.4.2_12
The file ‘jogl.jar’ should be copied to &lt;JRE&gt;\lib\ext, and the other files should be copied to &lt;JRE&gt;\bin.

==== Mac OS X ====
When operating from the command terminal, you should copy all files to /Library/Java/Extensions. When operating through the graphical interface, the above destination folder is shown as ‘Macintosh HD/Library/Java/Extensions’. In this operation, the password for root is required.

==== Linux ====
The directory that JRE has been installed is denoted by &lt;JRE&gt;. It depends on the environment, however it is typically as follows.
 &lt;JRE&gt;=/usr/java/j2sdk1.4.2_12/jre
file ‘jogl.jar’ should be copied to &lt;JRE&gt;/lib/ext, and the other files should be copied to &lt;JRE&gt;/lib/i386.</text>
    <sha1>b3abeb860b8b4b6dd80f5f35348bb54d655cc3f8</sha1>
  </revision>
  <revision>
    <id>321</id>
    <parentid>316</parentid>
    <timestamp>2009-06-05T06:19:58Z</timestamp>
    <contributor>
      <username>WikiSysop</username>
      <id>1</id>
    </contributor>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="2453" xml:space="preserve">__NOTOC__
== System requirements ==
jV3 runs on the Java Runtime Environment (JRE) with JOGL API. The version requirements are as follows.
* [http://java.sun.com/j2se/ JRE] (includes Java Plug-in) 1.4.2 or later
* [https://jogl.dev.java.net/ JOGL] API JSR-231 1.0.0 or later 
These softwares are available on typical operation systems such as Windows (2000/XP/Vista), Mac OS X 10.3 or later, and Red Hat Linux 7.3 or later.

== Installing JOGL API ==
=== Automatic install ===
It is assumed that JRE 1.4.2 or later has been installed on your computer. Installing JOGL is just deploying several files to JRE. A tool that automatically performs the JOGL installation with a graphical user interface is available here.

* JSR-231 1.0.0 [[http://ef-site.hgc.jp/eF-site/jV/JOGL_JSR231_win32.zip Windows], [http://ef-site.hgc.jp/eF-site/jV/JOGL_JSR231_macosx_ppc.tar.gz Mac OS X ppc], [http://ef-site.hgc.jp/eF-site/jV/JOGL_JSR231_macosx_universal.tar.gz Mac OS X universal], [http://ef-site.hgc.jp/eF-site/jV/JOGL_JSR231_linux_i586.tar.gz Linux]]

=== Manual install ===
It is also possible to install JOGL manually. According to the kind of your operation system, you should get the following files from [https://jogl.dev.java.net/ JOGL].

{| class="wikitable" border="1"
 ! !! Windows !! Mac OS X !! Linux
 |-
 | JSR-231 1.0.0
 | jogl.jar&lt;br /&gt;jogl.dll&lt;br /&gt;jogl_cg.dll&lt;br /&gt;jogl_awt.dll
 | jogl.jar&lt;br /&gt;libjogl.jnilib&lt;br /&gt;libjogl_cg.jnilib&lt;br /&gt;libjogl_awt.jnilib
 | jogl.jar&lt;br /&gt;libjogl.so&lt;br /&gt;libjogl_cg.so&lt;br /&gt;libjogl_awt.so&lt;br /&gt;libjogl_drihack.so
 |}

==== Windows ====
The folder that JRE has been installed is denoted by &lt;JRE&gt;. It depends on the environment, however it is typically as follows.
 &lt;JRE&gt;=C:\Program Files\Java\j2re1.4.2_12
The file ‘jogl.jar’ should be copied to &lt;JRE&gt;\lib\ext, and the other files should be copied to &lt;JRE&gt;\bin.

==== Mac OS X ====
When operating from the command terminal, you should copy all files to /Library/Java/Extensions. When operating through the graphical interface, the above destination folder is shown as ‘Macintosh HD/Library/Java/Extensions’. In this operation, the password for root is required.

==== Linux ====
The directory that JRE has been installed is denoted by &lt;JRE&gt;. It depends on the environment, however it is typically as follows.
 &lt;JRE&gt;=/usr/java/j2sdk1.4.2_12/jre
file ‘jogl.jar’ should be copied to &lt;JRE&gt;/lib/ext, and the other files should be copied to &lt;JRE&gt;/lib/i386.</text>
    <sha1>51e20580051665bb1aa484f6b8b749326d6d247e</sha1>
  </revision>
  <revision>
    <id>326</id>
    <parentid>321</parentid>
    <timestamp>2009-07-07T02:06:17Z</timestamp>
    <contributor>
      <username>WikiSysop</username>
      <id>1</id>
    </contributor>
    <comment>/* Automatic install */</comment>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="2517" xml:space="preserve">__NOTOC__
== System requirements ==
jV3 runs on the Java Runtime Environment (JRE) with JOGL API. The version requirements are as follows.
* [http://java.sun.com/j2se/ JRE] (includes Java Plug-in) 1.4.2 or later
* [https://jogl.dev.java.net/ JOGL] API JSR-231 1.0.0 or later 
These softwares are available on typical operation systems such as Windows (2000/XP/Vista), Mac OS X 10.3 or later, and Red Hat Linux 7.3 or later.

== Installing JOGL API ==
=== Automatic install ===
It is assumed that JRE 1.4.2 or later has been installed on your computer. Installing JOGL is just deploying several files to JRE. A tool that automatically performs the JOGL installation with a graphical user interface is available here.

* JSR-231 1.0.0
** for [http://ef-site.hgc.jp/eF-site/jV/JOGL_JSR231_win32.zip Windows/x86]
** for [http://ef-site.hgc.jp/eF-site/jV/JOGL_JSR231_macosx_universal.tar.gz Mac OS X 10.4+ (Universal binaries)]
** for [http://ef-site.hgc.jp/eF-site/jV/JOGL_JSR231_macosx_ppc.tar.gz Mac OS X 10.3 (PowerPC only)]
** for [http://ef-site.hgc.jp/eF-site/jV/JOGL_JSR231_linux_i586.tar.gz Linux/x86]

=== Manual install ===
It is also possible to install JOGL manually. According to the kind of your operation system, you should get the following files from [https://jogl.dev.java.net/ JOGL].

{| class="wikitable" border="1"
 ! !! Windows !! Mac OS X !! Linux
 |-
 | JSR-231 1.0.0
 | jogl.jar&lt;br /&gt;jogl.dll&lt;br /&gt;jogl_cg.dll&lt;br /&gt;jogl_awt.dll
 | jogl.jar&lt;br /&gt;libjogl.jnilib&lt;br /&gt;libjogl_cg.jnilib&lt;br /&gt;libjogl_awt.jnilib
 | jogl.jar&lt;br /&gt;libjogl.so&lt;br /&gt;libjogl_cg.so&lt;br /&gt;libjogl_awt.so&lt;br /&gt;libjogl_drihack.so
 |}

==== Windows ====
The folder that JRE has been installed is denoted by &lt;JRE&gt;. It depends on the environment, however it is typically as follows.
 &lt;JRE&gt;=C:\Program Files\Java\j2re1.4.2_12
The file ‘jogl.jar’ should be copied to &lt;JRE&gt;\lib\ext, and the other files should be copied to &lt;JRE&gt;\bin.

==== Mac OS X ====
When operating from the command terminal, you should copy all files to /Library/Java/Extensions. When operating through the graphical interface, the above destination folder is shown as ‘Macintosh HD/Library/Java/Extensions’. In this operation, the password for root is required.

==== Linux ====
The directory that JRE has been installed is denoted by &lt;JRE&gt;. It depends on the environment, however it is typically as follows.
 &lt;JRE&gt;=/usr/java/j2sdk1.4.2_12/jre
file ‘jogl.jar’ should be copied to &lt;JRE&gt;/lib/ext, and the other files should be copied to &lt;JRE&gt;/lib/i386.</text>
    <sha1>211c1d06c4fef6d4d62f4f7c586e72fabf75502a</sha1>
  </revision>
  <revision>
    <id>327</id>
    <parentid>326</parentid>
    <timestamp>2009-07-07T02:06:41Z</timestamp>
    <contributor>
      <username>WikiSysop</username>
      <id>1</id>
    </contributor>
    <comment>/* Mac OS X */</comment>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="2660" xml:space="preserve">__NOTOC__
== System requirements ==
jV3 runs on the Java Runtime Environment (JRE) with JOGL API. The version requirements are as follows.
* [http://java.sun.com/j2se/ JRE] (includes Java Plug-in) 1.4.2 or later
* [https://jogl.dev.java.net/ JOGL] API JSR-231 1.0.0 or later 
These softwares are available on typical operation systems such as Windows (2000/XP/Vista), Mac OS X 10.3 or later, and Red Hat Linux 7.3 or later.

== Installing JOGL API ==
=== Automatic install ===
It is assumed that JRE 1.4.2 or later has been installed on your computer. Installing JOGL is just deploying several files to JRE. A tool that automatically performs the JOGL installation with a graphical user interface is available here.

* JSR-231 1.0.0
** for [http://ef-site.hgc.jp/eF-site/jV/JOGL_JSR231_win32.zip Windows/x86]
** for [http://ef-site.hgc.jp/eF-site/jV/JOGL_JSR231_macosx_universal.tar.gz Mac OS X 10.4+ (Universal binaries)]
** for [http://ef-site.hgc.jp/eF-site/jV/JOGL_JSR231_macosx_ppc.tar.gz Mac OS X 10.3 (PowerPC only)]
** for [http://ef-site.hgc.jp/eF-site/jV/JOGL_JSR231_linux_i586.tar.gz Linux/x86]

=== Manual install ===
It is also possible to install JOGL manually. According to the kind of your operation system, you should get the following files from [https://jogl.dev.java.net/ JOGL].

{| class="wikitable" border="1"
 ! !! Windows !! Mac OS X !! Linux
 |-
 | JSR-231 1.0.0
 | jogl.jar&lt;br /&gt;jogl.dll&lt;br /&gt;jogl_cg.dll&lt;br /&gt;jogl_awt.dll
 | jogl.jar&lt;br /&gt;libjogl.jnilib&lt;br /&gt;libjogl_cg.jnilib&lt;br /&gt;libjogl_awt.jnilib
 | jogl.jar&lt;br /&gt;libjogl.so&lt;br /&gt;libjogl_cg.so&lt;br /&gt;libjogl_awt.so&lt;br /&gt;libjogl_drihack.so
 |}

==== Windows ====
The folder that JRE has been installed is denoted by &lt;JRE&gt;. It depends on the environment, however it is typically as follows.
 &lt;JRE&gt;=C:\Program Files\Java\j2re1.4.2_12
The file ‘jogl.jar’ should be copied to &lt;JRE&gt;\lib\ext, and the other files should be copied to &lt;JRE&gt;\bin.

==== Mac OS X ====
Note that two kinds of libraries are available for Mac OS X; 'Universal' and 'PowerPC only'.
Intel Mac users should choose the universal binaries.
When operating from the command terminal, you should copy all files to /Library/Java/Extensions. When operating through the graphical interface, the above destination folder is shown as 'Macintosh HD/Library/Java/Extensions'. In this operation, the password for root is required.

==== Linux ====
The directory that JRE has been installed is denoted by &lt;JRE&gt;. It depends on the environment, however it is typically as follows.
 &lt;JRE&gt;=/usr/java/j2sdk1.4.2_12/jre
file ‘jogl.jar’ should be copied to &lt;JRE&gt;/lib/ext, and the other files should be copied to &lt;JRE&gt;/lib/i386.</text>
    <sha1>0749b8f44e8b4eaa561d6dad2c03ece216d0ba9b</sha1>
  </revision>
</page>
<page arvcontinue="20090423011428|304">
  <title>Main Page</title>
  <ns>0</ns>
  <id>1</id>
  <revision>
    <id>305</id>
    <parentid>292</parentid>
    <timestamp>2009-04-23T01:17:57Z</timestamp>
    <contributor>
      <username>WikiSysop</username>
      <id>1</id>
    </contributor>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="1615" xml:space="preserve">&lt;big&gt;'''Welcome to jV wiki.'''&lt;/big&gt;

jV version3 (formerly known as PDBjViewer) is a program to display molecular graphics of protein and nucleic acids. 
jV supports the following features:
* jV can read and display PDBML files, the canonical XML format for the Protein Data Bank.
* Of course, jV can read and display the traditional PDB format files, too.
* RasMol-like usability.
* jV can process more than one molecules.
* jV can display polygons specified by XML. ([http://ef-site.hgc.jp/eF-site/schema/polygon12.xsd XML Schema for polygons] is available.)
* Multiple polygons can be processed simultaneously, and be superimposed onto molecular images.
* Animation can be realized.
* jV runs on the Java Runtime Environment ([http://java.sun.com/javase/index.jsp JRE]) so that it can work as a stand-alone application as well as an applet.
* The graphics of jV is based on OpenGL [https://jogl.dev.java.net/ JOGL]), thereby producing fairly beautiful pictures.


The program 'jV' has been developed by [http://www.hgc.jp/~kinosita/TOP.html Kengo Kinoshita] ([http://www.hgc.jp/english/ Human Genome Center], [http://www.ims.u-tokyo.ac.jp/imsut/en/ Insutitute for Medical Science],[http://www.u-tokyo.ac.jp/index_e.html University of Tokyo]) and [http://www.protein.osaka-u.ac.jp/rcsfp/pi/ Haruki Nakamura] ([http://www.protein.osaka-u.ac.jp/index_e.php Institute for Protein Research], [http://www.osaka-u.ac.jp/eng/index.html Osaka Univeristy]), with the support from [http://www-bird.jst.go.jp/index_e.html JST-BIRD].


&lt;gallery&gt;
File:Spacefill.jpg
File:Cartoon.jpg
File:Surface.jpg
File:edmap.jpg
&lt;/gallery&gt;</text>
    <sha1>cfc98d3387914262ac5489a2e60e6434d1b9ec94</sha1>
  </revision>
  <revision>
    <id>310</id>
    <parentid>305</parentid>
    <timestamp>2009-04-23T02:21:50Z</timestamp>
    <contributor>
      <username>WikiSysop</username>
      <id>1</id>
    </contributor>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="1920" xml:space="preserve">&lt;big&gt;'''Welcome to jV wiki.'''&lt;/big&gt;

jV version3 (formerly known as PDBjViewer) is a program to display molecular graphics of protein and nucleic acids. 
jV supports the following features:
* jV can read and display PDBML files, the canonical XML format for the Protein Data Bank.
* Of course, jV can read and display the traditional PDB format files, too.
* RasMol-like usability.
* jV can process more than one molecules.
* jV can display polygons specified by XML. ([http://ef-site.hgc.jp/eF-site/schema/polygon12.xsd XML Schema for polygons] is available.)
* Multiple polygons can be processed simultaneously, and be superimposed onto molecular images.
* Animation can be realized.
* jV runs on the Java Runtime Environment ([http://java.sun.com/javase/index.jsp JRE]) so that it can work as a stand-alone application as well as an applet.
* The graphics of jV is based on OpenGL [https://jogl.dev.java.net/ JOGL]), thereby producing fairly beautiful pictures.


The program 'jV' has been developed by [http://www.hgc.jp/~kinosita/TOP.html Kengo Kinoshita] ([http://www.hgc.jp/english/ Human Genome Center], [http://www.ims.u-tokyo.ac.jp/imsut/en/ Insutitute for Medical Science],[http://www.u-tokyo.ac.jp/index_e.html University of Tokyo]) and [http://www.protein.osaka-u.ac.jp/rcsfp/pi/ Haruki Nakamura] ([http://www.protein.osaka-u.ac.jp/index_e.php Institute for Protein Research], [http://www.osaka-u.ac.jp/eng/index.html Osaka Univeristy]), with the support from [http://www-bird.jst.go.jp/index_e.html JST-BIRD].


&lt;gallery&gt;
File:Spacefill.jpg
File:Cartoon.jpg
File:Surface.jpg
File:edmap.jpg
&lt;/gallery&gt;


== Download ==
The following links take you to the download pages.
* [http://ef-site.hgc.jp/eF-site/servlet/DownloadViewerBinary binary]
* [http://ef-site.hgc.jp/eF-site/servlet/Registration source code]
* [http://ef-site.hgc.jp/jV/stable/jV.jnlp Java WebStart version] for stable version.(recommended)</text>
    <sha1>b6478efb1973a8dcfe0c7a48276f0c019b2593ba</sha1>
  </revision>
  <revision>
    <id>311</id>
    <parentid>310</parentid>
    <timestamp>2009-04-23T02:55:54Z</timestamp>
    <contributor>
      <username>WikiSysop</username>
      <id>1</id>
    </contributor>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="2252" xml:space="preserve">&lt;big&gt;'''Welcome to jV wiki.'''&lt;/big&gt;

jV version 3 (formerly known as PDBjViewer) is a program to display molecular graphics of protein and nucleic acids. 
jV supports the following features:
* jV can read and display PDBML files, the canonical XML format for the Protein Data Bank.
* Of course, jV can read and display the traditional PDB format files, too.
* RasMol-like usability.
* jV can process more than one molecules.
* jV can display polygons specified by XML. ([http://ef-site.hgc.jp/eF-site/schema/polygon12.xsd XML Schema for polygons] is available.)
* Multiple polygons can be processed simultaneously, and be superimposed onto molecular images.
* Animation can be realized.
* jV runs on the Java Runtime Environment ([http://java.sun.com/javase/index.jsp JRE]) so that it can work as a stand-alone application as well as an applet.
* The graphics of jV is based on OpenGL ([https://jogl.dev.java.net/ JOGL]), thereby producing fairly beautiful pictures.


The program 'jV' has been developed by [http://www.hgc.jp/~kinosita/TOP.html Kengo Kinoshita] ([http://www.hgc.jp/english/ Human Genome Center], [http://www.ims.u-tokyo.ac.jp/imsut/en/ Insutitute for Medical Science],[http://www.u-tokyo.ac.jp/index_e.html University of Tokyo]) and [http://www.protein.osaka-u.ac.jp/rcsfp/pi/ Haruki Nakamura] ([http://www.protein.osaka-u.ac.jp/index_e.php Institute for Protein Research], [http://www.osaka-u.ac.jp/eng/index.html Osaka Univeristy]), with the support from [http://www-bird.jst.go.jp/index_e.html JST-BIRD].


&lt;gallery&gt;
File:Spacefill.jpg
File:Cartoon.jpg
File:Surface.jpg
File:edmap.jpg
&lt;/gallery&gt;


== Start up ==
You can start up jV with Java Web Start technology immediately from here.
* [http://ef-site.hgc.jp/jV/stable/jV.jnlp stable JOGL version] (recommended)
* [http://ef-site.hgc.jp/jV/current/jV.jnlp recent JOGL version] 

== Download ==
You can also download the program and start up it locally.
In this case, installing JOGL is required in advance (see [[Installation_of_jV3 | Installation]] page).
The following links take you to the download pages.
* [http://ef-site.hgc.jp/eF-site/servlet/DownloadViewerBinary binary]
* [http://ef-site.hgc.jp/eF-site/servlet/Registration source code] (registration will be required)</text>
    <sha1>ee5aec53b135039bf974f24e20964daf6afb3a70</sha1>
  </revision>
  <revision>
    <id>315</id>
    <parentid>311</parentid>
    <timestamp>2009-04-23T03:03:41Z</timestamp>
    <contributor>
      <username>WikiSysop</username>
      <id>1</id>
    </contributor>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="2252" xml:space="preserve">&lt;big&gt;'''Welcome to jV wiki.'''&lt;/big&gt;

jV version 3 (formerly known as PDBjViewer) is a program to display molecular graphics of protein and nucleic acids. 
jV supports the following features:
* jV can read and display PDBML files, the canonical XML format for the Protein Data Bank.
* Of course, jV can read and display the traditional PDB format files, too.
* RasMol-like usability.
* jV can process more than one molecules.
* jV can display polygons specified by XML. ([http://ef-site.hgc.jp/eF-site/schema/polygon12.xsd XML Schema for polygons] is available.)
* Multiple polygons can be processed simultaneously, and be superimposed onto molecular images.
* Animation can be realized.
* jV runs on the Java Runtime Environment ([http://java.sun.com/javase/index.jsp JRE]) so that it can work as a stand-alone application as well as an applet.
* The graphics of jV is based on OpenGL ([https://jogl.dev.java.net/ JOGL]), thereby producing fairly beautiful pictures.


The program 'jV' has been developed by [http://www.hgc.jp/~kinosita/TOP.html Kengo Kinoshita] ([http://www.hgc.jp/english/ Human Genome Center], [http://www.ims.u-tokyo.ac.jp/imsut/en/ Insutitute for Medical Science],[http://www.u-tokyo.ac.jp/index_e.html University of Tokyo]) and [http://www.protein.osaka-u.ac.jp/rcsfp/pi/ Haruki Nakamura] ([http://www.protein.osaka-u.ac.jp/index_e.php Institute for Protein Research], [http://www.osaka-u.ac.jp/eng/index.html Osaka Univeristy]), with the support from [http://www-bird.jst.go.jp/index_e.html JST-BIRD].


&lt;gallery&gt;
File:Spacefill.jpg
File:Cartoon.jpg
File:Surface.jpg
File:edmap.jpg
&lt;/gallery&gt;


== Start up ==
You can start up jV with Java Web Start technology immediately from here.
* [http://ef-site.hgc.jp/jV/stable/jV.jnlp stable JOGL version] (recommended)
* [http://ef-site.hgc.jp/jV/current/jV.jnlp recent JOGL version] 

== Download ==
You can also download the program and start it up locally.
In this case, installing JOGL is required in advance (see [[Installation_of_jV3 | Installation]] page).
The following links take you to the download pages.
* [http://ef-site.hgc.jp/eF-site/servlet/DownloadViewerBinary binary]
* [http://ef-site.hgc.jp/eF-site/servlet/Registration source code] (registration will be required)</text>
    <sha1>c743e7321e7b7d3a94fa4eec58304191ab7eb3fc</sha1>
  </revision>
  <revision>
    <id>332</id>
    <parentid>315</parentid>
    <timestamp>2009-07-31T02:48:40Z</timestamp>
    <contributor>
      <username>Kinoshita</username>
      <id>3</id>
    </contributor>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="2289" xml:space="preserve">&lt;big&gt;'''Welcome to jV wiki.'''&lt;/big&gt;

jV version 3 (formerly known as PDBjViewer) is a program to display molecular graphics of protein and nucleic acids. 
jV supports the following features:
* jV can read and display PDBML files, the canonical XML format for the Protein Data Bank.
* Of course, jV can read and display the traditional PDB format files, too.
* RasMol-like usability.
* jV can process more than one molecules.
* jV can display polygons specified by XML. ([http://ef-site.hgc.jp/eF-site/schema/polygon12.xsd XML Schema for polygons] is available.)
* Multiple polygons can be processed simultaneously, and be superimposed onto molecular images.
* Animation can be realized.
* jV runs on the Java Runtime Environment ([http://java.sun.com/javase/index.jsp JRE]) so that it can work as a stand-alone application as well as an applet.
* The graphics of jV is based on OpenGL ([https://jogl.dev.java.net/ JOGL]), thereby producing fairly beautiful pictures.


The program 'jV' has been developed by [http://www.hgc.jp/~kinosita/TOP.html Kengo Kinoshita] ([http://www.hgc.jp/english/ Human Genome Center], [http://www.ims.u-tokyo.ac.jp/imsut/en/ Insutitute for Medical Science],[http://www.u-tokyo.ac.jp/index_e.html University of Tokyo]) and [http://www.protein.osaka-u.ac.jp/rcsfp/pi/ Haruki Nakamura] ([http://www.protein.osaka-u.ac.jp/index_e.php Institute for Protein Research], [http://www.osaka-u.ac.jp/eng/index.html Osaka Univeristy]), with the support from [http://www-bird.jst.go.jp/index_e.html JST-BIRD].


&lt;gallery&gt;
File:Spacefill.jpg
File:Cartoon.jpg
File:Surface.jpg
File:edmap.jpg
&lt;/gallery&gt;


== Start up ==
You can start up jV with Java Web Start technology immediately from here.
* [http://ef-site.hgc.jp/jV/stable/jV.jnlp stable JOGL version] (recommended)
* [http://ef-site.hgc.jp/jV/current/jV.jnlp recent JOGL version] 

== Download ==
You can also download the program and start it up locally.
In this case, installing JOGL is required in advance (see [[Installation_of_jV3 | Installation]] page).
The following links take you to the download pages. (latest version is 3.6.3@2009/7/31)
* [http://ef-site.hgc.jp/eF-site/servlet/DownloadViewerBinary binary] 
* [http://ef-site.hgc.jp/eF-site/servlet/Registration source code] (registration will be required)</text>
    <sha1>6c1190bcbe0f4cd8f27efe721464c84e3acb66ac</sha1>
  </revision>
  <revision>
    <id>333</id>
    <parentid>332</parentid>
    <timestamp>2009-07-31T04:47:03Z</timestamp>
    <contributor>
      <username>IMSsato</username>
      <id>4</id>
    </contributor>
    <comment>/* Download */</comment>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="2289" xml:space="preserve">&lt;big&gt;'''Welcome to jV wiki.'''&lt;/big&gt;

jV version 3 (formerly known as PDBjViewer) is a program to display molecular graphics of protein and nucleic acids. 
jV supports the following features:
* jV can read and display PDBML files, the canonical XML format for the Protein Data Bank.
* Of course, jV can read and display the traditional PDB format files, too.
* RasMol-like usability.
* jV can process more than one molecules.
* jV can display polygons specified by XML. ([http://ef-site.hgc.jp/eF-site/schema/polygon12.xsd XML Schema for polygons] is available.)
* Multiple polygons can be processed simultaneously, and be superimposed onto molecular images.
* Animation can be realized.
* jV runs on the Java Runtime Environment ([http://java.sun.com/javase/index.jsp JRE]) so that it can work as a stand-alone application as well as an applet.
* The graphics of jV is based on OpenGL ([https://jogl.dev.java.net/ JOGL]), thereby producing fairly beautiful pictures.


The program 'jV' has been developed by [http://www.hgc.jp/~kinosita/TOP.html Kengo Kinoshita] ([http://www.hgc.jp/english/ Human Genome Center], [http://www.ims.u-tokyo.ac.jp/imsut/en/ Insutitute for Medical Science],[http://www.u-tokyo.ac.jp/index_e.html University of Tokyo]) and [http://www.protein.osaka-u.ac.jp/rcsfp/pi/ Haruki Nakamura] ([http://www.protein.osaka-u.ac.jp/index_e.php Institute for Protein Research], [http://www.osaka-u.ac.jp/eng/index.html Osaka Univeristy]), with the support from [http://www-bird.jst.go.jp/index_e.html JST-BIRD].


&lt;gallery&gt;
File:Spacefill.jpg
File:Cartoon.jpg
File:Surface.jpg
File:edmap.jpg
&lt;/gallery&gt;


== Start up ==
You can start up jV with Java Web Start technology immediately from here.
* [http://ef-site.hgc.jp/jV/stable/jV.jnlp stable JOGL version] (recommended)
* [http://ef-site.hgc.jp/jV/current/jV.jnlp recent JOGL version] 

== Download ==
You can also download the program and start it up locally.
In this case, installing JOGL is required in advance (see [[Installation_of_jV3 | Installation]] page).
The following links take you to the download pages. (latest version is 3.6.4@2009/7/31)
* [http://ef-site.hgc.jp/eF-site/servlet/DownloadViewerBinary binary] 
* [http://ef-site.hgc.jp/eF-site/servlet/Registration source code] (registration will be required)</text>
    <sha1>f19d961cb0e242f04a1369aab775a4c40e753471</sha1>
  </revision>
  <revision>
    <id>334</id>
    <parentid>333</parentid>
    <timestamp>2009-08-22T02:42:38Z</timestamp>
    <contributor>
      <username>IMSsato</username>
      <id>4</id>
    </contributor>
    <comment>/* Download */</comment>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="2289" xml:space="preserve">&lt;big&gt;'''Welcome to jV wiki.'''&lt;/big&gt;

jV version 3 (formerly known as PDBjViewer) is a program to display molecular graphics of protein and nucleic acids. 
jV supports the following features:
* jV can read and display PDBML files, the canonical XML format for the Protein Data Bank.
* Of course, jV can read and display the traditional PDB format files, too.
* RasMol-like usability.
* jV can process more than one molecules.
* jV can display polygons specified by XML. ([http://ef-site.hgc.jp/eF-site/schema/polygon12.xsd XML Schema for polygons] is available.)
* Multiple polygons can be processed simultaneously, and be superimposed onto molecular images.
* Animation can be realized.
* jV runs on the Java Runtime Environment ([http://java.sun.com/javase/index.jsp JRE]) so that it can work as a stand-alone application as well as an applet.
* The graphics of jV is based on OpenGL ([https://jogl.dev.java.net/ JOGL]), thereby producing fairly beautiful pictures.


The program 'jV' has been developed by [http://www.hgc.jp/~kinosita/TOP.html Kengo Kinoshita] ([http://www.hgc.jp/english/ Human Genome Center], [http://www.ims.u-tokyo.ac.jp/imsut/en/ Insutitute for Medical Science],[http://www.u-tokyo.ac.jp/index_e.html University of Tokyo]) and [http://www.protein.osaka-u.ac.jp/rcsfp/pi/ Haruki Nakamura] ([http://www.protein.osaka-u.ac.jp/index_e.php Institute for Protein Research], [http://www.osaka-u.ac.jp/eng/index.html Osaka Univeristy]), with the support from [http://www-bird.jst.go.jp/index_e.html JST-BIRD].


&lt;gallery&gt;
File:Spacefill.jpg
File:Cartoon.jpg
File:Surface.jpg
File:edmap.jpg
&lt;/gallery&gt;


== Start up ==
You can start up jV with Java Web Start technology immediately from here.
* [http://ef-site.hgc.jp/jV/stable/jV.jnlp stable JOGL version] (recommended)
* [http://ef-site.hgc.jp/jV/current/jV.jnlp recent JOGL version] 

== Download ==
You can also download the program and start it up locally.
In this case, installing JOGL is required in advance (see [[Installation_of_jV3 | Installation]] page).
The following links take you to the download pages. (latest version is 3.6.5@2009/8/22)
* [http://ef-site.hgc.jp/eF-site/servlet/DownloadViewerBinary binary] 
* [http://ef-site.hgc.jp/eF-site/servlet/Registration source code] (registration will be required)</text>
    <sha1>1f0b8cb2465ddfbd1ac5f2932b3a72aab6912948</sha1>
  </revision>
  <revision>
    <id>337</id>
    <parentid>334</parentid>
    <timestamp>2009-09-16T02:10:47Z</timestamp>
    <contributor>
      <username>Cudo29</username>
      <id>5</id>
    </contributor>
    <minor/>
    <comment>The URL to the JOGL page was changed because it is redirected to another page.</comment>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="2293" xml:space="preserve">&lt;big&gt;'''Welcome to jV wiki.'''&lt;/big&gt;

jV version 3 (formerly known as PDBjViewer) is a program to display molecular graphics of protein and nucleic acids. 
jV supports the following features:
* jV can read and display PDBML files, the canonical XML format for the Protein Data Bank.
* Of course, jV can read and display the traditional PDB format files, too.
* RasMol-like usability.
* jV can process more than one molecules.
* jV can display polygons specified by XML. ([http://ef-site.hgc.jp/eF-site/schema/polygon12.xsd XML Schema for polygons] is available.)
* Multiple polygons can be processed simultaneously, and be superimposed onto molecular images.
* Animation can be realized.
* jV runs on the Java Runtime Environment ([http://java.sun.com/javase/index.jsp JRE]) so that it can work as a stand-alone application as well as an applet.
* The graphics of jV is based on OpenGL ([http://kenai.com/projects/jogl JOGL]), thereby producing fairly beautiful pictures.


The program 'jV' has been developed by [http://www.hgc.jp/~kinosita/TOP.html Kengo Kinoshita] ([http://www.hgc.jp/english/ Human Genome Center], [http://www.ims.u-tokyo.ac.jp/imsut/en/ Insutitute for Medical Science],[http://www.u-tokyo.ac.jp/index_e.html University of Tokyo]) and [http://www.protein.osaka-u.ac.jp/rcsfp/pi/ Haruki Nakamura] ([http://www.protein.osaka-u.ac.jp/index_e.php Institute for Protein Research], [http://www.osaka-u.ac.jp/eng/index.html Osaka Univeristy]), with the support from [http://www-bird.jst.go.jp/index_e.html JST-BIRD].


&lt;gallery&gt;
File:Spacefill.jpg
File:Cartoon.jpg
File:Surface.jpg
File:edmap.jpg
&lt;/gallery&gt;


== Start up ==
You can start up jV with Java Web Start technology immediately from here.
* [http://ef-site.hgc.jp/jV/stable/jV.jnlp stable JOGL version] (recommended)
* [http://ef-site.hgc.jp/jV/current/jV.jnlp recent JOGL version] 

== Download ==
You can also download the program and start it up locally.
In this case, installing JOGL is required in advance (see [[Installation_of_jV3 | Installation]] page).
The following links take you to the download pages. (latest version is 3.6.5@2009/8/22)
* [http://ef-site.hgc.jp/eF-site/servlet/DownloadViewerBinary binary] 
* [http://ef-site.hgc.jp/eF-site/servlet/Registration source code] (registration will be required)</text>
    <sha1>c2f2007a01db4bf6fffaf4a16c20e26f11b64736</sha1>
  </revision>
  <revision>
    <id>340</id>
    <parentid>337</parentid>
    <timestamp>2009-09-16T02:37:49Z</timestamp>
    <contributor>
      <username>Cudo29</username>
      <id>5</id>
    </contributor>
    <comment>Some links of other document resources were added.</comment>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="2505" xml:space="preserve">&lt;big&gt;'''Welcome to jV wiki.'''&lt;/big&gt;

jV version 3 (formerly known as PDBjViewer) is a program to display molecular graphics of protein and nucleic acids. 
jV supports the following features:
* jV can read and display PDBML files, the canonical XML format for the Protein Data Bank.
* Of course, jV can read and display the traditional PDB format files, too.
* RasMol-like usability.
* jV can process more than one molecules.
* jV can display polygons specified by XML. ([http://ef-site.hgc.jp/eF-site/schema/polygon12.xsd XML Schema for polygons] is available.)
* Multiple polygons can be processed simultaneously, and be superimposed onto molecular images.
* Animation can be realized.
* jV runs on the Java Runtime Environment ([http://java.sun.com/javase/index.jsp JRE]) so that it can work as a stand-alone application as well as an applet.
* The graphics of jV is based on OpenGL ([http://kenai.com/projects/jogl JOGL]), thereby producing fairly beautiful pictures.


The program 'jV' has been developed by [http://www.hgc.jp/~kinosita/TOP.html Kengo Kinoshita] ([http://www.hgc.jp/english/ Human Genome Center], [http://www.ims.u-tokyo.ac.jp/imsut/en/ Insutitute for Medical Science],[http://www.u-tokyo.ac.jp/index_e.html University of Tokyo]) and [http://www.protein.osaka-u.ac.jp/rcsfp/pi/ Haruki Nakamura] ([http://www.protein.osaka-u.ac.jp/index_e.php Institute for Protein Research], [http://www.osaka-u.ac.jp/eng/index.html Osaka Univeristy]), with the support from [http://www-bird.jst.go.jp/index_e.html JST-BIRD].


&lt;gallery&gt;
File:Spacefill.jpg
File:Cartoon.jpg
File:Surface.jpg
File:edmap.jpg
&lt;/gallery&gt;


== Start up ==
You can start up jV with Java Web Start technology immediately from here.
* [http://ef-site.hgc.jp/jV/stable/jV.jnlp stable JOGL version] (recommended)
* [http://ef-site.hgc.jp/jV/current/jV.jnlp recent JOGL version] 

== Download ==
You can also download the program and start it up locally.
In this case, installing JOGL is required in advance (see [[Installation_of_jV3 | Installation]] page).
The following links take you to the download pages. (latest version is 3.6.5@2009/8/22)
* [http://ef-site.hgc.jp/eF-site/servlet/DownloadViewerBinary binary] 
* [http://ef-site.hgc.jp/eF-site/servlet/Registration source code] (registration will be required)

== Other resources ==

* PDBj Help page in [http://doc.pdbj.org/help?jV English]/[http://doc.pdbj.org/help_jp.cgi?jV Japanese].
* [http://doc.pdbj.org/jV/manual.html Japanese documents] with some usage samples.</text>
    <sha1>a70604fd5a768fd397d13788307671e37467cb22</sha1>
  </revision>
  <revision>
    <id>341</id>
    <parentid>340</parentid>
    <timestamp>2009-10-06T05:52:08Z</timestamp>
    <contributor>
      <username>IMSsato</username>
      <id>4</id>
    </contributor>
    <comment>/* Start up */</comment>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="2530" xml:space="preserve">&lt;big&gt;'''Welcome to jV wiki.'''&lt;/big&gt;

jV version 3 (formerly known as PDBjViewer) is a program to display molecular graphics of protein and nucleic acids. 
jV supports the following features:
* jV can read and display PDBML files, the canonical XML format for the Protein Data Bank.
* Of course, jV can read and display the traditional PDB format files, too.
* RasMol-like usability.
* jV can process more than one molecules.
* jV can display polygons specified by XML. ([http://ef-site.hgc.jp/eF-site/schema/polygon12.xsd XML Schema for polygons] is available.)
* Multiple polygons can be processed simultaneously, and be superimposed onto molecular images.
* Animation can be realized.
* jV runs on the Java Runtime Environment ([http://java.sun.com/javase/index.jsp JRE]) so that it can work as a stand-alone application as well as an applet.
* The graphics of jV is based on OpenGL ([http://kenai.com/projects/jogl JOGL]), thereby producing fairly beautiful pictures.


The program 'jV' has been developed by [http://www.hgc.jp/~kinosita/TOP.html Kengo Kinoshita] ([http://www.hgc.jp/english/ Human Genome Center], [http://www.ims.u-tokyo.ac.jp/imsut/en/ Insutitute for Medical Science],[http://www.u-tokyo.ac.jp/index_e.html University of Tokyo]) and [http://www.protein.osaka-u.ac.jp/rcsfp/pi/ Haruki Nakamura] ([http://www.protein.osaka-u.ac.jp/index_e.php Institute for Protein Research], [http://www.osaka-u.ac.jp/eng/index.html Osaka Univeristy]), with the support from [http://www-bird.jst.go.jp/index_e.html JST-BIRD].


&lt;gallery&gt;
File:Spacefill.jpg
File:Cartoon.jpg
File:Surface.jpg
File:edmap.jpg
&lt;/gallery&gt;


== Start up ==
You can start up jV with Java Web Start technology immediately from here.
* [http://ef-site.hgc.jp/eF-site/servlet/stable/jV.jnlp stable JOGL version] (recommended)
* [http://ef-site.hgc.jp/eF-site/servlet/current/jV.jnlp recent JOGL version]

== Download ==
You can also download the program and start it up locally.
In this case, installing JOGL is required in advance (see [[Installation_of_jV3 | Installation]] page).
The following links take you to the download pages. (latest version is 3.6.5@2009/8/22)
* [http://ef-site.hgc.jp/eF-site/servlet/DownloadViewerBinary binary] 
* [http://ef-site.hgc.jp/eF-site/servlet/Registration source code] (registration will be required)

== Other resources ==

* PDBj Help page in [http://doc.pdbj.org/help?jV English]/[http://doc.pdbj.org/help_jp.cgi?jV Japanese].
* [http://doc.pdbj.org/jV/manual.html Japanese documents] with some usage samples.</text>
    <sha1>c1f5143a42b55044194e3a6733dadd2e504959dd</sha1>
  </revision>
  <revision>
    <id>342</id>
    <parentid>341</parentid>
    <timestamp>2009-10-06T05:54:39Z</timestamp>
    <contributor>
      <username>IMSsato</username>
      <id>4</id>
    </contributor>
    <comment>/* Start up */</comment>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="2517" xml:space="preserve">&lt;big&gt;'''Welcome to jV wiki.'''&lt;/big&gt;

jV version 3 (formerly known as PDBjViewer) is a program to display molecular graphics of protein and nucleic acids. 
jV supports the following features:
* jV can read and display PDBML files, the canonical XML format for the Protein Data Bank.
* Of course, jV can read and display the traditional PDB format files, too.
* RasMol-like usability.
* jV can process more than one molecules.
* jV can display polygons specified by XML. ([http://ef-site.hgc.jp/eF-site/schema/polygon12.xsd XML Schema for polygons] is available.)
* Multiple polygons can be processed simultaneously, and be superimposed onto molecular images.
* Animation can be realized.
* jV runs on the Java Runtime Environment ([http://java.sun.com/javase/index.jsp JRE]) so that it can work as a stand-alone application as well as an applet.
* The graphics of jV is based on OpenGL ([http://kenai.com/projects/jogl JOGL]), thereby producing fairly beautiful pictures.


The program 'jV' has been developed by [http://www.hgc.jp/~kinosita/TOP.html Kengo Kinoshita] ([http://www.hgc.jp/english/ Human Genome Center], [http://www.ims.u-tokyo.ac.jp/imsut/en/ Insutitute for Medical Science],[http://www.u-tokyo.ac.jp/index_e.html University of Tokyo]) and [http://www.protein.osaka-u.ac.jp/rcsfp/pi/ Haruki Nakamura] ([http://www.protein.osaka-u.ac.jp/index_e.php Institute for Protein Research], [http://www.osaka-u.ac.jp/eng/index.html Osaka Univeristy]), with the support from [http://www-bird.jst.go.jp/index_e.html JST-BIRD].


&lt;gallery&gt;
File:Spacefill.jpg
File:Cartoon.jpg
File:Surface.jpg
File:edmap.jpg
&lt;/gallery&gt;


== Start up ==
You can start up jV with Java Web Start technology immediately from here.
* [http://ef-site.hgc.jp/jV/stable/jV.jnlp stable JOGL version] (recommended)
* [http://ef-site.hgc.jp/eF-site/servlet/current/jV.jnlp recent JOGL version]

== Download ==
You can also download the program and start it up locally.
In this case, installing JOGL is required in advance (see [[Installation_of_jV3 | Installation]] page).
The following links take you to the download pages. (latest version is 3.6.5@2009/8/22)
* [http://ef-site.hgc.jp/eF-site/servlet/DownloadViewerBinary binary] 
* [http://ef-site.hgc.jp/eF-site/servlet/Registration source code] (registration will be required)

== Other resources ==

* PDBj Help page in [http://doc.pdbj.org/help?jV English]/[http://doc.pdbj.org/help_jp.cgi?jV Japanese].
* [http://doc.pdbj.org/jV/manual.html Japanese documents] with some usage samples.</text>
    <sha1>39f8a9cd0965d2a45e4232d0db4d1db3e0be133f</sha1>
  </revision>
  <revision>
    <id>343</id>
    <parentid>342</parentid>
    <timestamp>2009-10-06T06:00:24Z</timestamp>
    <contributor>
      <username>IMSsato</username>
      <id>4</id>
    </contributor>
    <comment>/* Start up */</comment>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="2504" xml:space="preserve">&lt;big&gt;'''Welcome to jV wiki.'''&lt;/big&gt;

jV version 3 (formerly known as PDBjViewer) is a program to display molecular graphics of protein and nucleic acids. 
jV supports the following features:
* jV can read and display PDBML files, the canonical XML format for the Protein Data Bank.
* Of course, jV can read and display the traditional PDB format files, too.
* RasMol-like usability.
* jV can process more than one molecules.
* jV can display polygons specified by XML. ([http://ef-site.hgc.jp/eF-site/schema/polygon12.xsd XML Schema for polygons] is available.)
* Multiple polygons can be processed simultaneously, and be superimposed onto molecular images.
* Animation can be realized.
* jV runs on the Java Runtime Environment ([http://java.sun.com/javase/index.jsp JRE]) so that it can work as a stand-alone application as well as an applet.
* The graphics of jV is based on OpenGL ([http://kenai.com/projects/jogl JOGL]), thereby producing fairly beautiful pictures.


The program 'jV' has been developed by [http://www.hgc.jp/~kinosita/TOP.html Kengo Kinoshita] ([http://www.hgc.jp/english/ Human Genome Center], [http://www.ims.u-tokyo.ac.jp/imsut/en/ Insutitute for Medical Science],[http://www.u-tokyo.ac.jp/index_e.html University of Tokyo]) and [http://www.protein.osaka-u.ac.jp/rcsfp/pi/ Haruki Nakamura] ([http://www.protein.osaka-u.ac.jp/index_e.php Institute for Protein Research], [http://www.osaka-u.ac.jp/eng/index.html Osaka Univeristy]), with the support from [http://www-bird.jst.go.jp/index_e.html JST-BIRD].


&lt;gallery&gt;
File:Spacefill.jpg
File:Cartoon.jpg
File:Surface.jpg
File:edmap.jpg
&lt;/gallery&gt;


== Start up ==
You can start up jV with Java Web Start technology immediately from here.
* [http://ef-site.hgc.jp/jV/stable/jV.jnlp stable JOGL version] (recommended)
* [http://ef-site.hgc.jp/jV/current/jV.jnlp recent JOGL version]

== Download ==
You can also download the program and start it up locally.
In this case, installing JOGL is required in advance (see [[Installation_of_jV3 | Installation]] page).
The following links take you to the download pages. (latest version is 3.6.5@2009/8/22)
* [http://ef-site.hgc.jp/eF-site/servlet/DownloadViewerBinary binary] 
* [http://ef-site.hgc.jp/eF-site/servlet/Registration source code] (registration will be required)

== Other resources ==

* PDBj Help page in [http://doc.pdbj.org/help?jV English]/[http://doc.pdbj.org/help_jp.cgi?jV Japanese].
* [http://doc.pdbj.org/jV/manual.html Japanese documents] with some usage samples.</text>
    <sha1>927a162096e6ce525713027ab1c1109ebf915080</sha1>
  </revision>
  <revision>
    <id>344</id>
    <parentid>343</parentid>
    <timestamp>2009-10-06T06:09:25Z</timestamp>
    <contributor>
      <username>IMSsato</username>
      <id>4</id>
    </contributor>
    <comment>/* Start up */</comment>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="2530" xml:space="preserve">&lt;big&gt;'''Welcome to jV wiki.'''&lt;/big&gt;

jV version 3 (formerly known as PDBjViewer) is a program to display molecular graphics of protein and nucleic acids. 
jV supports the following features:
* jV can read and display PDBML files, the canonical XML format for the Protein Data Bank.
* Of course, jV can read and display the traditional PDB format files, too.
* RasMol-like usability.
* jV can process more than one molecules.
* jV can display polygons specified by XML. ([http://ef-site.hgc.jp/eF-site/schema/polygon12.xsd XML Schema for polygons] is available.)
* Multiple polygons can be processed simultaneously, and be superimposed onto molecular images.
* Animation can be realized.
* jV runs on the Java Runtime Environment ([http://java.sun.com/javase/index.jsp JRE]) so that it can work as a stand-alone application as well as an applet.
* The graphics of jV is based on OpenGL ([http://kenai.com/projects/jogl JOGL]), thereby producing fairly beautiful pictures.


The program 'jV' has been developed by [http://www.hgc.jp/~kinosita/TOP.html Kengo Kinoshita] ([http://www.hgc.jp/english/ Human Genome Center], [http://www.ims.u-tokyo.ac.jp/imsut/en/ Insutitute for Medical Science],[http://www.u-tokyo.ac.jp/index_e.html University of Tokyo]) and [http://www.protein.osaka-u.ac.jp/rcsfp/pi/ Haruki Nakamura] ([http://www.protein.osaka-u.ac.jp/index_e.php Institute for Protein Research], [http://www.osaka-u.ac.jp/eng/index.html Osaka Univeristy]), with the support from [http://www-bird.jst.go.jp/index_e.html JST-BIRD].


&lt;gallery&gt;
File:Spacefill.jpg
File:Cartoon.jpg
File:Surface.jpg
File:edmap.jpg
&lt;/gallery&gt;


== Start up ==
You can start up jV with Java Web Start technology immediately from here.
* [http://ef-site.hgc.jp/eF-site/servlet/stable/jV.jnlp stable JOGL version] (recommended)
* [http://ef-site.hgc.jp/eF-site/servlet/current/jV.jnlp recent JOGL version]

== Download ==
You can also download the program and start it up locally.
In this case, installing JOGL is required in advance (see [[Installation_of_jV3 | Installation]] page).
The following links take you to the download pages. (latest version is 3.6.5@2009/8/22)
* [http://ef-site.hgc.jp/eF-site/servlet/DownloadViewerBinary binary] 
* [http://ef-site.hgc.jp/eF-site/servlet/Registration source code] (registration will be required)

== Other resources ==

* PDBj Help page in [http://doc.pdbj.org/help?jV English]/[http://doc.pdbj.org/help_jp.cgi?jV Japanese].
* [http://doc.pdbj.org/jV/manual.html Japanese documents] with some usage samples.</text>
    <sha1>c1f5143a42b55044194e3a6733dadd2e504959dd</sha1>
  </revision>
</page>
<page arvcontinue="20090423011428|304">
  <title>MediaWiki:Sidebar</title>
  <ns>8</ns>
  <id>5</id>
  <revision>
    <id>308</id>
    <parentid>303</parentid>
    <timestamp>2009-04-23T02:17:37Z</timestamp>
    <contributor>
      <username>WikiSysop</username>
      <id>1</id>
    </contributor>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="329" xml:space="preserve">* contents
** How to use|How to use
** Installation_of_jV3 | Installation
** Links|Links
** old version|Old version
* navigation
** mainpage|mainpage-description
** portal-url|portal
** currentevents-url|currentevents
** recentchanges-url|recentchanges
** randompage-url|randompage
** helppage|help
* SEARCH
* TOOLBOX
* LANGUAGES</text>
    <sha1>c4d579457f2d7cf8b500c29191204e1c874fbcc0</sha1>
  </revision>
</page>
<page arvcontinue="20090423011428|304">
  <title>Old version</title>
  <ns>0</ns>
  <id>6</id>
  <revision>
    <id>314</id>
    <parentid>270</parentid>
    <timestamp>2009-04-23T03:02:34Z</timestamp>
    <contributor>
      <username>WikiSysop</username>
      <id>1</id>
    </contributor>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="1440" xml:space="preserve">== jV version 1 (PDBjViewer) ==
Visualization of structure and surface of molecules is performed by a Java applet program called 'PDBjViewer'.

In order to use PDBjViewer, [http://java.sun.com/products/plugin/ Java Plug-in] and
[http://java.sun.com/products/java-media/3D/ Java 3D API] must be installed on your computer.
The version requirements are as follows.&lt;br /&gt;
* JRE (includes Java Plug-in) 1.4.1 or later (recommend 1.4.2)
* Java 3D API (OpenGL) 1.2.1 or later (recommend 1.2.1_04)
Important notes
# You can select two kinds of implementation of Java 3D, OpenGL version and DirectX version. But, PDBjViewer only work with OpenGL version at present.
# PDBjViewer does not work with JRE from 1.4.1_03 to 1.4.1_06.&lt;br /&gt;

== jV version 2 ==
jV version 2 is an advanced version of PDBjViewer, which can be used only as a stand-alone program. It enables to display more than one molecule images at the same time and their display models and transforms can be operated separately. An animation of molecules can be also performed. jV version 2 runs with .NET framework 1.1 on the Windows platform. Therefore the .NET framework must be installed on your computer.

== Download ==
You can download the older versions from the same download pages with the current version.
* [http://ef-site.hgc.jp/eF-site/servlet/DownloadViewerBinary binary]
* [http://ef-site.hgc.jp/eF-site/servlet/Registration source code] (registration will be required)</text>
    <sha1>3b95554e6a1662b8f1cf27a2575da1346151d173</sha1>
  </revision>
</page>
<page arvcontinue="20090423011428|304">
  <title>How to use</title>
  <ns>0</ns>
  <id>11</id>
  <revision>
    <id>317</id>
    <parentid>299</parentid>
    <timestamp>2009-04-23T03:10:59Z</timestamp>
    <contributor>
      <username>WikiSysop</username>
      <id>1</id>
    </contributor>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="1120" xml:space="preserve">The following table shows how to do the minimum things with jV; the mouse controls.
For the detail, see the reference manual and User's guide.&lt;br /&gt;
{| class="wikitable" border="1" style="margin:0 auto" 
 ! Action !! Window, Linux !! Mac OS X 
 |-
 ! style="text-align:left" | rotate around X,Y axes
 | left drag || drag
 |-
 ! style="text-align:left" | rotate around Z axis
 | Shift + right drag || Shift + command + drag
 |-
 ! style="text-align:left" | translate along X,Y axes
 | right drag || command + drag
 |-
 ! style="text-align:left" | translate along Z axis (zoom in/out)
 | Shift + left drag || Shift + drag
 |-
 ! style="text-align:left" | translate slab plane along Z axis
 | (Alt or Ctrl) + left drag || Alt + drag
 |}


; The reference manual
# [[Introduction]]
# [[Command List]]
# [[Atom Expression]]
# [[Vertex Expression]]
# [[Color Expression]]
# [[Use as Applet]]


; User's Guide ([[Media:JV3_User'sGuide.pdf|PDF]])
# [[Tutorials]]
# [[GUI]]
# [[Document type of the polygon file]]
# [[Functional site information for molecules]]


;Some examples
# [[Animation]]
# [[User jV with applet launcher]]</text>
    <sha1>49cb7d092c66c5a53dac43bef888a58874c42cbd</sha1>
  </revision>
  <revision>
    <id>318</id>
    <parentid>317</parentid>
    <timestamp>2009-04-23T03:12:03Z</timestamp>
    <contributor>
      <username>WikiSysop</username>
      <id>1</id>
    </contributor>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="1084" xml:space="preserve">The following table shows how to do the minimum things with jV; the mouse controls.
For the detail, see the reference manual and User's guide.&lt;br /&gt;
{| class="wikitable" border="1" style="margin:0 auto" 
 ! Action !! Window, Linux !! Mac OS X 
 |-
 ! style="text-align:left" | rotate around X,Y axes
 | left drag || drag
 |-
 ! style="text-align:left" | rotate around Z axis
 | Shift + right drag || Shift + command + drag
 |-
 ! style="text-align:left" | translate along X,Y axes
 | right drag || command + drag
 |-
 ! style="text-align:left" | translate along Z axis (zoom in/out)
 | Shift + left drag || Shift + drag
 |-
 ! style="text-align:left" | translate slab plane along Z axis
 | (Alt or Ctrl) + left drag || Alt + drag
 |}


; The reference manual
# [[Introduction]]
# [[Command List]]
# [[Atom Expression]]
# [[Vertex Expression]]
# [[Color Expression]]
# [[Use as Applet]]


; User's Guide
# [[Tutorials]]
# [[GUI]]
# [[Document type of the polygon file]]
# [[Functional site information for molecules]]


;Some examples
# [[Animation]]
# [[User jV with applet launcher]]</text>
    <sha1>c8e716d1ba61d4525e7ac33a08b1a918e2c07031</sha1>
  </revision>
  <revision>
    <id>325</id>
    <parentid>318</parentid>
    <timestamp>2009-07-07T02:05:47Z</timestamp>
    <contributor>
      <username>WikiSysop</username>
      <id>1</id>
    </contributor>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="1083" xml:space="preserve">The following table shows how to do the minimum things with jV; the mouse controls.
For the detail, see the reference manual and User's guide.&lt;br /&gt;
{| class="wikitable" border="1" style="margin:0 auto" 
 ! Action !! Window, Linux !! Mac OS X 
 |-
 ! style="text-align:left" | rotate around X,Y axes
 | left drag || drag
 |-
 ! style="text-align:left" | rotate around Z axis
 | Shift + right drag || Shift + command + drag
 |-
 ! style="text-align:left" | translate along X,Y axes
 | right drag || command + drag
 |-
 ! style="text-align:left" | translate along Z axis (zoom in/out)
 | Shift + left drag || Shift + drag
 |-
 ! style="text-align:left" | translate slab plane along Z axis
 | (Alt or Ctrl) + left drag || Alt + drag
 |}


; The reference manual
# [[Introduction]]
# [[Command List]]
# [[Atom Expression]]
# [[Vertex Expression]]
# [[Color Expression]]
# [[Use as Applet]]


; User's Guide
# [[Tutorials]]
# [[GUI]]
# [[Document type of the polygon file]]
# [[Functional site information for molecules]]


;Some examples
# [[Animation]]
# [[Use jV with applet launcher]]</text>
    <sha1>1b03d1a77c84c4595d46bee0d39f0d9a683f8ab5</sha1>
  </revision>
  <revision>
    <id>329</id>
    <parentid>325</parentid>
    <timestamp>2009-07-07T07:26:12Z</timestamp>
    <contributor>
      <username>WikiSysop</username>
      <id>1</id>
    </contributor>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="1315" xml:space="preserve">The following table shows how to do the minimum things with jV; the mouse controls.
For the detail, see the reference manual and User's guide.&lt;br /&gt;
{| class="wikitable" border="1" style="margin:0 auto" 
 ! Action !! Window, Linux !! Mac OS X 
 |-
 ! style="text-align:left" | rotate around X,Y axes
 | left drag || drag
 |-
 ! style="text-align:left" | rotate around Z axis
 | Shift + right drag || Shift + command + drag
 |-
 ! style="text-align:left" | translate along X,Y axes
 | right drag || command + drag
 |-
 ! style="text-align:left" | translate along Z axis (zoom in/out)
 | Shift + left drag || Shift + drag
 |-
 ! style="text-align:left" | translate slab plane along Z axis
 | (Alt or Ctrl) + left drag || Alt + drag
 |}


'''Note''': when visiting a web page that contains a jV applet with Internet Explorer,
there sometimes occurs trouble in working with native JOGL libraries especially on Windows Vista.
Please use Firefox web browser in that case.


; The reference manual
# [[Introduction]]
# [[Command List]]
# [[Atom Expression]]
# [[Vertex Expression]]
# [[Color Expression]]
# [[Use as Applet]]


; User's Guide
# [[Tutorials]]
# [[GUI]]
# [[Document type of the polygon file]]
# [[Functional site information for molecules]]


;Some examples
# [[Animation]]
# [[Use jV with applet launcher]]</text>
    <sha1>1bd9e6a7ce6b5551f77e6de5f4380786c2630a48</sha1>
  </revision>
  <revision>
    <id>345</id>
    <parentid>329</parentid>
    <timestamp>2009-10-09T15:17:08Z</timestamp>
    <contributor>
      <username>Nancy</username>
      <id>6</id>
    </contributor>
    <minor/>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="1362" xml:space="preserve">The following table shows how to do the minimum things with jV; the mouse controls.
For the detail, see the reference manual and User's guide.&lt;br /&gt;
{| class="wikitable" border="1" style="margin:0 auto" 
 ! Action !! Window, Linux !! Mac OS X 
 |-
 ! style="text-align:left" | rotate around X,Y axes
 | left drag || drag
 |-
 ! style="text-align:left" | rotate around Z axis
 | Shift + right drag || Shift + command + drag
 |-
 ! style="text-align:left" | translate along X,Y axes
 | right drag || command + drag
 |-
 ! style="text-align:left" | translate along Z axis (zoom in/out)
 | Shift + left drag || Shift + drag
 |-
 ! style="text-align:left" | translate slab plane along Z axis
 | (Alt or Ctrl) + left drag || Alt + drag
 |}


'''Note''': when visiting a web page that contains a jV applet with Internet Explorer,
there sometimes occurs trouble in working with native JOGL libraries especially on Windows Vista.
Please use Firefox web browser in that case.


; The reference manual
# [[Introduction]]
# [[Command List]]
# [[Atom Expression]]
# [[Vertex Expression]]
# [[Color Expression]]
# [[Use as Applet]]


; User's Guide
# [[Tutorials]]
# [[GUI]]
# [[Document type of the polygon file]]
# [[Functional site information for molecules]]
# [http://www.superiorpapers.com/ term papers]


;Some examples
# [[Animation]]
# [[Use jV with applet launcher]]</text>
    <sha1>554656125dbcc7756fd4ef9ed5046e0610c12d0d</sha1>
  </revision>
  <revision>
    <id>346</id>
    <parentid>345</parentid>
    <timestamp>2009-11-10T01:06:36Z</timestamp>
    <contributor>
      <username>IMSsato</username>
      <id>4</id>
    </contributor>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="1315" xml:space="preserve">The following table shows how to do the minimum things with jV; the mouse controls.
For the detail, see the reference manual and User's guide.&lt;br /&gt;
{| class="wikitable" border="1" style="margin:0 auto" 
 ! Action !! Window, Linux !! Mac OS X 
 |-
 ! style="text-align:left" | rotate around X,Y axes
 | left drag || drag
 |-
 ! style="text-align:left" | rotate around Z axis
 | Shift + right drag || Shift + command + drag
 |-
 ! style="text-align:left" | translate along X,Y axes
 | right drag || command + drag
 |-
 ! style="text-align:left" | translate along Z axis (zoom in/out)
 | Shift + left drag || Shift + drag
 |-
 ! style="text-align:left" | translate slab plane along Z axis
 | (Alt or Ctrl) + left drag || Alt + drag
 |}


'''Note''': when visiting a web page that contains a jV applet with Internet Explorer,
there sometimes occurs trouble in working with native JOGL libraries especially on Windows Vista.
Please use Firefox web browser in that case.


; The reference manual
# [[Introduction]]
# [[Command List]]
# [[Atom Expression]]
# [[Vertex Expression]]
# [[Color Expression]]
# [[Use as Applet]]


; User's Guide
# [[Tutorials]]
# [[GUI]]
# [[Document type of the polygon file]]
# [[Functional site information for molecules]]


;Some examples
# [[Animation]]
# [[Use jV with applet launcher]]</text>
    <sha1>1bd9e6a7ce6b5551f77e6de5f4380786c2630a48</sha1>
  </revision>
  <revision>
    <id>353</id>
    <parentid>346</parentid>
    <timestamp>2009-11-13T08:29:41Z</timestamp>
    <contributor>
      <username>IMSsato</username>
      <id>4</id>
    </contributor>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="1079" xml:space="preserve">The following table shows how to do the minimum things with jV; the mouse controls.
For the detail, see the reference manual and User's guide.&lt;br /&gt;
{| class="wikitable" border="1" style="margin:0 auto" 
 ! Action !! Window, Linux !! Mac OS X 
 |-
 ! style="text-align:left" | rotate around X,Y axes
 | left drag || drag
 |-
 ! style="text-align:left" | rotate around Z axis
 | Shift + right drag || Shift + command + drag
 |-
 ! style="text-align:left" | translate along X,Y axes
 | right drag || command + drag
 |-
 ! style="text-align:left" | translate along Z axis (zoom in/out)
 | Shift + left drag || Shift + drag
 |-
 ! style="text-align:left" | translate slab plane along Z axis
 | (Alt or Ctrl) + left drag || Alt + drag
 |}


; Reference manual
# [[Introduction]]
# [[Command List]]
# [[Atom Expression]]
# [[Vertex Expression]]
# [[Color Expression]]
# [[Use as Applet]]


; User's Guide
# [[Tutorials]]
# [[GUI]]
# [[Document type of the polygon file]]
# [[Functional site information for molecules]]


;Some examples
# [[Animation]]
# [[Use jV with applet launcher]]</text>
    <sha1>81df095754e7e56181d5fafbd35300d69d70314e</sha1>
  </revision>
</page>
<page arvcontinue="20090423011428|304">
  <title>Release note</title>
  <ns>0</ns>
  <id>17</id>
  <revision>
    <id>319</id>
    <parentid>272</parentid>
    <timestamp>2009-04-23T03:13:42Z</timestamp>
    <contributor>
      <username>WikiSysop</username>
      <id>1</id>
    </contributor>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="2807" xml:space="preserve">Changes and improvements have been made as follows.

* version 3.1
** The following commands have been added; 'animrange', 'set adjustview', 'show godata', and 'show xps3'.
** The xPSSS expression has been added in order to select a group of atoms.
** Several public methods have been added to the applet so as to append molecule or polygon files after the applet started.
** The applet can send information about mouse-picked atoms to JavaScript.
* version 3.1.1
** Some problems in GUI menu [Options]-[Hetero Atoms] and [Hydrogens] have been fixed.
** Some problems in 'trace' command have been fixed.
* version 3.1.2
** eF-site ID has been changed to a new format.
* version 3.1.3
** Some problems in xps3 atom selection have been fixed.
* version 3.1.4
** Some problems in finalization process of openGL rendering have been fixed.
* version 3.1.5
** The output of 'show xps3' command has been modified.
** Some problems in 'save png/jpeg' command have been fixed.
* version 3.1.6
** Some problems in loading an empty polygon file have been fixed.
* version 3.1.7
** Some problems in initialization process of the applet have been fixed.
* version 3.2
** 'show site' command has been added.
* version 3.3 beta 1
** Availabe JOGL version is restricted to JSR-231 beta 5 only.
* version 3.3
** Both the previous JOGL (version 1.1.1) and JSR-231 are available.
** The following commands have been added; 'set viewpoint', 'show viewpoint', 'set imagesize', and 'show imagesize'.
* version 3.3.1
** Some problems in reading a pdbMLplus file have been fixed.
* version 3.4
** PDB format version 3 can be processed.
* version 3.5
** Discrimination of DNA and RNA linking nucleotides is based on [http://remediation.wwpdb.org/downloads.html Chemical Component Dictionary] for PDB format version 3.
** The default representation of the cartoon model has been changed. Commands 'set cartoon_loop_tube', 'set cartoon_round' and 'set ribbonback' have been added.
** The default parameters of lighting have been changed. Commands 'set ambient', 'set diffuse1', 'set diffuse1_direction', 'set diffuse2' and 'set diffuse1_direction' have been added.
** Commands 'set pdbml_noatom_url', 'set pdbml_extatom_url', 'set pdbml_plus_url', 'set efsite_url', 'set ext_site_url', 'show pdbml_url', 'show efsite_url' and 'show ext_site_url' have been added.
** The command-line option '-stdin' has been added to receive commands from stdin stream.
* version 3.6
** Users can specify the JavaScript function name used in Applet-to-JavaScript Communication.
** Applet parameter 'file_load_message' has been added.
* version 3.6.1
** Predefined set of residues has been modified.
** Old JOGL API is not supported.
* version 3.6.2
** Latest version of PDBML can be processed.
** Some problems in mouse control on Mac have been fixed.</text>
    <sha1>ddc5ac9bea24101504779d487bdc0a501a99a150</sha1>
  </revision>
</page>
<page arvcontinue="20090423011428|304">
  <title>Introduction</title>
  <ns>0</ns>
  <id>44</id>
  <revision>
    <id>320</id>
    <parentid>300</parentid>
    <timestamp>2009-04-23T03:14:57Z</timestamp>
    <contributor>
      <username>WikiSysop</username>
      <id>1</id>
    </contributor>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="1923" xml:space="preserve">jV is an interactive 3D viewer program to visualize protein and nucleic acid molecules. The program reads in a PDBML file that is an XML format for PDB. Usual PDB format files are also accepted. More than one molecule files can be opened and displayed at the same time and their display models and transforms can be operated separately. In addition to molecule files, a polygon file written in XML can be read and displayed. More than one polygon files can be opened at the same time and superposed on molecule images. The [http://ef-site.hgc.jp/eF-site/schema/polygon12.xsd XML schema] of the polygon file is available. jV can perform an animation of molecules. The animation file is a PDB format file in which each frame is separated by a MODEL line.

jV runs on Java Runtime Environment ([http://java.sun.com/j2se/1.4.2/download.html JRE]) and can be used both as a standalone program and an applet. The 3D rendering is performed with the use of [https://jogl.dev.java.net/ JOGL] API. The version requirements are as follows.

* JRE (includes Java Plug-in) 1.4.2 or later
* JOGL JSR-231 1.0.0 or later

Here, [http://java.sun.com/products/plugin/ Java Plug-in] is required in order to use the program as an applet.

The program allows an interactive mouse control and command execution. The commnad syntax follows that of [http://www.rasmol.org/ Rasmol] with some modifications. In order to handle the transform of each molecule and polygon separately, every files are set to be either selected or not selected. The transform operation commands, such as rotate or translate, act only on selected files. On the other hand, every atoms in a molecule are also set to be either selected or not selected independently of whether the molecule itself is selected or not selected. Only selected atoms are the target of display model operations, such as wireframe or spacefill commands, and coloring operations.

[[Release note]]</text>
    <sha1>60ebf37efd5a73d8746330656470c0afbd8de626</sha1>
  </revision>
  <revision>
    <id>338</id>
    <parentid>320</parentid>
    <timestamp>2009-09-16T02:12:25Z</timestamp>
    <contributor>
      <username>Cudo29</username>
      <id>5</id>
    </contributor>
    <minor/>
    <comment>The URL to the JOGL page was changed because it is redirected to another page.</comment>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="1927" xml:space="preserve">jV is an interactive 3D viewer program to visualize protein and nucleic acid molecules. The program reads in a PDBML file that is an XML format for PDB. Usual PDB format files are also accepted. More than one molecule files can be opened and displayed at the same time and their display models and transforms can be operated separately. In addition to molecule files, a polygon file written in XML can be read and displayed. More than one polygon files can be opened at the same time and superposed on molecule images. The [http://ef-site.hgc.jp/eF-site/schema/polygon12.xsd XML schema] of the polygon file is available. jV can perform an animation of molecules. The animation file is a PDB format file in which each frame is separated by a MODEL line.

jV runs on Java Runtime Environment ([http://java.sun.com/j2se/1.4.2/download.html JRE]) and can be used both as a standalone program and an applet. The 3D rendering is performed with the use of [http://kenai.com/projects/jogl JOGL] API. The version requirements are as follows.

* JRE (includes Java Plug-in) 1.4.2 or later
* JOGL JSR-231 1.0.0 or later

Here, [http://java.sun.com/products/plugin/ Java Plug-in] is required in order to use the program as an applet.

The program allows an interactive mouse control and command execution. The commnad syntax follows that of [http://www.rasmol.org/ Rasmol] with some modifications. In order to handle the transform of each molecule and polygon separately, every files are set to be either selected or not selected. The transform operation commands, such as rotate or translate, act only on selected files. On the other hand, every atoms in a molecule are also set to be either selected or not selected independently of whether the molecule itself is selected or not selected. Only selected atoms are the target of display model operations, such as wireframe or spacefill commands, and coloring operations.

[[Release note]]</text>
    <sha1>1557e3dff4487d238da0206e11d40956671b8172</sha1>
  </revision>
</page>
<page arvcontinue="20090423011428|304">
  <title>Atom Expression</title>
  <ns>0</ns>
  <id>21</id>
  <revision>
    <id>322</id>
    <parentid>162</parentid>
    <timestamp>2009-06-05T07:47:54Z</timestamp>
    <contributor>
      <username>WikiSysop</username>
      <id>1</id>
    </contributor>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="9238" xml:space="preserve">{| style="float:right"
 |__TOC__
 |}
In order to specify a group of atoms in a molecule, the following five expressions are available.

The standard boolean connectives 'and', 'or' and 'not', and brackets can be used to construct a complex expression. The boolean connectives may be abbreviated as '&amp;', '|', and '|', respectively. 

== predefined set ==
=== element name ===
Element names, such as carbon or nitrogen, can be used to select atoms. 
=== set based on residue property ===
a) amino acids in protein molecule
&lt;table border="1"&gt;
&lt;tr&gt;
&lt;td&gt;&lt;/td&gt;
&lt;td&gt;ALA&lt;/td&gt;&lt;td&gt;ARG&lt;/td&gt;&lt;td&gt;ASN&lt;/td&gt;&lt;td&gt;ASP&lt;/td&gt;&lt;td&gt;CYS&lt;/td&gt;
&lt;td&gt;GLU&lt;/td&gt;&lt;td&gt;GLN&lt;/td&gt;&lt;td&gt;GLY&lt;/td&gt;&lt;td&gt;HIS&lt;/td&gt;&lt;td&gt;ILE&lt;/td&gt;
&lt;td&gt;LEU&lt;/td&gt;&lt;td&gt;LYS&lt;/td&gt;&lt;td&gt;MET&lt;/td&gt;&lt;td&gt;PHE&lt;/td&gt;&lt;td&gt;PRO&lt;/td&gt;
&lt;td&gt;SER&lt;/td&gt;&lt;td&gt;THR&lt;/td&gt;&lt;td&gt;TRP&lt;/td&gt;&lt;td&gt;TYR&lt;/td&gt;&lt;td&gt;VAL&lt;/td&gt;
&lt;/tr&gt;
&lt;tr&gt;
&lt;td&gt;Acidic&lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;/tr&gt;
&lt;tr&gt;
&lt;td&gt;Acyclic&lt;/td&gt;
&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;
&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;
&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;&lt;/td&gt;&lt;td&gt;&lt;/td&gt;
&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;&lt;/td&gt;&lt;td&gt;&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;
&lt;/tr&gt;
&lt;tr&gt;
&lt;td&gt;Aliphatic&lt;/td&gt;
&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;
&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;
&lt;/tr&gt;
&lt;tr&gt;
&lt;td&gt;Aromatic&lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;/tr&gt;
&lt;tr&gt;
&lt;td&gt;Basic&lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;/tr&gt;
&lt;tr&gt;
&lt;td&gt;Buried&lt;/td&gt;
&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;
&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;
&lt;/tr&gt;
&lt;tr&gt;
&lt;td&gt;Charged&lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;/tr&gt;
&lt;tr&gt;
&lt;td&gt;Cyclic&lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;/tr&gt;
&lt;tr&gt;
&lt;td&gt;Hydrophobic&lt;/td&gt;
&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;
&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;
&lt;/tr&gt;
&lt;tr&gt;
&lt;td&gt;Large&lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;
&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;/tr&gt;
&lt;tr&gt;
&lt;td&gt;Medium&lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;
&lt;/tr&gt;
&lt;tr&gt;
&lt;td&gt;Negative&lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;/tr&gt;
&lt;tr&gt;
&lt;td&gt;Neutral&lt;/td&gt;
&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;
&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;
&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;
&lt;/tr&gt;
&lt;tr&gt;
&lt;td&gt;Polar&lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;
&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;/tr&gt;
&lt;tr&gt;
&lt;td&gt;Positive&lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;/tr&gt;
&lt;tr&gt;
&lt;td&gt;Small&lt;/td&gt;
&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;/tr&gt;
&lt;tr&gt;
&lt;td&gt;Surface&lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;
&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;/tr&gt;
&lt;tr&gt;
&lt;td&gt;Cysteine&lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;/tr&gt;
&lt;tr&gt;
&lt;td&gt;Amino&lt;/td&gt;
&lt;td colspan="20"&gt;above 20 amino acids + ASX, GLX, PCA, HYP&lt;/td&gt;
&lt;/tr&gt;
&lt;tr&gt;
&lt;td&gt;Protein&lt;/td&gt;
&lt;td colspan="20"&gt;above 20 amino acids + ASX, GLX, PCA, HYP, UNK, ACE, FOR&lt;/td&gt;
&lt;/tr&gt;
&lt;/table&gt;

b) nucleotides
&lt;table border="1"&gt;
&lt;tr&gt;
&lt;td&gt;&lt;/td&gt;
&lt;td&gt;  A&lt;/td&gt;&lt;td&gt;  C&lt;/td&gt;&lt;td&gt;  G&lt;/td&gt;&lt;td&gt;  T&lt;/td&gt;&lt;td&gt;  U&lt;/td&gt;
&lt;td&gt; +U&lt;/td&gt;&lt;td&gt;  I&lt;/td&gt;&lt;td&gt;1MA&lt;/td&gt;&lt;td&gt;5MC&lt;/td&gt;&lt;td&gt;OMC&lt;/td&gt;
&lt;td&gt;1MG&lt;/td&gt;&lt;td&gt;2MG&lt;/td&gt;&lt;td&gt;M2G&lt;/td&gt;&lt;td&gt;7MG&lt;/td&gt;&lt;td&gt;OMG&lt;/td&gt;
&lt;td&gt; YG&lt;/td&gt;&lt;td&gt;H2U&lt;/td&gt;&lt;td&gt;5MU&lt;/td&gt;&lt;td&gt;PSU&lt;/td&gt;
&lt;/tr&gt;
&lt;tr&gt;
&lt;td&gt;AT&lt;/td&gt;
&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;/tr&gt;
&lt;tr&gt;
&lt;td&gt;CG&lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;/tr&gt;
&lt;tr&gt;
&lt;td&gt;Purine&lt;/td&gt;
&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;/tr&gt;
&lt;tr&gt;
&lt;td&gt;Pyrimidine&lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;/tr&gt;
&lt;tr&gt;
&lt;td&gt;DNA&lt;/td&gt;
&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;/tr&gt;
&lt;tr&gt;
&lt;td&gt;RNA&lt;/td&gt;
&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;
&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;
&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;
&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;
&lt;/tr&gt;
&lt;tr&gt;
&lt;td&gt;Nucleic&lt;/td&gt;
&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;
&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;
&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;
&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;
&lt;/tr&gt;
&lt;/table&gt;

c) others
&lt;table border="1"&gt;
&lt;tr&gt;
&lt;td&gt;&lt;/td&gt;
&lt;td&gt;HOH&lt;/td&gt;&lt;td&gt;DOD&lt;/td&gt;&lt;td&gt;SO4&lt;/td&gt;&lt;td&gt;PO4&lt;/td&gt;
&lt;/tr&gt;
&lt;tr&gt;
&lt;td&gt;Water&lt;/td&gt;
&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;/tr&gt;
&lt;tr&gt;
&lt;td&gt;Ions&lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;
&lt;/tr&gt;
&lt;tr&gt;
&lt;td&gt;Solvent&lt;/td&gt;
&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;
&lt;/tr&gt;
&lt;/table&gt;

=== others ===


== comparison operators ==
Parts of a molecule can be selected using equality, inequality and ordering operators on their properties. Possible operators are =, ==, &lt;&gt;, !=, /=, &lt;, &lt;=, &gt; and &gt;=, and possible property names are as follows.
{| border="1"
 |-
 | AtomNo || atom ID in PDB files.
 |-
 | ElemNo || atomic number.
 |-
 | ResNo || residue ID in PDB files.
 |-
 | Radius || radius of a ball image of atoms.
 |-
 | Temperature || temperature factor of atoms.
 |-
 | Model || model ID in PDB files.
 |-
 | File || File ID.
 |}

== residue range ==
A group of atoms in a molecule can be selected by the residue ID. For example, command 'select 3' selects atoms whose residue ID is 3, and 'select 3-10' selects atoms whose residue ID is larger than or equal to 3 and smaller than or equal to 10. 
Optionally, the chain ID can be specified after residue range with a colon.
For example, command 'select 3:A' selects atoms
whose residue ID is 3 in the A chain.

== within expression ==
A within expression selects atoms that exist within a specified distance from another set of atoms. For example, 'select within(3.0, backbone) selects atoms within a 3.0 Angstrom radius of any atom in a protein or nucleic acid backbone. 

== xPSSS expression ==
A xPSSS expression selects a group of atoms according to molecule's properties defined in the 'PDBML plus' file. It takes the following form;
 xps3:keyword
For example, 'select xps3:binding'. The keywords available for each molecule are obtained by the 'show xps3' command.

== primitive expression ==
A primitive expression takes such a form as
 residue name[residue ID][:chain ID][.atom name][;alternate location][/model ID][@file ID]
Here, residue name and atom name are three letter and four letter name, respectively, and terms in square brackets can be omitted. For example, command 'select SER.CA' selects all alpha carbon atoms in serine.</text>
    <sha1>b60892afad22074c2bc99ae4a06ccc828c10b713</sha1>
  </revision>
</page>
<page arvcontinue="20090423011428|304">
  <title>Use jV applet with applet launcher</title>
  <ns>0</ns>
  <id>16</id>
  <revision>
    <id>323</id>
    <parentid>118</parentid>
    <timestamp>2009-07-07T02:05:37Z</timestamp>
    <contributor>
      <username>WikiSysop</username>
      <id>1</id>
    </contributor>
    <minor/>
    <comment>moved [[User jV with applet launcher]] to [[Use jV with applet launcher]]</comment>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="1809" xml:space="preserve">A brief introduction to use jV in applet.

== Minimum Example ==
To use jV applet, the best way is to with applet-launcher. jV after v3.6 is fully compatible with applet-launcher.

 &lt;applet
   hspace="0" vspace="0" align="middle"
   name="jVwindow" height="600" width="600"
   archive="applet-launcher.jar,
   http://download.java.net/media/jogl/builds/archive/jsr-231-webstart-current/jogl.jar,
   http://download.java.net/media/gluegen/webstart/gluegen-rt.jar,jv3_6.jar"
   code="org.jdesktop.applet.util.JNLPAppletLauncher"&gt;
 &lt;!-- param for applet-launcher --&gt;
   &lt;param name="subapplet.classname" value="org.pdbj.viewer.gui.ViewerApplet"&gt;
   &lt;param name="subapplet.displayname" value="jV applet"&gt;
   &lt;param name="noddraw.check" value="true"/&gt;
   &lt;param name="noddraw.check.silent" value="true"/&gt;
   &lt;param name="progressbar" value="true"/&gt;
   &lt;param name="jnlpNumExtensions" value="1"/&gt;
   &lt;param name="jnlpExtension1"
    value="http://download.java.net/media/jogl/builds/archive/jsr-231-webstart-current/jogl.jnlp"/&gt;
 &lt;!-- param for jV --&gt;
   &lt;param value="" name="pdbURL"&gt;
    &lt;!-- replace the following with an appropriate URL --&gt;
   &lt;param name="pdbmlURL" value="http://eprots.protein.osaka-u.ac.jp/Rep_PDBML/1ashA1.xml.gz"&gt;
   &lt;param value="" name="polygonURL"&gt;
   &lt;param value="set picking ident;background black;wireframe off;cartoon;color group" name="commands"&gt;
 &lt;/applet&gt;

Upper part is almost same as the usual usage of applet launcher. See the [https://applet-launcher.dev.java.net/ applet-launcher page] for details. The latter part is for jV parameters.

Only the &lt;B&gt;bold face&lt;/B&gt; part is specific for jV.

To use this template, you need to get applet-launcher.jar from http://download.java.net/media/applet-launcher/applet-launcher.jar, and put it in the same server that jv.jar is placed.</text>
    <sha1>e09af424ae486de899890049d36488828393cd3e</sha1>
  </revision>
  <revision>
    <id>328</id>
    <parentid>323</parentid>
    <timestamp>2009-07-07T02:27:04Z</timestamp>
    <contributor>
      <username>WikiSysop</username>
      <id>1</id>
    </contributor>
    <comment>/* Minimum Example */</comment>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="1866" xml:space="preserve">A brief introduction to use jV in applet.

== Minimum Example ==
To use jV applet, the best way is to with applet-launcher. jV after v3.6 is fully compatible with applet-launcher.

 &lt;applet
   hspace="0" vspace="0" align="middle"
   name="jVwindow" height="600" width="600"
   archive="applet-launcher.jar,
   http://download.java.net/media/jogl/builds/archive/jsr-231-webstart-current/jogl.jar,
   http://download.java.net/media/gluegen/webstart/gluegen-rt.jar,'''jv3_6.jar'''"
   code="org.jdesktop.applet.util.JNLPAppletLauncher"&gt;
 &amp;lt;!-- param for applet-launcher --&gt;
   &lt;param name="subapplet.classname" value="'''org.pdbj.viewer.gui.ViewerApplet'''"&gt;
   &lt;param name="subapplet.displayname" value="jV applet"&gt;
   &lt;param name="noddraw.check" value="true"/&gt;
   &lt;param name="noddraw.check.silent" value="true"/&gt;
   &lt;param name="progressbar" value="true"/&gt;
   &lt;param name="jnlpNumExtensions" value="1"/&gt;
   &lt;param name="jnlpExtension1"
    value="http://download.java.net/media/jogl/builds/archive/jsr-231-webstart-current/jogl.jnlp"/&gt;
 '''&amp;lt;!-- param for jV --&gt;'''
   '''&lt;param value="" name="pdbURL"&gt;'''
    '''&amp;lt;!-- replace the following with an appropriate URL --&gt;'''
   '''&lt;param name="pdbmlURL" value="http://eprots.protein.osaka-u.ac.jp/Rep_PDBML/1ashA1.xml.gz"&gt;'''
   '''&lt;param value="" name="polygonURL"&gt;'''
   '''&lt;param value="set picking ident;background black;wireframe off;cartoon;color group" name="commands"&gt;'''
 &lt;/applet&gt;

Upper part is almost same as the usual usage of applet launcher. See the [https://applet-launcher.dev.java.net/ applet-launcher page] for details. The latter part is for jV parameters.

Only the &lt;B&gt;bold face&lt;/B&gt; part is specific for jV.

To use this template, you need to get applet-launcher.jar from http://download.java.net/media/applet-launcher/applet-launcher.jar, and put it in the same server that jv.jar is placed.</text>
    <sha1>f01610660b3a6c8317dc80063c6f99a5ef5d4b6b</sha1>
  </revision>
</page>
<page arvcontinue="20090423011428|304">
  <title>User jV with applet launcher</title>
  <ns>0</ns>
  <id>45</id>
  <revision>
    <id>324</id>
    <timestamp>2009-07-07T02:05:37Z</timestamp>
    <contributor>
      <username>WikiSysop</username>
      <id>1</id>
    </contributor>
    <comment>moved [[User jV with applet launcher]] to [[Use jV with applet launcher]]</comment>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="41" xml:space="preserve">#REDIRECT [[Use jV with applet launcher]]</text>
    <sha1>1261cc7bc82e40caa0b81868492652a51eaaca15</sha1>
  </revision>
</page>
<page arvcontinue="20090423011428|304">
  <title>Use as Applet</title>
  <ns>0</ns>
  <id>24</id>
  <revision>
    <id>330</id>
    <parentid>180</parentid>
    <timestamp>2009-07-09T05:34:11Z</timestamp>
    <contributor>
      <username>WikiSysop</username>
      <id>1</id>
    </contributor>
    <comment>/* Parameters */</comment>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="3481" xml:space="preserve">{| style="float:right"
 |__TOC__
 |}

== Introduction ==
In order to use jV as an applet, [http://java.sun.com/products/plugin/ Java Plug-in] must be installed on client computers. The applet is called from usual APPLET tags, or OBJECT and EMBED tags in HTML (see [http://java.sun.com/products/plugin/ Java Plug-in] homepage), where class name that should be called is "org.pdbj.viewer.gui.ViewerApplet" class. The program has following features.
* whether to use the command line interface or not can be specified
* whether to use the file control panel or not can be specified
* whether to use the popup menu or not can be specified
* witihin applets in the same web page, mouse events can be shared
* applet can receive a command string from JaveScript
* applet can send information about mouse-picked atoms to JavaScript.

== Parameters ==
To initialize the applet, the following parameters can be specified in HTML.
{| class="wikitable" border="1"
 ! parameter !! value 
 |-
 | pdbmlURL || URL of the PDBML files to be loaded (delimited by comma for more than one files).
 |-
 | pdbURL || URL of the PDB files to be loaded (delimited by comma for more than one files).
 |-
 | polygonURL || URL of the polygon files to be loaded (delimited by comma for more than one files).
 |-
 | animURL || URL of the animation files to be loaded (delimited by comma for more than one files).
 |-
 | command_area || whether to use the command line interface or not (true or false).
 |-
 | file_control || whether to use the file control panel or not (true or false).
 |-
 | popup_menu || whether to use the popup menu or not (true or false).
 |-
 | mouse_send_to || name property of applets with which mouse events are shared (delimited by comma for more than one applets).
 |-
 | commands || initial commands that are executed when the applet starts (delimited by semicolon for more than one commands).
 |-
 | report_picking || whether to send information about mouse-picked atoms to JavaScript or not (true or false).
 |-
 | picking_receiver || JavaScript function name that receives mouse-picking data.
 |-
 | file_load_message || whether to show a message dialog while loading a file (true or false).
|}

== JavaScript-to-Applet Communication ==
The ViewerApplet class has some public methods, which can be called from JavaScript.

 void executeCommand(String commands)

Through this method, the applet can receive some arbitrary commands (delimited by semicolon).

 void loadPDB(String fileLocation)
 void loadPDBML(String fileLocation)
 void loadPolygon(String fileLocation)
 void loadAnim(String fileLocation)

Using these methods, PDB file, PDBML file, polygon file, and animation file specified by URL can be loaded respectively.

 void loadPDB(String fileLocation, int fitTo)
 void loadPDBML(String fileLocation, int fitTo)
 void loadPolygon(String fileLocation, int fitTo)
 void loadAnim(String fileLocation, int fitTo)

When these methods are used, the transform matrix of the loaded file is set identical to that of the specified file. 

== Applet-to-JavaScript Communication ==
In order to send the result of mouse-picking to JavaScript, the following function must be defined in JavaScript.

 function receiveMousePick(file, model, chain, res, atom, altloc, resName, atomName, x, y, z)

In addition, a new attribute 'MAYSCRIPT' is required in APPLET or OBJECT/EMBED tags (see [http://java.sun.com/j2se/1.4.2/docs/guide/plugin/developer_guide/java_js.html Java Plug-in guide]).</text>
    <sha1>07d12822f838618db9bf52468ef56500fa36a065</sha1>
  </revision>
  <revision>
    <id>331</id>
    <parentid>330</parentid>
    <timestamp>2009-07-09T05:34:35Z</timestamp>
    <contributor>
      <username>WikiSysop</username>
      <id>1</id>
    </contributor>
    <comment>/* Applet-to-JavaScript Communication */</comment>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="3634" xml:space="preserve">{| style="float:right"
 |__TOC__
 |}

== Introduction ==
In order to use jV as an applet, [http://java.sun.com/products/plugin/ Java Plug-in] must be installed on client computers. The applet is called from usual APPLET tags, or OBJECT and EMBED tags in HTML (see [http://java.sun.com/products/plugin/ Java Plug-in] homepage), where class name that should be called is "org.pdbj.viewer.gui.ViewerApplet" class. The program has following features.
* whether to use the command line interface or not can be specified
* whether to use the file control panel or not can be specified
* whether to use the popup menu or not can be specified
* witihin applets in the same web page, mouse events can be shared
* applet can receive a command string from JaveScript
* applet can send information about mouse-picked atoms to JavaScript.

== Parameters ==
To initialize the applet, the following parameters can be specified in HTML.
{| class="wikitable" border="1"
 ! parameter !! value 
 |-
 | pdbmlURL || URL of the PDBML files to be loaded (delimited by comma for more than one files).
 |-
 | pdbURL || URL of the PDB files to be loaded (delimited by comma for more than one files).
 |-
 | polygonURL || URL of the polygon files to be loaded (delimited by comma for more than one files).
 |-
 | animURL || URL of the animation files to be loaded (delimited by comma for more than one files).
 |-
 | command_area || whether to use the command line interface or not (true or false).
 |-
 | file_control || whether to use the file control panel or not (true or false).
 |-
 | popup_menu || whether to use the popup menu or not (true or false).
 |-
 | mouse_send_to || name property of applets with which mouse events are shared (delimited by comma for more than one applets).
 |-
 | commands || initial commands that are executed when the applet starts (delimited by semicolon for more than one commands).
 |-
 | report_picking || whether to send information about mouse-picked atoms to JavaScript or not (true or false).
 |-
 | picking_receiver || JavaScript function name that receives mouse-picking data.
 |-
 | file_load_message || whether to show a message dialog while loading a file (true or false).
|}

== JavaScript-to-Applet Communication ==
The ViewerApplet class has some public methods, which can be called from JavaScript.

 void executeCommand(String commands)

Through this method, the applet can receive some arbitrary commands (delimited by semicolon).

 void loadPDB(String fileLocation)
 void loadPDBML(String fileLocation)
 void loadPolygon(String fileLocation)
 void loadAnim(String fileLocation)

Using these methods, PDB file, PDBML file, polygon file, and animation file specified by URL can be loaded respectively.

 void loadPDB(String fileLocation, int fitTo)
 void loadPDBML(String fileLocation, int fitTo)
 void loadPolygon(String fileLocation, int fitTo)
 void loadAnim(String fileLocation, int fitTo)

When these methods are used, the transform matrix of the loaded file is set identical to that of the specified file. 

== Applet-to-JavaScript Communication ==
In order to send the result of mouse-picking to JavaScript, the following function must be defined in JavaScript.

 function receiveMousePick(file, model, chain, res, atom, altloc, resName, atomName, x, y, z)

In addition, a new attribute 'MAYSCRIPT' is required in APPLET or OBJECT/EMBED tags (see [http://java.sun.com/j2se/1.4.2/docs/guide/plugin/developer_guide/java_js.html Java Plug-in guide]).
The function name 'receiveMousePick' is a default name. It can be changed by specifying the 'picking_receiver' parameter in APPLET or OBJECT/EMBED tags.</text>
    <sha1>9ca566285e1f9c46e004e749b1b067e692910cfb</sha1>
  </revision>
  <revision>
    <id>335</id>
    <parentid>331</parentid>
    <timestamp>2009-08-22T02:46:26Z</timestamp>
    <contributor>
      <username>IMSsato</username>
      <id>4</id>
    </contributor>
    <comment>/* Parameters */</comment>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="3737" xml:space="preserve">{| style="float:right"
 |__TOC__
 |}

== Introduction ==
In order to use jV as an applet, [http://java.sun.com/products/plugin/ Java Plug-in] must be installed on client computers. The applet is called from usual APPLET tags, or OBJECT and EMBED tags in HTML (see [http://java.sun.com/products/plugin/ Java Plug-in] homepage), where class name that should be called is "org.pdbj.viewer.gui.ViewerApplet" class. The program has following features.
* whether to use the command line interface or not can be specified
* whether to use the file control panel or not can be specified
* whether to use the popup menu or not can be specified
* witihin applets in the same web page, mouse events can be shared
* applet can receive a command string from JaveScript
* applet can send information about mouse-picked atoms to JavaScript.

== Parameters ==
To initialize the applet, the following parameters can be specified in HTML.
{| class="wikitable" border="1"
 ! parameter !! value 
 |-
 | pdbmlURL || URL of the PDBML files to be loaded (delimited by comma for more than one files).
 |-
 | pdbURL || URL of the PDB files to be loaded (delimited by comma for more than one files).
 |-
 | polygonURL || URL of the polygon files to be loaded (delimited by comma for more than one files).
 |-
 | animURL || URL of the animation files to be loaded (delimited by comma for more than one files).
 |-
 | command_area || whether to use the command line interface or not (true or false).
 |-
 | file_control || whether to use the file control panel or not (true or false).
 |-
 | popup_menu || whether to use the popup menu or not (true or false).
 |-
 | mouse_send_to || name property of applets with which mouse events are shared (delimited by comma for more than one applets).
 |-
 | commands || initial commands that are executed when the applet starts (delimited by semicolon for more than one commands).
 |-
 | report_picking || whether to send information about mouse-picked atoms to JavaScript or not (true or false).
 |-
 | picking_receiver || JavaScript function name that receives mouse-picking data.
 |-
 | file_load_message || whether to show a message dialog while loading a file (true or false).
 |-
 | call_on_start || whether to call a JavaScript function when the applet started (true or false).
|}

== JavaScript-to-Applet Communication ==
The ViewerApplet class has some public methods, which can be called from JavaScript.

 void executeCommand(String commands)

Through this method, the applet can receive some arbitrary commands (delimited by semicolon).

 void loadPDB(String fileLocation)
 void loadPDBML(String fileLocation)
 void loadPolygon(String fileLocation)
 void loadAnim(String fileLocation)

Using these methods, PDB file, PDBML file, polygon file, and animation file specified by URL can be loaded respectively.

 void loadPDB(String fileLocation, int fitTo)
 void loadPDBML(String fileLocation, int fitTo)
 void loadPolygon(String fileLocation, int fitTo)
 void loadAnim(String fileLocation, int fitTo)

When these methods are used, the transform matrix of the loaded file is set identical to that of the specified file. 

== Applet-to-JavaScript Communication ==
In order to send the result of mouse-picking to JavaScript, the following function must be defined in JavaScript.

 function receiveMousePick(file, model, chain, res, atom, altloc, resName, atomName, x, y, z)

In addition, a new attribute 'MAYSCRIPT' is required in APPLET or OBJECT/EMBED tags (see [http://java.sun.com/j2se/1.4.2/docs/guide/plugin/developer_guide/java_js.html Java Plug-in guide]).
The function name 'receiveMousePick' is a default name. It can be changed by specifying the 'picking_receiver' parameter in APPLET or OBJECT/EMBED tags.</text>
    <sha1>44f48ac388f6c3609e75ef36a52bf086681b0bad</sha1>
  </revision>
  <revision>
    <id>336</id>
    <parentid>335</parentid>
    <timestamp>2009-08-22T02:48:51Z</timestamp>
    <contributor>
      <username>IMSsato</username>
      <id>4</id>
    </contributor>
    <comment>/* Applet-to-JavaScript Communication */</comment>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="4018" xml:space="preserve">{| style="float:right"
 |__TOC__
 |}

== Introduction ==
In order to use jV as an applet, [http://java.sun.com/products/plugin/ Java Plug-in] must be installed on client computers. The applet is called from usual APPLET tags, or OBJECT and EMBED tags in HTML (see [http://java.sun.com/products/plugin/ Java Plug-in] homepage), where class name that should be called is "org.pdbj.viewer.gui.ViewerApplet" class. The program has following features.
* whether to use the command line interface or not can be specified
* whether to use the file control panel or not can be specified
* whether to use the popup menu or not can be specified
* witihin applets in the same web page, mouse events can be shared
* applet can receive a command string from JaveScript
* applet can send information about mouse-picked atoms to JavaScript.

== Parameters ==
To initialize the applet, the following parameters can be specified in HTML.
{| class="wikitable" border="1"
 ! parameter !! value 
 |-
 | pdbmlURL || URL of the PDBML files to be loaded (delimited by comma for more than one files).
 |-
 | pdbURL || URL of the PDB files to be loaded (delimited by comma for more than one files).
 |-
 | polygonURL || URL of the polygon files to be loaded (delimited by comma for more than one files).
 |-
 | animURL || URL of the animation files to be loaded (delimited by comma for more than one files).
 |-
 | command_area || whether to use the command line interface or not (true or false).
 |-
 | file_control || whether to use the file control panel or not (true or false).
 |-
 | popup_menu || whether to use the popup menu or not (true or false).
 |-
 | mouse_send_to || name property of applets with which mouse events are shared (delimited by comma for more than one applets).
 |-
 | commands || initial commands that are executed when the applet starts (delimited by semicolon for more than one commands).
 |-
 | report_picking || whether to send information about mouse-picked atoms to JavaScript or not (true or false).
 |-
 | picking_receiver || JavaScript function name that receives mouse-picking data.
 |-
 | file_load_message || whether to show a message dialog while loading a file (true or false).
 |-
 | call_on_start || whether to call a JavaScript function when the applet started (true or false).
|}

== JavaScript-to-Applet Communication ==
The ViewerApplet class has some public methods, which can be called from JavaScript.

 void executeCommand(String commands)

Through this method, the applet can receive some arbitrary commands (delimited by semicolon).

 void loadPDB(String fileLocation)
 void loadPDBML(String fileLocation)
 void loadPolygon(String fileLocation)
 void loadAnim(String fileLocation)

Using these methods, PDB file, PDBML file, polygon file, and animation file specified by URL can be loaded respectively.

 void loadPDB(String fileLocation, int fitTo)
 void loadPDBML(String fileLocation, int fitTo)
 void loadPolygon(String fileLocation, int fitTo)
 void loadAnim(String fileLocation, int fitTo)

When these methods are used, the transform matrix of the loaded file is set identical to that of the specified file. 

== Applet-to-JavaScript Communication ==
In order to send the result of mouse-picking to JavaScript, the following function must be defined in JavaScript.

 function receiveMousePick(file, model, chain, res, atom, altloc, resName, atomName, x, y, z)

The function name 'receiveMousePick' is a default name. It can be changed by specifying the 'picking_receiver' parameter in APPLET or OBJECT/EMBED tags.

When the applet started, it invokes the following JavScript function 

 function jvOnStart(name)

if it is configured to do so by the applet parameter 'call_on_start'. Here the function receives the name of the applet as its argument. 

In order to enable applet-to-JavaScript communications, a new attribute 'MAYSCRIPT' is required in APPLET or OBJECT/EMBED tags (see [http://java.sun.com/j2se/1.4.2/docs/guide/plugin/developer_guide/java_js.html Java Plug-in guide]).</text>
    <sha1>375d091509e6591e035949a16d13c2008cb82fdc</sha1>
  </revision>
</page>
<page arvcontinue="20090423011428|304">
  <title>Links</title>
  <ns>0</ns>
  <id>4</id>
  <revision>
    <id>339</id>
    <parentid>56</parentid>
    <timestamp>2009-09-16T02:18:03Z</timestamp>
    <contributor>
      <username>Cudo29</username>
      <id>5</id>
    </contributor>
    <minor/>
    <comment>The URL of eProtS was changed to the redirect destination address.</comment>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="1254" xml:space="preserve">== Organization ==
* [http://www-bird.jst.go.jp/index_e.html JST-BIRD]
* [http://www.hgc.jp/english/ Human Genome Center]
* [http://www.protein.osaka-u.ac.jp/home_e/index_e.html Institute for Protein Research]
&lt;br /&gt;

== DBs ==
* [http://ef-site.hgc.jp/eF-site/ eF-site] (DB of electrostatic surface of functional site of proteins)
* [http://ef-site.hgc.jp/eF-seek/ eF-seek] (Prediction of ligand binding site of proteins)
* [http://ef-site.hgc.jp/eF-surf/ eF-surf] (Calculate the molecular surface and electrostatic potential of proteins)
&lt;br /&gt;
* [http://pre-s.protein.osaka-u.ac.jp/~preds/ P&lt;i&gt;re&lt;/i&gt;D&lt;i&gt;s&lt;/i&gt;] (Prediction of DNA-binding site)
* [http://pre-s.protein.osaka-u.ac.jp/~prebi/ PreBI] (Prediction of biological interface of proteins homo-interface)
* [http://pre-s.protein.osaka-u.ac.jp/~preds classPPI] (Classification of homo protein-protein interfaces)
&lt;br /&gt;
* [http://p-cats.hgc.jp/p-cats/ P-cats] (Prediction of Catalytic residues in proteins)
&lt;br /&gt;
* [http://pdbjs3.protein.osaka-u.ac.jp/xPSSS/index.html xPSSS] (xml-based protein structure search service)
* [http://eprots.pdbj.org/ eProtS] (Encyclopedia of protein structures)
* [http://cube.socs.waseda.ac.jp/pages/jsp/index.jsp ProMode] (DB of normal mode analysis of proteins)</text>
    <sha1>440e8e63f534018859e92d66c643d8f49b247759</sha1>
  </revision>
</page>
<page arvcontinue="20090423011428|304">
  <title>File:Java prefs1.png</title>
  <ns>6</ns>
  <id>46</id>
  <revision>
    <id>347</id>
    <timestamp>2009-11-13T05:33:15Z</timestamp>
    <contributor>
      <username>IMSsato</username>
      <id>4</id>
    </contributor>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="0" xml:space="preserve"></text>
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  </revision>
</page>
<page arvcontinue="20090423011428|304">
  <title>File:Java prefs2.png</title>
  <ns>6</ns>
  <id>47</id>
  <revision>
    <id>348</id>
    <timestamp>2009-11-13T05:34:24Z</timestamp>
    <contributor>
      <username>IMSsato</username>
      <id>4</id>
    </contributor>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="0" xml:space="preserve"></text>
    <sha1>da39a3ee5e6b4b0d3255bfef95601890afd80709</sha1>
  </revision>
</page>
<page arvcontinue="20090423011428|304">
  <title>Trouble shooting</title>
  <ns>0</ns>
  <id>48</id>
  <revision>
    <id>349</id>
    <timestamp>2009-11-13T05:35:02Z</timestamp>
    <contributor>
      <username>IMSsato</username>
      <id>4</id>
    </contributor>
    <comment>Created page with '{| style="left"  |__TOC__  |}  == JOGL library conflict ==  If you cannot start jV via Java Web Start or view jV applets due to a failure of locating the JOGL library, try the fo...'</comment>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="2379" xml:space="preserve">{| style="left"
 |__TOC__
 |}

== JOGL library conflict ==

If you cannot start jV via Java Web Start or view jV applets due to a failure of locating the JOGL library, try the followings.

===clear cached files===

On JRE of version 1.6.0_15 and 1.6.0_16, previously cached JOGL files cause a problem
even if newer files are placed on the server.
JRE of version 1.6.0_17 (and later) is recommended.
On Mac OS X Snow Leopard, however, the latest JRE is of version 1.6.0_15 at the moment.
The following steps show how to clear cached files.

1) Double-click the [Macintosh HD]-[Applications]-[Utilities]-[Java Preferences] icon, then the Java Preferences window appears.

[[File:Java_prefs1.png|center|500px]]

2) Choose 'Network' tab.

[[File:Java_prefs2.png|center|500px]]

3) Press 'Delete Files...' button and click 'OK' on the subsequent confirm dialog.

===remove local JOGL library===

Locally-installed JOGL libraries of different version cause conflicts with Java Web Start technology.
JOGL library files are different between operation systems.

'''Mac OS X'''

Open the [Macintosh HD]-[Library]-[Java]-[Extensions] folder.
If some of the following files

* jogl.jar
* gluegen-rt.jar
* libjogl.jnilib
* libjogl_awt.jnilib
* libjogl_cg.jnilib
* libgluegen-rt.jnilib

exist in the folder, remove them.
Here, this operation requires root privilege.

'''Windows'''

Files that should be removed are follows.

* &lt;JRE&gt;\lib\ext\jogl.jar
* &lt;JRE&gt;\lib\ext\gluegen-rt.jar
* &lt;JRE&gt;\bin\jogl.dll
* &lt;JRE&gt;\bin\jogl_cg.dll
* &lt;JRE&gt;\bin\jogl_awt.dll
* &lt;JRE&gt;\bin\gluegen-rt.dll

Here, &lt;JRE&gt; denotes the folder that JRE has been installed; typically &lt;JRE&gt;=C:\Program Files\Java\jre6.

'''Linux'''

Files that should be removed are follows.

* &lt;JRE&gt;/lib/ext/jogl.jar
* &lt;JRE&gt;/lib/ext/gluegen-rt.jar
* &lt;JRE&gt;/lib/&lt;arch&gt;/libjogl.so
* &lt;JRE&gt;/lib/&lt;arch&gt;/libjogl_cg.so
* &lt;JRE&gt;/lib/&lt;arch&gt;/libjogl_awt.so
* &lt;JRE&gt;/lib/&lt;arch&gt;/libjogl_drihack.so
* &lt;JRE&gt;/lib/&lt;arch&gt;/libgluegen-rt.so

Here, &lt;JRE&gt; denotes the directory that JRE has been installed; typically &lt;JRE&gt;=/usr/java/jdk1.6.0_17/jre,
and &lt;arch&gt; the processor architecture such as &lt;arch&gt;=i386.

== jV applet with Internet Explorer ==

When visiting a web page that contains a jV applet with Internet Explorer, there sometimes occurs trouble in working with native JOGL libraries especially on Windows Vista. Please use Firefox web browser in that case.</text>
    <sha1>3607132bf722db22db1a18d57b0e8e730c5acc44</sha1>
  </revision>
  <revision>
    <id>350</id>
    <parentid>349</parentid>
    <timestamp>2009-11-13T05:44:57Z</timestamp>
    <contributor>
      <username>IMSsato</username>
      <id>4</id>
    </contributor>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="2385" xml:space="preserve">{| style="left"
 |__TOC__
 |}

== JOGL library conflict ==

If you cannot start jV via Java Web Start or view jV applets due to a failure of locating the JOGL library, try the followings.

===clear cached files===

On JRE of version 1.6.0_15 and 1.6.0_16, previously cached JOGL files cause a problem
even if newer files are placed on the server.
JRE of version 1.6.0_17 (and later) is recommended.
On Mac OS X Snow Leopard, however, the latest JRE is of version 1.6.0_15 at the moment.
The following steps show how to clear cached files.

1) Double-click the [Macintosh HD]-[Applications]-[Utilities]-[Java Preferences] icon, then the Java Preferences window appears.

[[File:Java_prefs1.png|center|500px]]

2) Choose 'Network' tab.

[[File:Java_prefs2.png|center|500px]]

3) Press 'Delete Files...' button and click 'OK' on the subsequent confirm dialog.

===remove local JOGL library===

Locally-installed JOGL libraries of different version cause conflicts with Java Web Start technology.
JOGL library files are different between operation systems.

'''Mac OS X'''

Open the [Macintosh HD]-[Library]-[Java]-[Extensions] folder.
If some of the following files

* jogl.jar
* gluegen-rt.jar
* libjogl.jnilib
* libjogl_awt.jnilib
* libjogl_cg.jnilib
* libgluegen-rt.jnilib

exist in the folder, remove them.
Here, this operation requires root privilege.

'''Windows'''

Files that should be removed are as follows.

* &lt;JRE&gt;\lib\ext\jogl.jar
* &lt;JRE&gt;\lib\ext\gluegen-rt.jar
* &lt;JRE&gt;\bin\jogl.dll
* &lt;JRE&gt;\bin\jogl_cg.dll
* &lt;JRE&gt;\bin\jogl_awt.dll
* &lt;JRE&gt;\bin\gluegen-rt.dll

Here, &lt;JRE&gt; denotes the folder that JRE has been installed; typically &lt;JRE&gt;=C:\Program Files\Java\jre6.

'''Linux'''

Files that should be removed are as follows.

* &lt;JRE&gt;/lib/ext/jogl.jar
* &lt;JRE&gt;/lib/ext/gluegen-rt.jar
* &lt;JRE&gt;/lib/&lt;arch&gt;/libjogl.so
* &lt;JRE&gt;/lib/&lt;arch&gt;/libjogl_cg.so
* &lt;JRE&gt;/lib/&lt;arch&gt;/libjogl_awt.so
* &lt;JRE&gt;/lib/&lt;arch&gt;/libjogl_drihack.so
* &lt;JRE&gt;/lib/&lt;arch&gt;/libgluegen-rt.so

Here, &lt;JRE&gt; denotes the directory that JRE has been installed; typically &lt;JRE&gt;=/usr/java/jdk1.6.0_17/jre,
and &lt;arch&gt; the processor architecture such as &lt;arch&gt;=i386.

== jV applet with Internet Explorer ==

When visiting a web page that contains a jV applet with Internet Explorer, there sometimes occurs trouble in working with native JOGL libraries especially on Windows Vista. Please use Firefox web browser in that case.</text>
    <sha1>4bff76453a20cee142fc5d8eb2a6cf5c899a7e7c</sha1>
  </revision>
  <revision>
    <id>351</id>
    <parentid>350</parentid>
    <timestamp>2009-11-13T06:21:52Z</timestamp>
    <contributor>
      <username>IMSsato</username>
      <id>4</id>
    </contributor>
    <comment>/* clear cached files */</comment>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="2384" xml:space="preserve">{| style="left"
 |__TOC__
 |}

== JOGL library conflict ==

If you cannot start jV via Java Web Start or view jV applets due to a failure of locating the JOGL library, try the followings.

===clear cached files===

On JRE of version 1.6.0_15 and 1.6.0_16, previously cached JOGL files cause a problem
even if newer files are placed on the server.
JRE of version 1.6.0_17 (or later) is recommended.
On Mac OS X Snow Leopard, however, the latest JRE is of version 1.6.0_15 at the moment.
The following steps show how to clear cached files.

1) Double-click the [Macintosh HD]-[Applications]-[Utilities]-[Java Preferences] icon, then the Java Preferences window appears.

[[File:Java_prefs1.png|center|500px]]

2) Choose 'Network' tab.

[[File:Java_prefs2.png|center|500px]]

3) Press 'Delete Files...' button and click 'OK' on the subsequent confirm dialog.

===remove local JOGL library===

Locally-installed JOGL libraries of different version cause conflicts with Java Web Start technology.
JOGL library files are different between operation systems.

'''Mac OS X'''

Open the [Macintosh HD]-[Library]-[Java]-[Extensions] folder.
If some of the following files

* jogl.jar
* gluegen-rt.jar
* libjogl.jnilib
* libjogl_awt.jnilib
* libjogl_cg.jnilib
* libgluegen-rt.jnilib

exist in the folder, remove them.
Here, this operation requires root privilege.

'''Windows'''

Files that should be removed are as follows.

* &lt;JRE&gt;\lib\ext\jogl.jar
* &lt;JRE&gt;\lib\ext\gluegen-rt.jar
* &lt;JRE&gt;\bin\jogl.dll
* &lt;JRE&gt;\bin\jogl_cg.dll
* &lt;JRE&gt;\bin\jogl_awt.dll
* &lt;JRE&gt;\bin\gluegen-rt.dll

Here, &lt;JRE&gt; denotes the folder that JRE has been installed; typically &lt;JRE&gt;=C:\Program Files\Java\jre6.

'''Linux'''

Files that should be removed are as follows.

* &lt;JRE&gt;/lib/ext/jogl.jar
* &lt;JRE&gt;/lib/ext/gluegen-rt.jar
* &lt;JRE&gt;/lib/&lt;arch&gt;/libjogl.so
* &lt;JRE&gt;/lib/&lt;arch&gt;/libjogl_cg.so
* &lt;JRE&gt;/lib/&lt;arch&gt;/libjogl_awt.so
* &lt;JRE&gt;/lib/&lt;arch&gt;/libjogl_drihack.so
* &lt;JRE&gt;/lib/&lt;arch&gt;/libgluegen-rt.so

Here, &lt;JRE&gt; denotes the directory that JRE has been installed; typically &lt;JRE&gt;=/usr/java/jdk1.6.0_17/jre,
and &lt;arch&gt; the processor architecture such as &lt;arch&gt;=i386.

== jV applet with Internet Explorer ==

When visiting a web page that contains a jV applet with Internet Explorer, there sometimes occurs trouble in working with native JOGL libraries especially on Windows Vista. Please use Firefox web browser in that case.</text>
    <sha1>f8391ba1b0954bad3d848b79a14556066371e757</sha1>
  </revision>
  <revision>
    <id>352</id>
    <parentid>351</parentid>
    <timestamp>2009-11-13T06:35:50Z</timestamp>
    <contributor>
      <username>IMSsato</username>
      <id>4</id>
    </contributor>
    <comment>/* remove local JOGL library */</comment>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="2384" xml:space="preserve">{| style="left"
 |__TOC__
 |}

== JOGL library conflict ==

If you cannot start jV via Java Web Start or view jV applets due to a failure of locating the JOGL library, try the followings.

===clear cached files===

On JRE of version 1.6.0_15 and 1.6.0_16, previously cached JOGL files cause a problem
even if newer files are placed on the server.
JRE of version 1.6.0_17 (or later) is recommended.
On Mac OS X Snow Leopard, however, the latest JRE is of version 1.6.0_15 at the moment.
The following steps show how to clear cached files.

1) Double-click the [Macintosh HD]-[Applications]-[Utilities]-[Java Preferences] icon, then the Java Preferences window appears.

[[File:Java_prefs1.png|center|500px]]

2) Choose 'Network' tab.

[[File:Java_prefs2.png|center|500px]]

3) Press 'Delete Files...' button and click 'OK' on the subsequent confirm dialog.

===remove local JOGL library===

Locally-installed JOGL libraries of different version cause conflicts with Java Web Start technology.
JOGL library files are different between operating systems.

'''Mac OS X'''

Open the [Macintosh HD]-[Library]-[Java]-[Extensions] folder.
If some of the following files

* jogl.jar
* gluegen-rt.jar
* libjogl.jnilib
* libjogl_awt.jnilib
* libjogl_cg.jnilib
* libgluegen-rt.jnilib

exist in the folder, remove them.
Here, this operation requires root privilege.

'''Windows'''

Files that should be removed are as follows.

* &lt;JRE&gt;\lib\ext\jogl.jar
* &lt;JRE&gt;\lib\ext\gluegen-rt.jar
* &lt;JRE&gt;\bin\jogl.dll
* &lt;JRE&gt;\bin\jogl_cg.dll
* &lt;JRE&gt;\bin\jogl_awt.dll
* &lt;JRE&gt;\bin\gluegen-rt.dll

Here, &lt;JRE&gt; denotes the folder that JRE has been installed; typically &lt;JRE&gt;=C:\Program Files\Java\jre6.

'''Linux'''

Files that should be removed are as follows.

* &lt;JRE&gt;/lib/ext/jogl.jar
* &lt;JRE&gt;/lib/ext/gluegen-rt.jar
* &lt;JRE&gt;/lib/&lt;arch&gt;/libjogl.so
* &lt;JRE&gt;/lib/&lt;arch&gt;/libjogl_cg.so
* &lt;JRE&gt;/lib/&lt;arch&gt;/libjogl_awt.so
* &lt;JRE&gt;/lib/&lt;arch&gt;/libjogl_drihack.so
* &lt;JRE&gt;/lib/&lt;arch&gt;/libgluegen-rt.so

Here, &lt;JRE&gt; denotes the directory that JRE has been installed; typically &lt;JRE&gt;=/usr/java/jdk1.6.0_17/jre,
and &lt;arch&gt; the processor architecture such as &lt;arch&gt;=i386.

== jV applet with Internet Explorer ==

When visiting a web page that contains a jV applet with Internet Explorer, there sometimes occurs trouble in working with native JOGL libraries especially on Windows Vista. Please use Firefox web browser in that case.</text>
    <sha1>77f2aab9d5322307423f489902539f0dff032036</sha1>
  </revision>
</page>
<page arvcontinue="20091113083303|354">
  <title>MediaWiki:Sidebar</title>
  <ns>8</ns>
  <id>5</id>
  <revision>
    <id>354</id>
    <parentid>308</parentid>
    <timestamp>2009-11-13T08:33:03Z</timestamp>
    <contributor>
      <username>WikiSysop</username>
      <id>1</id>
    </contributor>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="366" xml:space="preserve">* contents
** How to use|How to use
** Installation_of_jV3 | Installation
** Trouble shooting|Trouble shooting
** Links|Links
** old version|Old version
* navigation
** mainpage|mainpage-description
** portal-url|portal
** currentevents-url|currentevents
** recentchanges-url|recentchanges
** randompage-url|randompage
** helppage|help
* SEARCH
* TOOLBOX
* LANGUAGES</text>
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</page>
<page arvcontinue="20091113083303|354">
  <title>Trouble shooting</title>
  <ns>0</ns>
  <id>48</id>
  <revision>
    <id>355</id>
    <parentid>352</parentid>
    <timestamp>2009-11-26T06:04:21Z</timestamp>
    <contributor>
      <username>IMSsato</username>
      <id>4</id>
    </contributor>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="2713" xml:space="preserve">{| style="left"
 |__TOC__
 |}

== Certificate error on applet ==

When you use JRE6 Update15 (1.6.0_15) or JRE6 Update16 (1.6.0_16) on Windows or Linux,
jV applet and applet-launcher fail to start up with the following error.

 Error:java.io.IOException:Cannot find certificates for JNLP AppletLauncher class

Please use JRE6 Update17 (1.6.0_17) or later.

== JOGL library conflict ==

If you cannot start jV via Java Web Start or view jV applets due to a failure of locating the JOGL library, try the followings.

===clear cached files===

On JRE of version 1.6.0_15 and 1.6.0_16, previously cached JOGL files cause a problem
even if newer files are placed on the server.
JRE of version 1.6.0_17 or later is recommended.
On Mac OS X Snow Leopard, however, the latest JRE is of version 1.6.0_15 at the moment.
The following steps show how to clear cached files.

1) Double-click the [Macintosh HD]-[Applications]-[Utilities]-[Java Preferences] icon, then the Java Preferences window appears.

[[File:Java_prefs1.png|center|500px]]

2) Choose 'Network' tab.

[[File:Java_prefs2.png|center|500px]]

3) Press 'Delete Files...' button and click 'OK' on the subsequent confirmation dialog.

===remove local JOGL library===

Locally-installed JOGL libraries of different version cause conflicts with Java Web Start technology.
JOGL library files are different between operating systems.

'''Mac OS X'''

Open the [Macintosh HD]-[Library]-[Java]-[Extensions] folder.
If some of the following files

* jogl.jar
* gluegen-rt.jar
* libjogl.jnilib
* libjogl_awt.jnilib
* libjogl_cg.jnilib
* libgluegen-rt.jnilib

exist in the folder, remove them.
Here, this operation requires root privilege.

'''Windows'''

Files that should be removed are as follows.

* &lt;JRE&gt;\lib\ext\jogl.jar
* &lt;JRE&gt;\lib\ext\gluegen-rt.jar
* &lt;JRE&gt;\bin\jogl.dll
* &lt;JRE&gt;\bin\jogl_cg.dll
* &lt;JRE&gt;\bin\jogl_awt.dll
* &lt;JRE&gt;\bin\gluegen-rt.dll

Here, &lt;JRE&gt; denotes the folder that JRE has been installed; typically &lt;JRE&gt;=C:\Program Files\Java\jre6.

'''Linux'''

Files that should be removed are as follows.

* &lt;JRE&gt;/lib/ext/jogl.jar
* &lt;JRE&gt;/lib/ext/gluegen-rt.jar
* &lt;JRE&gt;/lib/&lt;arch&gt;/libjogl.so
* &lt;JRE&gt;/lib/&lt;arch&gt;/libjogl_cg.so
* &lt;JRE&gt;/lib/&lt;arch&gt;/libjogl_awt.so
* &lt;JRE&gt;/lib/&lt;arch&gt;/libjogl_drihack.so
* &lt;JRE&gt;/lib/&lt;arch&gt;/libgluegen-rt.so

Here, &lt;JRE&gt; denotes the directory that JRE has been installed; typically &lt;JRE&gt;=/usr/java/jdk1.6.0_17/jre,
and &lt;arch&gt; the processor architecture such as &lt;arch&gt;=i386.

== jV applet with Internet Explorer ==

When visiting a web page that contains a jV applet with Internet Explorer, there sometimes occurs trouble in working with native JOGL libraries especially on Windows Vista. Please use Firefox web browser in that case.</text>
    <sha1>80202768d89e68da08297b32da4cd0f7dc190995</sha1>
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</page>
<page arvcontinue="20091113083303|354">
  <title>Command List</title>
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  <id>20</id>
  <revision>
    <id>356</id>
    <parentid>273</parentid>
    <timestamp>2009-12-03T04:32:49Z</timestamp>
    <contributor>
      <username>Cudo29</username>
      <id>5</id>
    </contributor>
    <comment>Description about disabled command in applet circumstance was added.</comment>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="18715" xml:space="preserve"> {| style="float:right"
  |__TOC__
  |}
Command usage of jV follows that of [http://www.rasmol.org/ Rasmol] with some modifications. In the following part, command arguments that can take an arbitrary value are denoted as &lt;value&gt; for example, arguments restricted to several possible values are listed with / as a delimiter, and arguments that can be omitted are put in brackets {}. Commands, [[#exit|exit]], [[#load|load]], [[#quit|quit]], [[#save|save]], [[#script|script]], and [[#write|write]], are not available in applet circumstance.

== anim ==
 anim forward {&lt;value&gt;}
Starts animation forward. If the &lt;value&gt; is given, just move frames forward by the specified amount.

 anim backward {&lt;value&gt;}
Starts animation backward. If the &lt;value&gt; is given, just move frames backward by the specified amount.

 anim stop
Stops animation.

== animframe ==
 animframe &lt;frame&gt; {&lt;file_ID&gt;}
Sets the frame of all animation files for the specified value. When &lt;file_ID&gt; is given, only the specified file is processed.

== animmode ==
 animmode once
Sets the behavior of animation for 'once'. When the frame reaches the last one, animation is stopped.

 animmode loop
Sets the behavior of animation for 'loop'. When the frame reaches the last one, animation is reset to the first frame and continues playing.

 animmode swing
Sets the behavior of animation for 'swing'. When the frame reaches the last one, the direction of animation is reversed.

== animrange ==
 animrange &lt;init_frame&gt;-&lt;term_frame&gt; {&lt;file_IDs&gt;}
Sets the range of all animation files. When is given, only the specified file is processed.

== animselect ==
 animselect {-a/-r} &lt;file_IDs&gt;
Selects the specified files and makes the others not selected. More than one file IDs can be specified by putting commas as the delimiter. When the option -a or -r is specified, only the selection status of the specified files are modified, selected or not selected, respectively, and the others remain unchanged.

== animspeed ==
 animspeed &lt;speed&gt;
Sets the animation speed. The argument should be an integer value from 1 to 20.

== animstep ==
 animstep &lt;step&gt; {&lt;file_ID&gt;}
Sets the step of all animation files for the specified value. When &lt;file_ID&gt; is given, only the specified file is processed.

== backbone ==
 backbone {on/true}
Turns on the selected backbone bonds.

 backbone off/false
Turns off the selected backbone bonds.

 backbone &lt;radius&gt;
Turns on the selected backbone bonds with the specified raidus (angstrom or Rasmol unit). The maximum parameter value is 2.0.

== background ==
 background &lt;color&gt;
Changes the background color. The color may be given as RGB values [r,g,b], or predefined color names.

== cartoon ==
 cartoon {on/true}
Turns on the thick ribbons for the selected residues.

 cartoon off/false
Turns off the thick ribbons for the selected residues.

 cartoon &lt;half_width&gt;
Turns on the thick ribbons for the selected residues with the specified half width (angstrom or Rasmol unit). The maximum parameter value is 4.0.

== center ==
 center {-r/-s} {&lt;atom_expression&gt;}
Sets the center of rotation and the center of the screen to the center of a group of atoms specified by the atom expression. When the option -r or -s is specified, only the center of rotation or the center of the screen is modified, respectively.

 center {-r} [x, y, z]
Moves the center of rotation and the center of the screen from the current position by the specified amount. When the option -r is specified, only the center of rotation is modified.

 center {-r} {x, y, z}
Sets the center of rotation and the center of the screen to the specified coordinates. When the option -r is specified, only the center of rotation is modified.

 center -s [x, y]
Moves the center of the screen from the current position by the specified amount.

 center -s {x, y}
Sets the center of the screen to the specified coordinates.

== color ==
 color {atoms} &lt;color&gt;
Sets the color of the selected atoms. The color may be given as RGB values [r,g,b], predefined color names, or predefined color schemes; amino, chain, charge, cpk, group, shapely, structure, and temperature.

 color bonds/backbone/ribbons/hbonds/ssbonds &lt;color&gt;
Sets the color of the specified object. The color may be given as RGB values [r,g,b] or predefined color names. For hydrogen bonds, color scheme 'type' can be specified.

 color bonds/backbone/ribbons/hbonds/ssbonds none
Resets the color of the specified object.

== colorvertex ==
 colorvertex &lt;color&gt;
Sets the color of the selected vertices. The color may be given as RGB values [r,g,b] or predefined color names.

 colorvertex none
Resets the color of the selected vertices.

== cpk ==
 cpk
A synonym of the spacefill command.

== define ==
 define &lt;name&gt; &lt;atom_expression&gt;
Associates an arbitrary set of atoms with a unique name.

== display ==
 display all
Displays the image of all files.

 display none
Turns off the image of all files.

 display {-a/-r} &lt;file_IDs&gt;
Displays the image of the specified files and turns off the others. More than one file IDs can be specified by putting commas as the delimiter. When the option -a or -r is specified, turns the image of the specified files on or off, respectively, and the others remain unchanged.

== displayvertex ==
 displayvertex {on/true}
Displays the selected vertices.

 displayvertex off/false
Turns off the selected vertices.

== echo ==
 echo &lt;string&gt;
Echoes the specified message back to the message area.

== exit ==
 exit
Terminates the application.

== fit ==
 fit &lt;file1_ID&gt; &lt;file2_ID&gt;
Sets the transform matrix of file1 identical to that of file2. 

== fselect ==
 fselect all
Selects all files.

 fselect none
Selects no files.

 fselect {-a/-r} &lt;file_IDs&gt;
Selects the specified files and makes the others not selected. More than one file IDs can be specified by putting commas as the delimiter. When the option -a or -r is specified, only the selection status of the specified files are modified, selected or not selected, respectively, and the others remain unchanged.

== hbonds ==
 hbonds {on/true}
Turns on the selected hydrogen bonds.

 hbonds off/false
Turns off the selected hydrogen bonds.

 hbonds &lt;radius&gt;
Turns on the selected hydrogen bonds with the specified raidus (angstrom or Rasmol unit). The maximum parameter value is 2.0. 

== load ==
 load {pdbml} &lt;filename&gt; {fit &lt;file_ID&gt;}
Opens a PDBML file. URL can be used to open a remote file. On loading, the transform matrix can be set identical to that of the specified file.

 load pdb &lt;filename&gt; {fit &lt;file_ID&gt;}
Opens a PDB file. URL can be used to open a remote file. On loading, the transform matrix can be set identical to that of the specified file.

 load polygon &lt;filename&gt; {fit &lt;file_ID&gt;}
Opens a polygon file. URL can be used to open a remote file. On loading, the transform matrix can be set identical to that of the specified file.

 load animation &lt;filename&gt; {fit &lt;file_ID&gt;}
Opens an animation file. URL can be used to open a remote file. On loading, the transform matrix can be set identical to that of the specified file.

 load ftp &lt;PDB_code&gt; {fit &lt;file_ID&gt;}
Retrieves a PDBML file from the PDBj FTP site and opens it. On loading, the transform matrix can be set identical to that of the specified file. 

== pause ==
 pause
Stops the execution of a script file until any key is pressed to restart. 

== quit ==
 quit
A synonym of the exit command. 

== refresh ==
 refresh
Redraws all images. 

== reset ==
=== default ===
 reset
Restores the original viewing transformation of all images, the center of rotation, and the view point. 

=== cartoon ===
 reset cartoon
Restores the thickness of the cartoon representation. 

=== line_width ===
 reset line_width
Restores the width of lines in polygon images. 

=== pickradius ===
 reset pickradius
Restores the mouse-pickable region of each atom. 

=== point_size ===
 reset point_size
Restores the size of points in polygon images. 

=== polyline_width ===
 reset polyline_width
Restores the width of polylines in polygon images. 

=== transparency ===
 reset transparency
Restores the transparency of polygon images.

 reset point_transparency
Restores the transparency of points in polygon images.

 reset line_transparency
Restores the transparency of lines in polygon images.

 reset triangle_transparency
Restores the transparency of triangles in polygon images.

 reset quad_transparency
Restores the transparency of quads in polygon images.

 reset polyline_transparency
Restores the transparency of polylines in polygon images. 

== ribbons ==
 ribbons {on/true}
Turns on the ribbon surfaces for the selected residues.

 ribbons off/false
Turns off the ribbon surfaces for the selected residues.

 ribbons &lt;half_width&gt;
Turns on the ribbon surfaces for the selected residues with the specified half width (angstrom or Rasmol unit). The maximum parameter value is 4.0. 

== rotate ==
 rotate x/y/z &lt;angle&gt;
Rotates images about the specified axis by the specified angle in degrees. 

== save ==
 save {pdb} &lt;filename&gt;
Saves the currently selected set of atoms in a PDB format file.

 save script &lt;filename&gt;
Creates a script file that reproduces the currently displayed image.

 save png &lt;filename&gt;
Creates a PNG image file of the currently displayed image.

 save jpeg &lt;filename&gt; {&lt;quality&gt;}
Creates a JPEG image file of the currently displayed image. The compression quality can be specified, 0 &lt; quality &lt;= 1, where 'quality = 1' means no compression. 

== script ==
 script &lt;filename&gt;
Opens and executes the specified script file. URL can be used to open a remote file. 

== select ==
 select
Selects all atoms. Whether hetero atoms and hydrogens are selected or not depends on the internal parameters, hetero and hydrogen, respectively.

 select all
Selects all atoms including hetero atoms and hydrogens.

 select none
Selects no atoms.

 select &lt;atom_expression&gt;
Selects a group of atoms specified by the atom expression. 

== selectvertex ==
 selectvertex {all}
Selects all vertices.

 selectvertex none
Selects no vertices.

 selectvertex &lt;vertex_expression&gt;
Selects a group of vertices specified by the vertex expression. 

== set ==
=== adjustview ===
 set adjustview on
The view point is automatically adjusted when a new file is loaded.

 set adjustview off
The view point is kept unchanged when a new file is loaded. 

=== background ===
 set background &lt;color&gt;
Changes the background color. The color may be given as RGB values [r,g,b], or predefined color names. 

=== bondmode ===
 set bondmode and
Specifies how to select an individual bonds. A bond is selected when both atoms connected by the bond are selected.

 set bondmode or
Specifies how to select an individual bonds. A bond is selected when either of the connected atoms is selected. 

=== cartoon ===
 set cartoon {&lt;value&gt;}
Specifies the thickness of the cartoon representation (angstrom or Rasmol unit). The maximum parameter value is 2.0. When the parameter is not specified, it is restored to the default value. 

=== center ===
 set center &lt;atom_expression&gt;
Sets the default center of the selected files to the center of the specified atoms.

 set center [x, y, z]
Sets the default center of the selected files to the specified coordinates. 

=== drawlevel ===
 set drawlevel &lt;value&gt;
Specifies precision of the rendering of spheres and cylinders. The value may be given as an integer (minimum 5) that stands for the number of straight line segments to represent an arc of 180 degrees. 

=== hbonds ===
 set hbonds backbone
Hydrogen bonds are displayed between backbones.

 set hbonds sidechain
Hydrogen bonds are displayed between sidechains. 

=== hetero ===
 set hetero on
Sets the default behavior of the select command such that hetero atoms are selected.

 set hetero off
Sets the default behavior of the select command such that hetero atoms are not selected. 

=== hydrogen ===
 set hydrogen on
Sets the default behavior of the select command such that hydrogens are selected.

 set hydrogen off
Sets the default behavior of the select command such that hydrogens are not selected. 

=== imagesize ===
 set imagesize &lt;width&gt; &lt;height&gt;
Sets the size of the 3D-rendering panel in pixels. The size will be set within the screen size with the width being an even integer. 

=== line_width ===
 set line_width &lt;value&gt;
Sets the width of lines in polygon images. The &lt;value&gt; should be larger than 0. 

=== loadcenter ===
 set loadcenter on
When a file is opened, sets the default center of that file to the center of all files that have already opened.

 set loadcenter off
When a file is opened, sets the default center of that file according to its own coordiantes. 

=== picking ===
 set picking off
Turns off the mouse picking.

 set picking ident
Sets the mouse picking behavior to show atom identification.

 set picking coord
Sets the mouse picking behavior to show atom coordinates with identification.

 set picking distance
Sets the mouse picking behavior to show the distance between atoms successively picked.

 set picking center
Sets the mouse picking behavior to specify the center of rotation and center of the screen.

 set picking select
Sets the mouse picking behavior to select the file that contains the atom picked. 

=== pickradius ===
 set pickradius &lt;value&gt;
Sets the mouse-pickable region of each atom to be the sphere centered to each atom with the specified radius (angstrom or Rasmol unit). 

=== point_size ===
 set point_size &lt;value&gt;
Sets the size of points in polygon images. The &lt;value&gt; should be larger than 0. 

=== polyline_width ===
 set polyline_width &lt;value&gt;
Sets the width of polylines in polygon images. The &lt;value&gt; should be larger than 0. 

=== projection ===
 set projection perspective
Sets the projection mode for a perspective projection.

 set projection parallel {&lt;size&gt;}
Sets the projection mode for a parallel projection. The size of image (fit to the height of the screen) can be specified (angstrom or Rasmol unit). 

=== specular ===
 set specular on/true
Enables the display of specular highlights on solid objects.

 set specular off/false
Disables the display of specular highlights on solid objects.

 set specular &lt;value&gt;
Enables the display of specular highlights on solid objects. The value between 0 and 100 specifies the specular color in gray scale with 0 and 100 being black and white, respectively. The default value is 50.0. 

=== specpower ===
 set specpower &lt;value&gt;
Sets the shininess of solid objects. The value between 0 and 100 specifies a material reflection coefficient with 0 being diffuse surfaces and 100 being shiny surfaces. 

=== ssbonds ===
 set ssbonds backbone
Disulfide bonds are displayed between backbones.

 set ssbonds sidechain
Disulfide bonds are displayed between sidechains. 

=== stereo ===
 set stereo
A synonym of the stereo command. 

=== transparency ===
 set transparency &lt;value&gt;
Sets the transparency of polygon images.

 set point_transparency &lt;value&gt;
Sets the transparency of points in polygon images.

 set line_transparency &lt;value&gt;
Sets the transparency of lines in polygon images.

 set triangle_transparency &lt;value&gt;
Sets the transparency of triangles in polygon images.

 set quad_transparency &lt;value&gt;
Sets the transparency of quads in polygon images.

 set polyline_transparency &lt;value&gt;
Sets the transparency of polylines in polygon images. 

=== viewpoint ===
 set viewpoint {x, y, z}
Sets the viewpoint to the specified coordinates. 

== show ==
 show godata
Displays gene ontology data of molecules.

 show imagesize
Displays the size of the 3D-rendering panel.

 show information
Displays a detail discription of molecules.

 show site {&lt;prefix&gt;:&lt;db&gt;:&lt;category&gt;}
Displays site information in an external database.

 show transform
Displays the transform matrix of molecules.

 show viewpoint
Displays the current viewpoint.

 show xps3
Displays keywords available in xps3 selection. 

== slab ==
 slab {on/true}
Enables the z-clipping plane of molecules and polygons.

 slab off/false
Disables the z-clipping plane of molecules and polygons.

 slab &lt;ratio&gt;
Sets the position of the z-clipping plane of molecules and polygons. The parameter may be given as a number from 0 to 100. The values 0 and 100 represent that image as a whole is completely invisible and visible, respectively.

 slab -v &lt;value&gt;
Sets the position of the z-clipping plane of molecules and polygons by specifying the z coordinate value. 

== spacefill ==
 spacefill {on/true}
Turns on the ball image of the selected atoms.

 spacefill off/false
Turns off the ball image of the selected atoms.

 spacefill &lt;radius&gt;
Turns on the ball image of the selected atoms with the specified radius (angstrom or Rasmol unit). The maximum parameter value is 3.0.

 spacefill temperature
Turns on the ball image of the selected atoms using the temperature factor as radius. 

== ssbonds ==
 ssbonds {on/true}
Turns on the selected disulfide bonds.

 ssbonds off/false
Turns off the selected disulfide bonds.

 ssbonds &lt;radius&gt;
Turns on the selected disulfide bonds with the specified raidus (angstrom or Rasmol unit). The maximum parameter value is 2.0. 

== stereo ==
 stereo {on/true}
Enables stereo display. This command without arguments cycles three state; 'stereo off', 'stereo on' in cross-eyed mode and 'stereo on' in parallel-eyed mode.

 stereo off/false
Disables stereo display.

 stereo &lt;angle&gt;
Enables stereo display with the specified separation angle. Positive and negative values represent cross-eyed and parallel-eyed viewing, respectively.


== structure ==
 structure
Estimates the secondary structure using Kabsch and Sander's DSSP algorithm. 

== trace ==
 trace {on/true}
Turns on a tube representation for the selected residues.

 trace off/false
Turns off a tube representation for the selected residues.

 trace &lt;radius&gt;
Turns on a tube representation for the selected residues with the specified radius (angstrom or Rasmol unit). The maximum parameter value is 2.0.


== translate ==
 translate x/y/z &lt;value&gt;
Moves images along the specified axis by the specified amount (angstrom). 

== wireframe ==
 wireframe {on/true}
Turns on the selected bonds.

 wireframe off/false
Turns off the selected bonds.

 wireframe &lt;radius&gt;
Turns on the selected bonds with the specified raidus (angstrom or Rasmol unit). The maximum parameter value is 2.0. 

== write ==
 write
A synonym of the save command. 

== zap ==
 zap {&lt;file_IDs&gt;}
Closes the specified files. More than one file IDs can be specified by putting commas as the delimiter. When the paraneter is absent, all files are closed. 

== zoom ==
 zoom {&lt;value&gt;}
Sets the magnification of the image as a whole. The value stands for the magnification as a percentage of the current scale. The minimum parameter value is 10.0.</text>
    <sha1>b47577635bd9f3b8f853c6ae98ce3efcac8fe259</sha1>
  </revision>
  <revision>
    <id>357</id>
    <parentid>356</parentid>
    <timestamp>2009-12-03T04:33:59Z</timestamp>
    <contributor>
      <username>Cudo29</username>
      <id>5</id>
    </contributor>
    <minor/>
    <comment>/* write */ A link to the save section was added.</comment>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="18724" xml:space="preserve"> {| style="float:right"
  |__TOC__
  |}
Command usage of jV follows that of [http://www.rasmol.org/ Rasmol] with some modifications. In the following part, command arguments that can take an arbitrary value are denoted as &lt;value&gt; for example, arguments restricted to several possible values are listed with / as a delimiter, and arguments that can be omitted are put in brackets {}. Commands, [[#exit|exit]], [[#load|load]], [[#quit|quit]], [[#save|save]], [[#script|script]], and [[#write|write]], are not available in applet circumstance.

== anim ==
 anim forward {&lt;value&gt;}
Starts animation forward. If the &lt;value&gt; is given, just move frames forward by the specified amount.

 anim backward {&lt;value&gt;}
Starts animation backward. If the &lt;value&gt; is given, just move frames backward by the specified amount.

 anim stop
Stops animation.

== animframe ==
 animframe &lt;frame&gt; {&lt;file_ID&gt;}
Sets the frame of all animation files for the specified value. When &lt;file_ID&gt; is given, only the specified file is processed.

== animmode ==
 animmode once
Sets the behavior of animation for 'once'. When the frame reaches the last one, animation is stopped.

 animmode loop
Sets the behavior of animation for 'loop'. When the frame reaches the last one, animation is reset to the first frame and continues playing.

 animmode swing
Sets the behavior of animation for 'swing'. When the frame reaches the last one, the direction of animation is reversed.

== animrange ==
 animrange &lt;init_frame&gt;-&lt;term_frame&gt; {&lt;file_IDs&gt;}
Sets the range of all animation files. When is given, only the specified file is processed.

== animselect ==
 animselect {-a/-r} &lt;file_IDs&gt;
Selects the specified files and makes the others not selected. More than one file IDs can be specified by putting commas as the delimiter. When the option -a or -r is specified, only the selection status of the specified files are modified, selected or not selected, respectively, and the others remain unchanged.

== animspeed ==
 animspeed &lt;speed&gt;
Sets the animation speed. The argument should be an integer value from 1 to 20.

== animstep ==
 animstep &lt;step&gt; {&lt;file_ID&gt;}
Sets the step of all animation files for the specified value. When &lt;file_ID&gt; is given, only the specified file is processed.

== backbone ==
 backbone {on/true}
Turns on the selected backbone bonds.

 backbone off/false
Turns off the selected backbone bonds.

 backbone &lt;radius&gt;
Turns on the selected backbone bonds with the specified raidus (angstrom or Rasmol unit). The maximum parameter value is 2.0.

== background ==
 background &lt;color&gt;
Changes the background color. The color may be given as RGB values [r,g,b], or predefined color names.

== cartoon ==
 cartoon {on/true}
Turns on the thick ribbons for the selected residues.

 cartoon off/false
Turns off the thick ribbons for the selected residues.

 cartoon &lt;half_width&gt;
Turns on the thick ribbons for the selected residues with the specified half width (angstrom or Rasmol unit). The maximum parameter value is 4.0.

== center ==
 center {-r/-s} {&lt;atom_expression&gt;}
Sets the center of rotation and the center of the screen to the center of a group of atoms specified by the atom expression. When the option -r or -s is specified, only the center of rotation or the center of the screen is modified, respectively.

 center {-r} [x, y, z]
Moves the center of rotation and the center of the screen from the current position by the specified amount. When the option -r is specified, only the center of rotation is modified.

 center {-r} {x, y, z}
Sets the center of rotation and the center of the screen to the specified coordinates. When the option -r is specified, only the center of rotation is modified.

 center -s [x, y]
Moves the center of the screen from the current position by the specified amount.

 center -s {x, y}
Sets the center of the screen to the specified coordinates.

== color ==
 color {atoms} &lt;color&gt;
Sets the color of the selected atoms. The color may be given as RGB values [r,g,b], predefined color names, or predefined color schemes; amino, chain, charge, cpk, group, shapely, structure, and temperature.

 color bonds/backbone/ribbons/hbonds/ssbonds &lt;color&gt;
Sets the color of the specified object. The color may be given as RGB values [r,g,b] or predefined color names. For hydrogen bonds, color scheme 'type' can be specified.

 color bonds/backbone/ribbons/hbonds/ssbonds none
Resets the color of the specified object.

== colorvertex ==
 colorvertex &lt;color&gt;
Sets the color of the selected vertices. The color may be given as RGB values [r,g,b] or predefined color names.

 colorvertex none
Resets the color of the selected vertices.

== cpk ==
 cpk
A synonym of the spacefill command.

== define ==
 define &lt;name&gt; &lt;atom_expression&gt;
Associates an arbitrary set of atoms with a unique name.

== display ==
 display all
Displays the image of all files.

 display none
Turns off the image of all files.

 display {-a/-r} &lt;file_IDs&gt;
Displays the image of the specified files and turns off the others. More than one file IDs can be specified by putting commas as the delimiter. When the option -a or -r is specified, turns the image of the specified files on or off, respectively, and the others remain unchanged.

== displayvertex ==
 displayvertex {on/true}
Displays the selected vertices.

 displayvertex off/false
Turns off the selected vertices.

== echo ==
 echo &lt;string&gt;
Echoes the specified message back to the message area.

== exit ==
 exit
Terminates the application.

== fit ==
 fit &lt;file1_ID&gt; &lt;file2_ID&gt;
Sets the transform matrix of file1 identical to that of file2. 

== fselect ==
 fselect all
Selects all files.

 fselect none
Selects no files.

 fselect {-a/-r} &lt;file_IDs&gt;
Selects the specified files and makes the others not selected. More than one file IDs can be specified by putting commas as the delimiter. When the option -a or -r is specified, only the selection status of the specified files are modified, selected or not selected, respectively, and the others remain unchanged.

== hbonds ==
 hbonds {on/true}
Turns on the selected hydrogen bonds.

 hbonds off/false
Turns off the selected hydrogen bonds.

 hbonds &lt;radius&gt;
Turns on the selected hydrogen bonds with the specified raidus (angstrom or Rasmol unit). The maximum parameter value is 2.0. 

== load ==
 load {pdbml} &lt;filename&gt; {fit &lt;file_ID&gt;}
Opens a PDBML file. URL can be used to open a remote file. On loading, the transform matrix can be set identical to that of the specified file.

 load pdb &lt;filename&gt; {fit &lt;file_ID&gt;}
Opens a PDB file. URL can be used to open a remote file. On loading, the transform matrix can be set identical to that of the specified file.

 load polygon &lt;filename&gt; {fit &lt;file_ID&gt;}
Opens a polygon file. URL can be used to open a remote file. On loading, the transform matrix can be set identical to that of the specified file.

 load animation &lt;filename&gt; {fit &lt;file_ID&gt;}
Opens an animation file. URL can be used to open a remote file. On loading, the transform matrix can be set identical to that of the specified file.

 load ftp &lt;PDB_code&gt; {fit &lt;file_ID&gt;}
Retrieves a PDBML file from the PDBj FTP site and opens it. On loading, the transform matrix can be set identical to that of the specified file. 

== pause ==
 pause
Stops the execution of a script file until any key is pressed to restart. 

== quit ==
 quit
A synonym of the exit command. 

== refresh ==
 refresh
Redraws all images. 

== reset ==
=== default ===
 reset
Restores the original viewing transformation of all images, the center of rotation, and the view point. 

=== cartoon ===
 reset cartoon
Restores the thickness of the cartoon representation. 

=== line_width ===
 reset line_width
Restores the width of lines in polygon images. 

=== pickradius ===
 reset pickradius
Restores the mouse-pickable region of each atom. 

=== point_size ===
 reset point_size
Restores the size of points in polygon images. 

=== polyline_width ===
 reset polyline_width
Restores the width of polylines in polygon images. 

=== transparency ===
 reset transparency
Restores the transparency of polygon images.

 reset point_transparency
Restores the transparency of points in polygon images.

 reset line_transparency
Restores the transparency of lines in polygon images.

 reset triangle_transparency
Restores the transparency of triangles in polygon images.

 reset quad_transparency
Restores the transparency of quads in polygon images.

 reset polyline_transparency
Restores the transparency of polylines in polygon images. 

== ribbons ==
 ribbons {on/true}
Turns on the ribbon surfaces for the selected residues.

 ribbons off/false
Turns off the ribbon surfaces for the selected residues.

 ribbons &lt;half_width&gt;
Turns on the ribbon surfaces for the selected residues with the specified half width (angstrom or Rasmol unit). The maximum parameter value is 4.0. 

== rotate ==
 rotate x/y/z &lt;angle&gt;
Rotates images about the specified axis by the specified angle in degrees. 

== save ==
 save {pdb} &lt;filename&gt;
Saves the currently selected set of atoms in a PDB format file.

 save script &lt;filename&gt;
Creates a script file that reproduces the currently displayed image.

 save png &lt;filename&gt;
Creates a PNG image file of the currently displayed image.

 save jpeg &lt;filename&gt; {&lt;quality&gt;}
Creates a JPEG image file of the currently displayed image. The compression quality can be specified, 0 &lt; quality &lt;= 1, where 'quality = 1' means no compression. 

== script ==
 script &lt;filename&gt;
Opens and executes the specified script file. URL can be used to open a remote file. 

== select ==
 select
Selects all atoms. Whether hetero atoms and hydrogens are selected or not depends on the internal parameters, hetero and hydrogen, respectively.

 select all
Selects all atoms including hetero atoms and hydrogens.

 select none
Selects no atoms.

 select &lt;atom_expression&gt;
Selects a group of atoms specified by the atom expression. 

== selectvertex ==
 selectvertex {all}
Selects all vertices.

 selectvertex none
Selects no vertices.

 selectvertex &lt;vertex_expression&gt;
Selects a group of vertices specified by the vertex expression. 

== set ==
=== adjustview ===
 set adjustview on
The view point is automatically adjusted when a new file is loaded.

 set adjustview off
The view point is kept unchanged when a new file is loaded. 

=== background ===
 set background &lt;color&gt;
Changes the background color. The color may be given as RGB values [r,g,b], or predefined color names. 

=== bondmode ===
 set bondmode and
Specifies how to select an individual bonds. A bond is selected when both atoms connected by the bond are selected.

 set bondmode or
Specifies how to select an individual bonds. A bond is selected when either of the connected atoms is selected. 

=== cartoon ===
 set cartoon {&lt;value&gt;}
Specifies the thickness of the cartoon representation (angstrom or Rasmol unit). The maximum parameter value is 2.0. When the parameter is not specified, it is restored to the default value. 

=== center ===
 set center &lt;atom_expression&gt;
Sets the default center of the selected files to the center of the specified atoms.

 set center [x, y, z]
Sets the default center of the selected files to the specified coordinates. 

=== drawlevel ===
 set drawlevel &lt;value&gt;
Specifies precision of the rendering of spheres and cylinders. The value may be given as an integer (minimum 5) that stands for the number of straight line segments to represent an arc of 180 degrees. 

=== hbonds ===
 set hbonds backbone
Hydrogen bonds are displayed between backbones.

 set hbonds sidechain
Hydrogen bonds are displayed between sidechains. 

=== hetero ===
 set hetero on
Sets the default behavior of the select command such that hetero atoms are selected.

 set hetero off
Sets the default behavior of the select command such that hetero atoms are not selected. 

=== hydrogen ===
 set hydrogen on
Sets the default behavior of the select command such that hydrogens are selected.

 set hydrogen off
Sets the default behavior of the select command such that hydrogens are not selected. 

=== imagesize ===
 set imagesize &lt;width&gt; &lt;height&gt;
Sets the size of the 3D-rendering panel in pixels. The size will be set within the screen size with the width being an even integer. 

=== line_width ===
 set line_width &lt;value&gt;
Sets the width of lines in polygon images. The &lt;value&gt; should be larger than 0. 

=== loadcenter ===
 set loadcenter on
When a file is opened, sets the default center of that file to the center of all files that have already opened.

 set loadcenter off
When a file is opened, sets the default center of that file according to its own coordiantes. 

=== picking ===
 set picking off
Turns off the mouse picking.

 set picking ident
Sets the mouse picking behavior to show atom identification.

 set picking coord
Sets the mouse picking behavior to show atom coordinates with identification.

 set picking distance
Sets the mouse picking behavior to show the distance between atoms successively picked.

 set picking center
Sets the mouse picking behavior to specify the center of rotation and center of the screen.

 set picking select
Sets the mouse picking behavior to select the file that contains the atom picked. 

=== pickradius ===
 set pickradius &lt;value&gt;
Sets the mouse-pickable region of each atom to be the sphere centered to each atom with the specified radius (angstrom or Rasmol unit). 

=== point_size ===
 set point_size &lt;value&gt;
Sets the size of points in polygon images. The &lt;value&gt; should be larger than 0. 

=== polyline_width ===
 set polyline_width &lt;value&gt;
Sets the width of polylines in polygon images. The &lt;value&gt; should be larger than 0. 

=== projection ===
 set projection perspective
Sets the projection mode for a perspective projection.

 set projection parallel {&lt;size&gt;}
Sets the projection mode for a parallel projection. The size of image (fit to the height of the screen) can be specified (angstrom or Rasmol unit). 

=== specular ===
 set specular on/true
Enables the display of specular highlights on solid objects.

 set specular off/false
Disables the display of specular highlights on solid objects.

 set specular &lt;value&gt;
Enables the display of specular highlights on solid objects. The value between 0 and 100 specifies the specular color in gray scale with 0 and 100 being black and white, respectively. The default value is 50.0. 

=== specpower ===
 set specpower &lt;value&gt;
Sets the shininess of solid objects. The value between 0 and 100 specifies a material reflection coefficient with 0 being diffuse surfaces and 100 being shiny surfaces. 

=== ssbonds ===
 set ssbonds backbone
Disulfide bonds are displayed between backbones.

 set ssbonds sidechain
Disulfide bonds are displayed between sidechains. 

=== stereo ===
 set stereo
A synonym of the stereo command. 

=== transparency ===
 set transparency &lt;value&gt;
Sets the transparency of polygon images.

 set point_transparency &lt;value&gt;
Sets the transparency of points in polygon images.

 set line_transparency &lt;value&gt;
Sets the transparency of lines in polygon images.

 set triangle_transparency &lt;value&gt;
Sets the transparency of triangles in polygon images.

 set quad_transparency &lt;value&gt;
Sets the transparency of quads in polygon images.

 set polyline_transparency &lt;value&gt;
Sets the transparency of polylines in polygon images. 

=== viewpoint ===
 set viewpoint {x, y, z}
Sets the viewpoint to the specified coordinates. 

== show ==
 show godata
Displays gene ontology data of molecules.

 show imagesize
Displays the size of the 3D-rendering panel.

 show information
Displays a detail discription of molecules.

 show site {&lt;prefix&gt;:&lt;db&gt;:&lt;category&gt;}
Displays site information in an external database.

 show transform
Displays the transform matrix of molecules.

 show viewpoint
Displays the current viewpoint.

 show xps3
Displays keywords available in xps3 selection. 

== slab ==
 slab {on/true}
Enables the z-clipping plane of molecules and polygons.

 slab off/false
Disables the z-clipping plane of molecules and polygons.

 slab &lt;ratio&gt;
Sets the position of the z-clipping plane of molecules and polygons. The parameter may be given as a number from 0 to 100. The values 0 and 100 represent that image as a whole is completely invisible and visible, respectively.

 slab -v &lt;value&gt;
Sets the position of the z-clipping plane of molecules and polygons by specifying the z coordinate value. 

== spacefill ==
 spacefill {on/true}
Turns on the ball image of the selected atoms.

 spacefill off/false
Turns off the ball image of the selected atoms.

 spacefill &lt;radius&gt;
Turns on the ball image of the selected atoms with the specified radius (angstrom or Rasmol unit). The maximum parameter value is 3.0.

 spacefill temperature
Turns on the ball image of the selected atoms using the temperature factor as radius. 

== ssbonds ==
 ssbonds {on/true}
Turns on the selected disulfide bonds.

 ssbonds off/false
Turns off the selected disulfide bonds.

 ssbonds &lt;radius&gt;
Turns on the selected disulfide bonds with the specified raidus (angstrom or Rasmol unit). The maximum parameter value is 2.0. 

== stereo ==
 stereo {on/true}
Enables stereo display. This command without arguments cycles three state; 'stereo off', 'stereo on' in cross-eyed mode and 'stereo on' in parallel-eyed mode.

 stereo off/false
Disables stereo display.

 stereo &lt;angle&gt;
Enables stereo display with the specified separation angle. Positive and negative values represent cross-eyed and parallel-eyed viewing, respectively.


== structure ==
 structure
Estimates the secondary structure using Kabsch and Sander's DSSP algorithm. 

== trace ==
 trace {on/true}
Turns on a tube representation for the selected residues.

 trace off/false
Turns off a tube representation for the selected residues.

 trace &lt;radius&gt;
Turns on a tube representation for the selected residues with the specified radius (angstrom or Rasmol unit). The maximum parameter value is 2.0.


== translate ==
 translate x/y/z &lt;value&gt;
Moves images along the specified axis by the specified amount (angstrom). 

== wireframe ==
 wireframe {on/true}
Turns on the selected bonds.

 wireframe off/false
Turns off the selected bonds.

 wireframe &lt;radius&gt;
Turns on the selected bonds with the specified raidus (angstrom or Rasmol unit). The maximum parameter value is 2.0. 

== write ==
 write
A synonym of the [[#save|save]] command.

== zap ==
 zap {&lt;file_IDs&gt;}
Closes the specified files. More than one file IDs can be specified by putting commas as the delimiter. When the paraneter is absent, all files are closed. 

== zoom ==
 zoom {&lt;value&gt;}
Sets the magnification of the image as a whole. The value stands for the magnification as a percentage of the current scale. The minimum parameter value is 10.0.</text>
    <sha1>f1e219a6a5c10c1102a006f2375559a1dc6d7909</sha1>
  </revision>
  <revision>
    <id>358</id>
    <parentid>357</parentid>
    <timestamp>2009-12-03T04:34:52Z</timestamp>
    <contributor>
      <username>Cudo29</username>
      <id>5</id>
    </contributor>
    <minor/>
    <comment>/* cpk */ A link to spacefill section was added.</comment>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="18739" xml:space="preserve"> {| style="float:right"
  |__TOC__
  |}
Command usage of jV follows that of [http://www.rasmol.org/ Rasmol] with some modifications. In the following part, command arguments that can take an arbitrary value are denoted as &lt;value&gt; for example, arguments restricted to several possible values are listed with / as a delimiter, and arguments that can be omitted are put in brackets {}. Commands, [[#exit|exit]], [[#load|load]], [[#quit|quit]], [[#save|save]], [[#script|script]], and [[#write|write]], are not available in applet circumstance.

== anim ==
 anim forward {&lt;value&gt;}
Starts animation forward. If the &lt;value&gt; is given, just move frames forward by the specified amount.

 anim backward {&lt;value&gt;}
Starts animation backward. If the &lt;value&gt; is given, just move frames backward by the specified amount.

 anim stop
Stops animation.

== animframe ==
 animframe &lt;frame&gt; {&lt;file_ID&gt;}
Sets the frame of all animation files for the specified value. When &lt;file_ID&gt; is given, only the specified file is processed.

== animmode ==
 animmode once
Sets the behavior of animation for 'once'. When the frame reaches the last one, animation is stopped.

 animmode loop
Sets the behavior of animation for 'loop'. When the frame reaches the last one, animation is reset to the first frame and continues playing.

 animmode swing
Sets the behavior of animation for 'swing'. When the frame reaches the last one, the direction of animation is reversed.

== animrange ==
 animrange &lt;init_frame&gt;-&lt;term_frame&gt; {&lt;file_IDs&gt;}
Sets the range of all animation files. When is given, only the specified file is processed.

== animselect ==
 animselect {-a/-r} &lt;file_IDs&gt;
Selects the specified files and makes the others not selected. More than one file IDs can be specified by putting commas as the delimiter. When the option -a or -r is specified, only the selection status of the specified files are modified, selected or not selected, respectively, and the others remain unchanged.

== animspeed ==
 animspeed &lt;speed&gt;
Sets the animation speed. The argument should be an integer value from 1 to 20.

== animstep ==
 animstep &lt;step&gt; {&lt;file_ID&gt;}
Sets the step of all animation files for the specified value. When &lt;file_ID&gt; is given, only the specified file is processed.

== backbone ==
 backbone {on/true}
Turns on the selected backbone bonds.

 backbone off/false
Turns off the selected backbone bonds.

 backbone &lt;radius&gt;
Turns on the selected backbone bonds with the specified raidus (angstrom or Rasmol unit). The maximum parameter value is 2.0.

== background ==
 background &lt;color&gt;
Changes the background color. The color may be given as RGB values [r,g,b], or predefined color names.

== cartoon ==
 cartoon {on/true}
Turns on the thick ribbons for the selected residues.

 cartoon off/false
Turns off the thick ribbons for the selected residues.

 cartoon &lt;half_width&gt;
Turns on the thick ribbons for the selected residues with the specified half width (angstrom or Rasmol unit). The maximum parameter value is 4.0.

== center ==
 center {-r/-s} {&lt;atom_expression&gt;}
Sets the center of rotation and the center of the screen to the center of a group of atoms specified by the atom expression. When the option -r or -s is specified, only the center of rotation or the center of the screen is modified, respectively.

 center {-r} [x, y, z]
Moves the center of rotation and the center of the screen from the current position by the specified amount. When the option -r is specified, only the center of rotation is modified.

 center {-r} {x, y, z}
Sets the center of rotation and the center of the screen to the specified coordinates. When the option -r is specified, only the center of rotation is modified.

 center -s [x, y]
Moves the center of the screen from the current position by the specified amount.

 center -s {x, y}
Sets the center of the screen to the specified coordinates.

== color ==
 color {atoms} &lt;color&gt;
Sets the color of the selected atoms. The color may be given as RGB values [r,g,b], predefined color names, or predefined color schemes; amino, chain, charge, cpk, group, shapely, structure, and temperature.

 color bonds/backbone/ribbons/hbonds/ssbonds &lt;color&gt;
Sets the color of the specified object. The color may be given as RGB values [r,g,b] or predefined color names. For hydrogen bonds, color scheme 'type' can be specified.

 color bonds/backbone/ribbons/hbonds/ssbonds none
Resets the color of the specified object.

== colorvertex ==
 colorvertex &lt;color&gt;
Sets the color of the selected vertices. The color may be given as RGB values [r,g,b] or predefined color names.

 colorvertex none
Resets the color of the selected vertices.

== cpk ==
 cpk
A synonym of the [[#spacefill|spacefill]] command.

== define ==
 define &lt;name&gt; &lt;atom_expression&gt;
Associates an arbitrary set of atoms with a unique name.

== display ==
 display all
Displays the image of all files.

 display none
Turns off the image of all files.

 display {-a/-r} &lt;file_IDs&gt;
Displays the image of the specified files and turns off the others. More than one file IDs can be specified by putting commas as the delimiter. When the option -a or -r is specified, turns the image of the specified files on or off, respectively, and the others remain unchanged.

== displayvertex ==
 displayvertex {on/true}
Displays the selected vertices.

 displayvertex off/false
Turns off the selected vertices.

== echo ==
 echo &lt;string&gt;
Echoes the specified message back to the message area.

== exit ==
 exit
Terminates the application.

== fit ==
 fit &lt;file1_ID&gt; &lt;file2_ID&gt;
Sets the transform matrix of file1 identical to that of file2. 

== fselect ==
 fselect all
Selects all files.

 fselect none
Selects no files.

 fselect {-a/-r} &lt;file_IDs&gt;
Selects the specified files and makes the others not selected. More than one file IDs can be specified by putting commas as the delimiter. When the option -a or -r is specified, only the selection status of the specified files are modified, selected or not selected, respectively, and the others remain unchanged.

== hbonds ==
 hbonds {on/true}
Turns on the selected hydrogen bonds.

 hbonds off/false
Turns off the selected hydrogen bonds.

 hbonds &lt;radius&gt;
Turns on the selected hydrogen bonds with the specified raidus (angstrom or Rasmol unit). The maximum parameter value is 2.0. 

== load ==
 load {pdbml} &lt;filename&gt; {fit &lt;file_ID&gt;}
Opens a PDBML file. URL can be used to open a remote file. On loading, the transform matrix can be set identical to that of the specified file.

 load pdb &lt;filename&gt; {fit &lt;file_ID&gt;}
Opens a PDB file. URL can be used to open a remote file. On loading, the transform matrix can be set identical to that of the specified file.

 load polygon &lt;filename&gt; {fit &lt;file_ID&gt;}
Opens a polygon file. URL can be used to open a remote file. On loading, the transform matrix can be set identical to that of the specified file.

 load animation &lt;filename&gt; {fit &lt;file_ID&gt;}
Opens an animation file. URL can be used to open a remote file. On loading, the transform matrix can be set identical to that of the specified file.

 load ftp &lt;PDB_code&gt; {fit &lt;file_ID&gt;}
Retrieves a PDBML file from the PDBj FTP site and opens it. On loading, the transform matrix can be set identical to that of the specified file. 

== pause ==
 pause
Stops the execution of a script file until any key is pressed to restart. 

== quit ==
 quit
A synonym of the exit command. 

== refresh ==
 refresh
Redraws all images. 

== reset ==
=== default ===
 reset
Restores the original viewing transformation of all images, the center of rotation, and the view point. 

=== cartoon ===
 reset cartoon
Restores the thickness of the cartoon representation. 

=== line_width ===
 reset line_width
Restores the width of lines in polygon images. 

=== pickradius ===
 reset pickradius
Restores the mouse-pickable region of each atom. 

=== point_size ===
 reset point_size
Restores the size of points in polygon images. 

=== polyline_width ===
 reset polyline_width
Restores the width of polylines in polygon images. 

=== transparency ===
 reset transparency
Restores the transparency of polygon images.

 reset point_transparency
Restores the transparency of points in polygon images.

 reset line_transparency
Restores the transparency of lines in polygon images.

 reset triangle_transparency
Restores the transparency of triangles in polygon images.

 reset quad_transparency
Restores the transparency of quads in polygon images.

 reset polyline_transparency
Restores the transparency of polylines in polygon images. 

== ribbons ==
 ribbons {on/true}
Turns on the ribbon surfaces for the selected residues.

 ribbons off/false
Turns off the ribbon surfaces for the selected residues.

 ribbons &lt;half_width&gt;
Turns on the ribbon surfaces for the selected residues with the specified half width (angstrom or Rasmol unit). The maximum parameter value is 4.0. 

== rotate ==
 rotate x/y/z &lt;angle&gt;
Rotates images about the specified axis by the specified angle in degrees. 

== save ==
 save {pdb} &lt;filename&gt;
Saves the currently selected set of atoms in a PDB format file.

 save script &lt;filename&gt;
Creates a script file that reproduces the currently displayed image.

 save png &lt;filename&gt;
Creates a PNG image file of the currently displayed image.

 save jpeg &lt;filename&gt; {&lt;quality&gt;}
Creates a JPEG image file of the currently displayed image. The compression quality can be specified, 0 &lt; quality &lt;= 1, where 'quality = 1' means no compression. 

== script ==
 script &lt;filename&gt;
Opens and executes the specified script file. URL can be used to open a remote file. 

== select ==
 select
Selects all atoms. Whether hetero atoms and hydrogens are selected or not depends on the internal parameters, hetero and hydrogen, respectively.

 select all
Selects all atoms including hetero atoms and hydrogens.

 select none
Selects no atoms.

 select &lt;atom_expression&gt;
Selects a group of atoms specified by the atom expression. 

== selectvertex ==
 selectvertex {all}
Selects all vertices.

 selectvertex none
Selects no vertices.

 selectvertex &lt;vertex_expression&gt;
Selects a group of vertices specified by the vertex expression. 

== set ==
=== adjustview ===
 set adjustview on
The view point is automatically adjusted when a new file is loaded.

 set adjustview off
The view point is kept unchanged when a new file is loaded. 

=== background ===
 set background &lt;color&gt;
Changes the background color. The color may be given as RGB values [r,g,b], or predefined color names. 

=== bondmode ===
 set bondmode and
Specifies how to select an individual bonds. A bond is selected when both atoms connected by the bond are selected.

 set bondmode or
Specifies how to select an individual bonds. A bond is selected when either of the connected atoms is selected. 

=== cartoon ===
 set cartoon {&lt;value&gt;}
Specifies the thickness of the cartoon representation (angstrom or Rasmol unit). The maximum parameter value is 2.0. When the parameter is not specified, it is restored to the default value. 

=== center ===
 set center &lt;atom_expression&gt;
Sets the default center of the selected files to the center of the specified atoms.

 set center [x, y, z]
Sets the default center of the selected files to the specified coordinates. 

=== drawlevel ===
 set drawlevel &lt;value&gt;
Specifies precision of the rendering of spheres and cylinders. The value may be given as an integer (minimum 5) that stands for the number of straight line segments to represent an arc of 180 degrees. 

=== hbonds ===
 set hbonds backbone
Hydrogen bonds are displayed between backbones.

 set hbonds sidechain
Hydrogen bonds are displayed between sidechains. 

=== hetero ===
 set hetero on
Sets the default behavior of the select command such that hetero atoms are selected.

 set hetero off
Sets the default behavior of the select command such that hetero atoms are not selected. 

=== hydrogen ===
 set hydrogen on
Sets the default behavior of the select command such that hydrogens are selected.

 set hydrogen off
Sets the default behavior of the select command such that hydrogens are not selected. 

=== imagesize ===
 set imagesize &lt;width&gt; &lt;height&gt;
Sets the size of the 3D-rendering panel in pixels. The size will be set within the screen size with the width being an even integer. 

=== line_width ===
 set line_width &lt;value&gt;
Sets the width of lines in polygon images. The &lt;value&gt; should be larger than 0. 

=== loadcenter ===
 set loadcenter on
When a file is opened, sets the default center of that file to the center of all files that have already opened.

 set loadcenter off
When a file is opened, sets the default center of that file according to its own coordiantes. 

=== picking ===
 set picking off
Turns off the mouse picking.

 set picking ident
Sets the mouse picking behavior to show atom identification.

 set picking coord
Sets the mouse picking behavior to show atom coordinates with identification.

 set picking distance
Sets the mouse picking behavior to show the distance between atoms successively picked.

 set picking center
Sets the mouse picking behavior to specify the center of rotation and center of the screen.

 set picking select
Sets the mouse picking behavior to select the file that contains the atom picked. 

=== pickradius ===
 set pickradius &lt;value&gt;
Sets the mouse-pickable region of each atom to be the sphere centered to each atom with the specified radius (angstrom or Rasmol unit). 

=== point_size ===
 set point_size &lt;value&gt;
Sets the size of points in polygon images. The &lt;value&gt; should be larger than 0. 

=== polyline_width ===
 set polyline_width &lt;value&gt;
Sets the width of polylines in polygon images. The &lt;value&gt; should be larger than 0. 

=== projection ===
 set projection perspective
Sets the projection mode for a perspective projection.

 set projection parallel {&lt;size&gt;}
Sets the projection mode for a parallel projection. The size of image (fit to the height of the screen) can be specified (angstrom or Rasmol unit). 

=== specular ===
 set specular on/true
Enables the display of specular highlights on solid objects.

 set specular off/false
Disables the display of specular highlights on solid objects.

 set specular &lt;value&gt;
Enables the display of specular highlights on solid objects. The value between 0 and 100 specifies the specular color in gray scale with 0 and 100 being black and white, respectively. The default value is 50.0. 

=== specpower ===
 set specpower &lt;value&gt;
Sets the shininess of solid objects. The value between 0 and 100 specifies a material reflection coefficient with 0 being diffuse surfaces and 100 being shiny surfaces. 

=== ssbonds ===
 set ssbonds backbone
Disulfide bonds are displayed between backbones.

 set ssbonds sidechain
Disulfide bonds are displayed between sidechains. 

=== stereo ===
 set stereo
A synonym of the stereo command. 

=== transparency ===
 set transparency &lt;value&gt;
Sets the transparency of polygon images.

 set point_transparency &lt;value&gt;
Sets the transparency of points in polygon images.

 set line_transparency &lt;value&gt;
Sets the transparency of lines in polygon images.

 set triangle_transparency &lt;value&gt;
Sets the transparency of triangles in polygon images.

 set quad_transparency &lt;value&gt;
Sets the transparency of quads in polygon images.

 set polyline_transparency &lt;value&gt;
Sets the transparency of polylines in polygon images. 

=== viewpoint ===
 set viewpoint {x, y, z}
Sets the viewpoint to the specified coordinates. 

== show ==
 show godata
Displays gene ontology data of molecules.

 show imagesize
Displays the size of the 3D-rendering panel.

 show information
Displays a detail discription of molecules.

 show site {&lt;prefix&gt;:&lt;db&gt;:&lt;category&gt;}
Displays site information in an external database.

 show transform
Displays the transform matrix of molecules.

 show viewpoint
Displays the current viewpoint.

 show xps3
Displays keywords available in xps3 selection. 

== slab ==
 slab {on/true}
Enables the z-clipping plane of molecules and polygons.

 slab off/false
Disables the z-clipping plane of molecules and polygons.

 slab &lt;ratio&gt;
Sets the position of the z-clipping plane of molecules and polygons. The parameter may be given as a number from 0 to 100. The values 0 and 100 represent that image as a whole is completely invisible and visible, respectively.

 slab -v &lt;value&gt;
Sets the position of the z-clipping plane of molecules and polygons by specifying the z coordinate value. 

== spacefill ==
 spacefill {on/true}
Turns on the ball image of the selected atoms.

 spacefill off/false
Turns off the ball image of the selected atoms.

 spacefill &lt;radius&gt;
Turns on the ball image of the selected atoms with the specified radius (angstrom or Rasmol unit). The maximum parameter value is 3.0.

 spacefill temperature
Turns on the ball image of the selected atoms using the temperature factor as radius. 

== ssbonds ==
 ssbonds {on/true}
Turns on the selected disulfide bonds.

 ssbonds off/false
Turns off the selected disulfide bonds.

 ssbonds &lt;radius&gt;
Turns on the selected disulfide bonds with the specified raidus (angstrom or Rasmol unit). The maximum parameter value is 2.0. 

== stereo ==
 stereo {on/true}
Enables stereo display. This command without arguments cycles three state; 'stereo off', 'stereo on' in cross-eyed mode and 'stereo on' in parallel-eyed mode.

 stereo off/false
Disables stereo display.

 stereo &lt;angle&gt;
Enables stereo display with the specified separation angle. Positive and negative values represent cross-eyed and parallel-eyed viewing, respectively.


== structure ==
 structure
Estimates the secondary structure using Kabsch and Sander's DSSP algorithm. 

== trace ==
 trace {on/true}
Turns on a tube representation for the selected residues.

 trace off/false
Turns off a tube representation for the selected residues.

 trace &lt;radius&gt;
Turns on a tube representation for the selected residues with the specified radius (angstrom or Rasmol unit). The maximum parameter value is 2.0.


== translate ==
 translate x/y/z &lt;value&gt;
Moves images along the specified axis by the specified amount (angstrom). 

== wireframe ==
 wireframe {on/true}
Turns on the selected bonds.

 wireframe off/false
Turns off the selected bonds.

 wireframe &lt;radius&gt;
Turns on the selected bonds with the specified raidus (angstrom or Rasmol unit). The maximum parameter value is 2.0. 

== write ==
 write
A synonym of the [[#save|save]] command.

== zap ==
 zap {&lt;file_IDs&gt;}
Closes the specified files. More than one file IDs can be specified by putting commas as the delimiter. When the paraneter is absent, all files are closed. 

== zoom ==
 zoom {&lt;value&gt;}
Sets the magnification of the image as a whole. The value stands for the magnification as a percentage of the current scale. The minimum parameter value is 10.0.</text>
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  <revision>
    <id>359</id>
    <parentid>358</parentid>
    <timestamp>2009-12-03T04:35:33Z</timestamp>
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      <username>Cudo29</username>
      <id>5</id>
    </contributor>
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Command usage of jV follows that of [http://www.rasmol.org/ Rasmol] with some modifications. In the following part, command arguments that can take an arbitrary value are denoted as &lt;value&gt; for example, arguments restricted to several possible values are listed with / as a delimiter, and arguments that can be omitted are put in brackets {}. Commands, [[#exit|exit]], [[#load|load]], [[#quit|quit]], [[#save|save]], [[#script|script]], and [[#write|write]], are not available in applet circumstance.

== anim ==
 anim forward {&lt;value&gt;}
Starts animation forward. If the &lt;value&gt; is given, just move frames forward by the specified amount.

 anim backward {&lt;value&gt;}
Starts animation backward. If the &lt;value&gt; is given, just move frames backward by the specified amount.

 anim stop
Stops animation.

== animframe ==
 animframe &lt;frame&gt; {&lt;file_ID&gt;}
Sets the frame of all animation files for the specified value. When &lt;file_ID&gt; is given, only the specified file is processed.

== animmode ==
 animmode once
Sets the behavior of animation for 'once'. When the frame reaches the last one, animation is stopped.

 animmode loop
Sets the behavior of animation for 'loop'. When the frame reaches the last one, animation is reset to the first frame and continues playing.

 animmode swing
Sets the behavior of animation for 'swing'. When the frame reaches the last one, the direction of animation is reversed.

== animrange ==
 animrange &lt;init_frame&gt;-&lt;term_frame&gt; {&lt;file_IDs&gt;}
Sets the range of all animation files. When is given, only the specified file is processed.

== animselect ==
 animselect {-a/-r} &lt;file_IDs&gt;
Selects the specified files and makes the others not selected. More than one file IDs can be specified by putting commas as the delimiter. When the option -a or -r is specified, only the selection status of the specified files are modified, selected or not selected, respectively, and the others remain unchanged.

== animspeed ==
 animspeed &lt;speed&gt;
Sets the animation speed. The argument should be an integer value from 1 to 20.

== animstep ==
 animstep &lt;step&gt; {&lt;file_ID&gt;}
Sets the step of all animation files for the specified value. When &lt;file_ID&gt; is given, only the specified file is processed.

== backbone ==
 backbone {on/true}
Turns on the selected backbone bonds.

 backbone off/false
Turns off the selected backbone bonds.

 backbone &lt;radius&gt;
Turns on the selected backbone bonds with the specified raidus (angstrom or Rasmol unit). The maximum parameter value is 2.0.

== background ==
 background &lt;color&gt;
Changes the background color. The color may be given as RGB values [r,g,b], or predefined color names.

== cartoon ==
 cartoon {on/true}
Turns on the thick ribbons for the selected residues.

 cartoon off/false
Turns off the thick ribbons for the selected residues.

 cartoon &lt;half_width&gt;
Turns on the thick ribbons for the selected residues with the specified half width (angstrom or Rasmol unit). The maximum parameter value is 4.0.

== center ==
 center {-r/-s} {&lt;atom_expression&gt;}
Sets the center of rotation and the center of the screen to the center of a group of atoms specified by the atom expression. When the option -r or -s is specified, only the center of rotation or the center of the screen is modified, respectively.

 center {-r} [x, y, z]
Moves the center of rotation and the center of the screen from the current position by the specified amount. When the option -r is specified, only the center of rotation is modified.

 center {-r} {x, y, z}
Sets the center of rotation and the center of the screen to the specified coordinates. When the option -r is specified, only the center of rotation is modified.

 center -s [x, y]
Moves the center of the screen from the current position by the specified amount.

 center -s {x, y}
Sets the center of the screen to the specified coordinates.

== color ==
 color {atoms} &lt;color&gt;
Sets the color of the selected atoms. The color may be given as RGB values [r,g,b], predefined color names, or predefined color schemes; amino, chain, charge, cpk, group, shapely, structure, and temperature.

 color bonds/backbone/ribbons/hbonds/ssbonds &lt;color&gt;
Sets the color of the specified object. The color may be given as RGB values [r,g,b] or predefined color names. For hydrogen bonds, color scheme 'type' can be specified.

 color bonds/backbone/ribbons/hbonds/ssbonds none
Resets the color of the specified object.

== colorvertex ==
 colorvertex &lt;color&gt;
Sets the color of the selected vertices. The color may be given as RGB values [r,g,b] or predefined color names.

 colorvertex none
Resets the color of the selected vertices.

== cpk ==
 cpk
A synonym of the [[#spacefill|spacefill]] command.

== define ==
 define &lt;name&gt; &lt;atom_expression&gt;
Associates an arbitrary set of atoms with a unique name.

== display ==
 display all
Displays the image of all files.

 display none
Turns off the image of all files.

 display {-a/-r} &lt;file_IDs&gt;
Displays the image of the specified files and turns off the others. More than one file IDs can be specified by putting commas as the delimiter. When the option -a or -r is specified, turns the image of the specified files on or off, respectively, and the others remain unchanged.

== displayvertex ==
 displayvertex {on/true}
Displays the selected vertices.

 displayvertex off/false
Turns off the selected vertices.

== echo ==
 echo &lt;string&gt;
Echoes the specified message back to the message area.

== exit ==
 exit
Terminates the application.

== fit ==
 fit &lt;file1_ID&gt; &lt;file2_ID&gt;
Sets the transform matrix of file1 identical to that of file2. 

== fselect ==
 fselect all
Selects all files.

 fselect none
Selects no files.

 fselect {-a/-r} &lt;file_IDs&gt;
Selects the specified files and makes the others not selected. More than one file IDs can be specified by putting commas as the delimiter. When the option -a or -r is specified, only the selection status of the specified files are modified, selected or not selected, respectively, and the others remain unchanged.

== hbonds ==
 hbonds {on/true}
Turns on the selected hydrogen bonds.

 hbonds off/false
Turns off the selected hydrogen bonds.

 hbonds &lt;radius&gt;
Turns on the selected hydrogen bonds with the specified raidus (angstrom or Rasmol unit). The maximum parameter value is 2.0. 

== load ==
 load {pdbml} &lt;filename&gt; {fit &lt;file_ID&gt;}
Opens a PDBML file. URL can be used to open a remote file. On loading, the transform matrix can be set identical to that of the specified file.

 load pdb &lt;filename&gt; {fit &lt;file_ID&gt;}
Opens a PDB file. URL can be used to open a remote file. On loading, the transform matrix can be set identical to that of the specified file.

 load polygon &lt;filename&gt; {fit &lt;file_ID&gt;}
Opens a polygon file. URL can be used to open a remote file. On loading, the transform matrix can be set identical to that of the specified file.

 load animation &lt;filename&gt; {fit &lt;file_ID&gt;}
Opens an animation file. URL can be used to open a remote file. On loading, the transform matrix can be set identical to that of the specified file.

 load ftp &lt;PDB_code&gt; {fit &lt;file_ID&gt;}
Retrieves a PDBML file from the PDBj FTP site and opens it. On loading, the transform matrix can be set identical to that of the specified file. 

== pause ==
 pause
Stops the execution of a script file until any key is pressed to restart. 

== quit ==
 quit
A synonym of the [[#exit|exit]] command.

== refresh ==
 refresh
Redraws all images. 

== reset ==
=== default ===
 reset
Restores the original viewing transformation of all images, the center of rotation, and the view point. 

=== cartoon ===
 reset cartoon
Restores the thickness of the cartoon representation. 

=== line_width ===
 reset line_width
Restores the width of lines in polygon images. 

=== pickradius ===
 reset pickradius
Restores the mouse-pickable region of each atom. 

=== point_size ===
 reset point_size
Restores the size of points in polygon images. 

=== polyline_width ===
 reset polyline_width
Restores the width of polylines in polygon images. 

=== transparency ===
 reset transparency
Restores the transparency of polygon images.

 reset point_transparency
Restores the transparency of points in polygon images.

 reset line_transparency
Restores the transparency of lines in polygon images.

 reset triangle_transparency
Restores the transparency of triangles in polygon images.

 reset quad_transparency
Restores the transparency of quads in polygon images.

 reset polyline_transparency
Restores the transparency of polylines in polygon images. 

== ribbons ==
 ribbons {on/true}
Turns on the ribbon surfaces for the selected residues.

 ribbons off/false
Turns off the ribbon surfaces for the selected residues.

 ribbons &lt;half_width&gt;
Turns on the ribbon surfaces for the selected residues with the specified half width (angstrom or Rasmol unit). The maximum parameter value is 4.0. 

== rotate ==
 rotate x/y/z &lt;angle&gt;
Rotates images about the specified axis by the specified angle in degrees. 

== save ==
 save {pdb} &lt;filename&gt;
Saves the currently selected set of atoms in a PDB format file.

 save script &lt;filename&gt;
Creates a script file that reproduces the currently displayed image.

 save png &lt;filename&gt;
Creates a PNG image file of the currently displayed image.

 save jpeg &lt;filename&gt; {&lt;quality&gt;}
Creates a JPEG image file of the currently displayed image. The compression quality can be specified, 0 &lt; quality &lt;= 1, where 'quality = 1' means no compression. 

== script ==
 script &lt;filename&gt;
Opens and executes the specified script file. URL can be used to open a remote file. 

== select ==
 select
Selects all atoms. Whether hetero atoms and hydrogens are selected or not depends on the internal parameters, hetero and hydrogen, respectively.

 select all
Selects all atoms including hetero atoms and hydrogens.

 select none
Selects no atoms.

 select &lt;atom_expression&gt;
Selects a group of atoms specified by the atom expression. 

== selectvertex ==
 selectvertex {all}
Selects all vertices.

 selectvertex none
Selects no vertices.

 selectvertex &lt;vertex_expression&gt;
Selects a group of vertices specified by the vertex expression. 

== set ==
=== adjustview ===
 set adjustview on
The view point is automatically adjusted when a new file is loaded.

 set adjustview off
The view point is kept unchanged when a new file is loaded. 

=== background ===
 set background &lt;color&gt;
Changes the background color. The color may be given as RGB values [r,g,b], or predefined color names. 

=== bondmode ===
 set bondmode and
Specifies how to select an individual bonds. A bond is selected when both atoms connected by the bond are selected.

 set bondmode or
Specifies how to select an individual bonds. A bond is selected when either of the connected atoms is selected. 

=== cartoon ===
 set cartoon {&lt;value&gt;}
Specifies the thickness of the cartoon representation (angstrom or Rasmol unit). The maximum parameter value is 2.0. When the parameter is not specified, it is restored to the default value. 

=== center ===
 set center &lt;atom_expression&gt;
Sets the default center of the selected files to the center of the specified atoms.

 set center [x, y, z]
Sets the default center of the selected files to the specified coordinates. 

=== drawlevel ===
 set drawlevel &lt;value&gt;
Specifies precision of the rendering of spheres and cylinders. The value may be given as an integer (minimum 5) that stands for the number of straight line segments to represent an arc of 180 degrees. 

=== hbonds ===
 set hbonds backbone
Hydrogen bonds are displayed between backbones.

 set hbonds sidechain
Hydrogen bonds are displayed between sidechains. 

=== hetero ===
 set hetero on
Sets the default behavior of the select command such that hetero atoms are selected.

 set hetero off
Sets the default behavior of the select command such that hetero atoms are not selected. 

=== hydrogen ===
 set hydrogen on
Sets the default behavior of the select command such that hydrogens are selected.

 set hydrogen off
Sets the default behavior of the select command such that hydrogens are not selected. 

=== imagesize ===
 set imagesize &lt;width&gt; &lt;height&gt;
Sets the size of the 3D-rendering panel in pixels. The size will be set within the screen size with the width being an even integer. 

=== line_width ===
 set line_width &lt;value&gt;
Sets the width of lines in polygon images. The &lt;value&gt; should be larger than 0. 

=== loadcenter ===
 set loadcenter on
When a file is opened, sets the default center of that file to the center of all files that have already opened.

 set loadcenter off
When a file is opened, sets the default center of that file according to its own coordiantes. 

=== picking ===
 set picking off
Turns off the mouse picking.

 set picking ident
Sets the mouse picking behavior to show atom identification.

 set picking coord
Sets the mouse picking behavior to show atom coordinates with identification.

 set picking distance
Sets the mouse picking behavior to show the distance between atoms successively picked.

 set picking center
Sets the mouse picking behavior to specify the center of rotation and center of the screen.

 set picking select
Sets the mouse picking behavior to select the file that contains the atom picked. 

=== pickradius ===
 set pickradius &lt;value&gt;
Sets the mouse-pickable region of each atom to be the sphere centered to each atom with the specified radius (angstrom or Rasmol unit). 

=== point_size ===
 set point_size &lt;value&gt;
Sets the size of points in polygon images. The &lt;value&gt; should be larger than 0. 

=== polyline_width ===
 set polyline_width &lt;value&gt;
Sets the width of polylines in polygon images. The &lt;value&gt; should be larger than 0. 

=== projection ===
 set projection perspective
Sets the projection mode for a perspective projection.

 set projection parallel {&lt;size&gt;}
Sets the projection mode for a parallel projection. The size of image (fit to the height of the screen) can be specified (angstrom or Rasmol unit). 

=== specular ===
 set specular on/true
Enables the display of specular highlights on solid objects.

 set specular off/false
Disables the display of specular highlights on solid objects.

 set specular &lt;value&gt;
Enables the display of specular highlights on solid objects. The value between 0 and 100 specifies the specular color in gray scale with 0 and 100 being black and white, respectively. The default value is 50.0. 

=== specpower ===
 set specpower &lt;value&gt;
Sets the shininess of solid objects. The value between 0 and 100 specifies a material reflection coefficient with 0 being diffuse surfaces and 100 being shiny surfaces. 

=== ssbonds ===
 set ssbonds backbone
Disulfide bonds are displayed between backbones.

 set ssbonds sidechain
Disulfide bonds are displayed between sidechains. 

=== stereo ===
 set stereo
A synonym of the stereo command. 

=== transparency ===
 set transparency &lt;value&gt;
Sets the transparency of polygon images.

 set point_transparency &lt;value&gt;
Sets the transparency of points in polygon images.

 set line_transparency &lt;value&gt;
Sets the transparency of lines in polygon images.

 set triangle_transparency &lt;value&gt;
Sets the transparency of triangles in polygon images.

 set quad_transparency &lt;value&gt;
Sets the transparency of quads in polygon images.

 set polyline_transparency &lt;value&gt;
Sets the transparency of polylines in polygon images. 

=== viewpoint ===
 set viewpoint {x, y, z}
Sets the viewpoint to the specified coordinates. 

== show ==
 show godata
Displays gene ontology data of molecules.

 show imagesize
Displays the size of the 3D-rendering panel.

 show information
Displays a detail discription of molecules.

 show site {&lt;prefix&gt;:&lt;db&gt;:&lt;category&gt;}
Displays site information in an external database.

 show transform
Displays the transform matrix of molecules.

 show viewpoint
Displays the current viewpoint.

 show xps3
Displays keywords available in xps3 selection. 

== slab ==
 slab {on/true}
Enables the z-clipping plane of molecules and polygons.

 slab off/false
Disables the z-clipping plane of molecules and polygons.

 slab &lt;ratio&gt;
Sets the position of the z-clipping plane of molecules and polygons. The parameter may be given as a number from 0 to 100. The values 0 and 100 represent that image as a whole is completely invisible and visible, respectively.

 slab -v &lt;value&gt;
Sets the position of the z-clipping plane of molecules and polygons by specifying the z coordinate value. 

== spacefill ==
 spacefill {on/true}
Turns on the ball image of the selected atoms.

 spacefill off/false
Turns off the ball image of the selected atoms.

 spacefill &lt;radius&gt;
Turns on the ball image of the selected atoms with the specified radius (angstrom or Rasmol unit). The maximum parameter value is 3.0.

 spacefill temperature
Turns on the ball image of the selected atoms using the temperature factor as radius. 

== ssbonds ==
 ssbonds {on/true}
Turns on the selected disulfide bonds.

 ssbonds off/false
Turns off the selected disulfide bonds.

 ssbonds &lt;radius&gt;
Turns on the selected disulfide bonds with the specified raidus (angstrom or Rasmol unit). The maximum parameter value is 2.0. 

== stereo ==
 stereo {on/true}
Enables stereo display. This command without arguments cycles three state; 'stereo off', 'stereo on' in cross-eyed mode and 'stereo on' in parallel-eyed mode.

 stereo off/false
Disables stereo display.

 stereo &lt;angle&gt;
Enables stereo display with the specified separation angle. Positive and negative values represent cross-eyed and parallel-eyed viewing, respectively.


== structure ==
 structure
Estimates the secondary structure using Kabsch and Sander's DSSP algorithm. 

== trace ==
 trace {on/true}
Turns on a tube representation for the selected residues.

 trace off/false
Turns off a tube representation for the selected residues.

 trace &lt;radius&gt;
Turns on a tube representation for the selected residues with the specified radius (angstrom or Rasmol unit). The maximum parameter value is 2.0.


== translate ==
 translate x/y/z &lt;value&gt;
Moves images along the specified axis by the specified amount (angstrom). 

== wireframe ==
 wireframe {on/true}
Turns on the selected bonds.

 wireframe off/false
Turns off the selected bonds.

 wireframe &lt;radius&gt;
Turns on the selected bonds with the specified raidus (angstrom or Rasmol unit). The maximum parameter value is 2.0. 

== write ==
 write
A synonym of the [[#save|save]] command.

== zap ==
 zap {&lt;file_IDs&gt;}
Closes the specified files. More than one file IDs can be specified by putting commas as the delimiter. When the paraneter is absent, all files are closed. 

== zoom ==
 zoom {&lt;value&gt;}
Sets the magnification of the image as a whole. The value stands for the magnification as a percentage of the current scale. The minimum parameter value is 10.0.</text>
    <sha1>a2bd91f9d01bb31fffd9508b768c5890f2a7a05e</sha1>
  </revision>
  <revision>
    <id>360</id>
    <parentid>359</parentid>
    <timestamp>2009-12-03T04:36:21Z</timestamp>
    <contributor>
      <username>Cudo29</username>
      <id>5</id>
    </contributor>
    <minor/>
    <comment>/* stereo */ A link to the stereo section was added.</comment>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="18759" xml:space="preserve"> {| style="float:right"
  |__TOC__
  |}
Command usage of jV follows that of [http://www.rasmol.org/ Rasmol] with some modifications. In the following part, command arguments that can take an arbitrary value are denoted as &lt;value&gt; for example, arguments restricted to several possible values are listed with / as a delimiter, and arguments that can be omitted are put in brackets {}. Commands, [[#exit|exit]], [[#load|load]], [[#quit|quit]], [[#save|save]], [[#script|script]], and [[#write|write]], are not available in applet circumstance.

== anim ==
 anim forward {&lt;value&gt;}
Starts animation forward. If the &lt;value&gt; is given, just move frames forward by the specified amount.

 anim backward {&lt;value&gt;}
Starts animation backward. If the &lt;value&gt; is given, just move frames backward by the specified amount.

 anim stop
Stops animation.

== animframe ==
 animframe &lt;frame&gt; {&lt;file_ID&gt;}
Sets the frame of all animation files for the specified value. When &lt;file_ID&gt; is given, only the specified file is processed.

== animmode ==
 animmode once
Sets the behavior of animation for 'once'. When the frame reaches the last one, animation is stopped.

 animmode loop
Sets the behavior of animation for 'loop'. When the frame reaches the last one, animation is reset to the first frame and continues playing.

 animmode swing
Sets the behavior of animation for 'swing'. When the frame reaches the last one, the direction of animation is reversed.

== animrange ==
 animrange &lt;init_frame&gt;-&lt;term_frame&gt; {&lt;file_IDs&gt;}
Sets the range of all animation files. When is given, only the specified file is processed.

== animselect ==
 animselect {-a/-r} &lt;file_IDs&gt;
Selects the specified files and makes the others not selected. More than one file IDs can be specified by putting commas as the delimiter. When the option -a or -r is specified, only the selection status of the specified files are modified, selected or not selected, respectively, and the others remain unchanged.

== animspeed ==
 animspeed &lt;speed&gt;
Sets the animation speed. The argument should be an integer value from 1 to 20.

== animstep ==
 animstep &lt;step&gt; {&lt;file_ID&gt;}
Sets the step of all animation files for the specified value. When &lt;file_ID&gt; is given, only the specified file is processed.

== backbone ==
 backbone {on/true}
Turns on the selected backbone bonds.

 backbone off/false
Turns off the selected backbone bonds.

 backbone &lt;radius&gt;
Turns on the selected backbone bonds with the specified raidus (angstrom or Rasmol unit). The maximum parameter value is 2.0.

== background ==
 background &lt;color&gt;
Changes the background color. The color may be given as RGB values [r,g,b], or predefined color names.

== cartoon ==
 cartoon {on/true}
Turns on the thick ribbons for the selected residues.

 cartoon off/false
Turns off the thick ribbons for the selected residues.

 cartoon &lt;half_width&gt;
Turns on the thick ribbons for the selected residues with the specified half width (angstrom or Rasmol unit). The maximum parameter value is 4.0.

== center ==
 center {-r/-s} {&lt;atom_expression&gt;}
Sets the center of rotation and the center of the screen to the center of a group of atoms specified by the atom expression. When the option -r or -s is specified, only the center of rotation or the center of the screen is modified, respectively.

 center {-r} [x, y, z]
Moves the center of rotation and the center of the screen from the current position by the specified amount. When the option -r is specified, only the center of rotation is modified.

 center {-r} {x, y, z}
Sets the center of rotation and the center of the screen to the specified coordinates. When the option -r is specified, only the center of rotation is modified.

 center -s [x, y]
Moves the center of the screen from the current position by the specified amount.

 center -s {x, y}
Sets the center of the screen to the specified coordinates.

== color ==
 color {atoms} &lt;color&gt;
Sets the color of the selected atoms. The color may be given as RGB values [r,g,b], predefined color names, or predefined color schemes; amino, chain, charge, cpk, group, shapely, structure, and temperature.

 color bonds/backbone/ribbons/hbonds/ssbonds &lt;color&gt;
Sets the color of the specified object. The color may be given as RGB values [r,g,b] or predefined color names. For hydrogen bonds, color scheme 'type' can be specified.

 color bonds/backbone/ribbons/hbonds/ssbonds none
Resets the color of the specified object.

== colorvertex ==
 colorvertex &lt;color&gt;
Sets the color of the selected vertices. The color may be given as RGB values [r,g,b] or predefined color names.

 colorvertex none
Resets the color of the selected vertices.

== cpk ==
 cpk
A synonym of the [[#spacefill|spacefill]] command.

== define ==
 define &lt;name&gt; &lt;atom_expression&gt;
Associates an arbitrary set of atoms with a unique name.

== display ==
 display all
Displays the image of all files.

 display none
Turns off the image of all files.

 display {-a/-r} &lt;file_IDs&gt;
Displays the image of the specified files and turns off the others. More than one file IDs can be specified by putting commas as the delimiter. When the option -a or -r is specified, turns the image of the specified files on or off, respectively, and the others remain unchanged.

== displayvertex ==
 displayvertex {on/true}
Displays the selected vertices.

 displayvertex off/false
Turns off the selected vertices.

== echo ==
 echo &lt;string&gt;
Echoes the specified message back to the message area.

== exit ==
 exit
Terminates the application.

== fit ==
 fit &lt;file1_ID&gt; &lt;file2_ID&gt;
Sets the transform matrix of file1 identical to that of file2. 

== fselect ==
 fselect all
Selects all files.

 fselect none
Selects no files.

 fselect {-a/-r} &lt;file_IDs&gt;
Selects the specified files and makes the others not selected. More than one file IDs can be specified by putting commas as the delimiter. When the option -a or -r is specified, only the selection status of the specified files are modified, selected or not selected, respectively, and the others remain unchanged.

== hbonds ==
 hbonds {on/true}
Turns on the selected hydrogen bonds.

 hbonds off/false
Turns off the selected hydrogen bonds.

 hbonds &lt;radius&gt;
Turns on the selected hydrogen bonds with the specified raidus (angstrom or Rasmol unit). The maximum parameter value is 2.0. 

== load ==
 load {pdbml} &lt;filename&gt; {fit &lt;file_ID&gt;}
Opens a PDBML file. URL can be used to open a remote file. On loading, the transform matrix can be set identical to that of the specified file.

 load pdb &lt;filename&gt; {fit &lt;file_ID&gt;}
Opens a PDB file. URL can be used to open a remote file. On loading, the transform matrix can be set identical to that of the specified file.

 load polygon &lt;filename&gt; {fit &lt;file_ID&gt;}
Opens a polygon file. URL can be used to open a remote file. On loading, the transform matrix can be set identical to that of the specified file.

 load animation &lt;filename&gt; {fit &lt;file_ID&gt;}
Opens an animation file. URL can be used to open a remote file. On loading, the transform matrix can be set identical to that of the specified file.

 load ftp &lt;PDB_code&gt; {fit &lt;file_ID&gt;}
Retrieves a PDBML file from the PDBj FTP site and opens it. On loading, the transform matrix can be set identical to that of the specified file. 

== pause ==
 pause
Stops the execution of a script file until any key is pressed to restart. 

== quit ==
 quit
A synonym of the [[#exit|exit]] command.

== refresh ==
 refresh
Redraws all images. 

== reset ==
=== default ===
 reset
Restores the original viewing transformation of all images, the center of rotation, and the view point. 

=== cartoon ===
 reset cartoon
Restores the thickness of the cartoon representation. 

=== line_width ===
 reset line_width
Restores the width of lines in polygon images. 

=== pickradius ===
 reset pickradius
Restores the mouse-pickable region of each atom. 

=== point_size ===
 reset point_size
Restores the size of points in polygon images. 

=== polyline_width ===
 reset polyline_width
Restores the width of polylines in polygon images. 

=== transparency ===
 reset transparency
Restores the transparency of polygon images.

 reset point_transparency
Restores the transparency of points in polygon images.

 reset line_transparency
Restores the transparency of lines in polygon images.

 reset triangle_transparency
Restores the transparency of triangles in polygon images.

 reset quad_transparency
Restores the transparency of quads in polygon images.

 reset polyline_transparency
Restores the transparency of polylines in polygon images. 

== ribbons ==
 ribbons {on/true}
Turns on the ribbon surfaces for the selected residues.

 ribbons off/false
Turns off the ribbon surfaces for the selected residues.

 ribbons &lt;half_width&gt;
Turns on the ribbon surfaces for the selected residues with the specified half width (angstrom or Rasmol unit). The maximum parameter value is 4.0. 

== rotate ==
 rotate x/y/z &lt;angle&gt;
Rotates images about the specified axis by the specified angle in degrees. 

== save ==
 save {pdb} &lt;filename&gt;
Saves the currently selected set of atoms in a PDB format file.

 save script &lt;filename&gt;
Creates a script file that reproduces the currently displayed image.

 save png &lt;filename&gt;
Creates a PNG image file of the currently displayed image.

 save jpeg &lt;filename&gt; {&lt;quality&gt;}
Creates a JPEG image file of the currently displayed image. The compression quality can be specified, 0 &lt; quality &lt;= 1, where 'quality = 1' means no compression. 

== script ==
 script &lt;filename&gt;
Opens and executes the specified script file. URL can be used to open a remote file. 

== select ==
 select
Selects all atoms. Whether hetero atoms and hydrogens are selected or not depends on the internal parameters, hetero and hydrogen, respectively.

 select all
Selects all atoms including hetero atoms and hydrogens.

 select none
Selects no atoms.

 select &lt;atom_expression&gt;
Selects a group of atoms specified by the atom expression. 

== selectvertex ==
 selectvertex {all}
Selects all vertices.

 selectvertex none
Selects no vertices.

 selectvertex &lt;vertex_expression&gt;
Selects a group of vertices specified by the vertex expression. 

== set ==
=== adjustview ===
 set adjustview on
The view point is automatically adjusted when a new file is loaded.

 set adjustview off
The view point is kept unchanged when a new file is loaded. 

=== background ===
 set background &lt;color&gt;
Changes the background color. The color may be given as RGB values [r,g,b], or predefined color names. 

=== bondmode ===
 set bondmode and
Specifies how to select an individual bonds. A bond is selected when both atoms connected by the bond are selected.

 set bondmode or
Specifies how to select an individual bonds. A bond is selected when either of the connected atoms is selected. 

=== cartoon ===
 set cartoon {&lt;value&gt;}
Specifies the thickness of the cartoon representation (angstrom or Rasmol unit). The maximum parameter value is 2.0. When the parameter is not specified, it is restored to the default value. 

=== center ===
 set center &lt;atom_expression&gt;
Sets the default center of the selected files to the center of the specified atoms.

 set center [x, y, z]
Sets the default center of the selected files to the specified coordinates. 

=== drawlevel ===
 set drawlevel &lt;value&gt;
Specifies precision of the rendering of spheres and cylinders. The value may be given as an integer (minimum 5) that stands for the number of straight line segments to represent an arc of 180 degrees. 

=== hbonds ===
 set hbonds backbone
Hydrogen bonds are displayed between backbones.

 set hbonds sidechain
Hydrogen bonds are displayed between sidechains. 

=== hetero ===
 set hetero on
Sets the default behavior of the select command such that hetero atoms are selected.

 set hetero off
Sets the default behavior of the select command such that hetero atoms are not selected. 

=== hydrogen ===
 set hydrogen on
Sets the default behavior of the select command such that hydrogens are selected.

 set hydrogen off
Sets the default behavior of the select command such that hydrogens are not selected. 

=== imagesize ===
 set imagesize &lt;width&gt; &lt;height&gt;
Sets the size of the 3D-rendering panel in pixels. The size will be set within the screen size with the width being an even integer. 

=== line_width ===
 set line_width &lt;value&gt;
Sets the width of lines in polygon images. The &lt;value&gt; should be larger than 0. 

=== loadcenter ===
 set loadcenter on
When a file is opened, sets the default center of that file to the center of all files that have already opened.

 set loadcenter off
When a file is opened, sets the default center of that file according to its own coordiantes. 

=== picking ===
 set picking off
Turns off the mouse picking.

 set picking ident
Sets the mouse picking behavior to show atom identification.

 set picking coord
Sets the mouse picking behavior to show atom coordinates with identification.

 set picking distance
Sets the mouse picking behavior to show the distance between atoms successively picked.

 set picking center
Sets the mouse picking behavior to specify the center of rotation and center of the screen.

 set picking select
Sets the mouse picking behavior to select the file that contains the atom picked. 

=== pickradius ===
 set pickradius &lt;value&gt;
Sets the mouse-pickable region of each atom to be the sphere centered to each atom with the specified radius (angstrom or Rasmol unit). 

=== point_size ===
 set point_size &lt;value&gt;
Sets the size of points in polygon images. The &lt;value&gt; should be larger than 0. 

=== polyline_width ===
 set polyline_width &lt;value&gt;
Sets the width of polylines in polygon images. The &lt;value&gt; should be larger than 0. 

=== projection ===
 set projection perspective
Sets the projection mode for a perspective projection.

 set projection parallel {&lt;size&gt;}
Sets the projection mode for a parallel projection. The size of image (fit to the height of the screen) can be specified (angstrom or Rasmol unit). 

=== specular ===
 set specular on/true
Enables the display of specular highlights on solid objects.

 set specular off/false
Disables the display of specular highlights on solid objects.

 set specular &lt;value&gt;
Enables the display of specular highlights on solid objects. The value between 0 and 100 specifies the specular color in gray scale with 0 and 100 being black and white, respectively. The default value is 50.0. 

=== specpower ===
 set specpower &lt;value&gt;
Sets the shininess of solid objects. The value between 0 and 100 specifies a material reflection coefficient with 0 being diffuse surfaces and 100 being shiny surfaces. 

=== ssbonds ===
 set ssbonds backbone
Disulfide bonds are displayed between backbones.

 set ssbonds sidechain
Disulfide bonds are displayed between sidechains. 

=== stereo ===
 set stereo
A synonym of the [[#stereo|stereo]] command.

=== transparency ===
 set transparency &lt;value&gt;
Sets the transparency of polygon images.

 set point_transparency &lt;value&gt;
Sets the transparency of points in polygon images.

 set line_transparency &lt;value&gt;
Sets the transparency of lines in polygon images.

 set triangle_transparency &lt;value&gt;
Sets the transparency of triangles in polygon images.

 set quad_transparency &lt;value&gt;
Sets the transparency of quads in polygon images.

 set polyline_transparency &lt;value&gt;
Sets the transparency of polylines in polygon images. 

=== viewpoint ===
 set viewpoint {x, y, z}
Sets the viewpoint to the specified coordinates. 

== show ==
 show godata
Displays gene ontology data of molecules.

 show imagesize
Displays the size of the 3D-rendering panel.

 show information
Displays a detail discription of molecules.

 show site {&lt;prefix&gt;:&lt;db&gt;:&lt;category&gt;}
Displays site information in an external database.

 show transform
Displays the transform matrix of molecules.

 show viewpoint
Displays the current viewpoint.

 show xps3
Displays keywords available in xps3 selection. 

== slab ==
 slab {on/true}
Enables the z-clipping plane of molecules and polygons.

 slab off/false
Disables the z-clipping plane of molecules and polygons.

 slab &lt;ratio&gt;
Sets the position of the z-clipping plane of molecules and polygons. The parameter may be given as a number from 0 to 100. The values 0 and 100 represent that image as a whole is completely invisible and visible, respectively.

 slab -v &lt;value&gt;
Sets the position of the z-clipping plane of molecules and polygons by specifying the z coordinate value. 

== spacefill ==
 spacefill {on/true}
Turns on the ball image of the selected atoms.

 spacefill off/false
Turns off the ball image of the selected atoms.

 spacefill &lt;radius&gt;
Turns on the ball image of the selected atoms with the specified radius (angstrom or Rasmol unit). The maximum parameter value is 3.0.

 spacefill temperature
Turns on the ball image of the selected atoms using the temperature factor as radius. 

== ssbonds ==
 ssbonds {on/true}
Turns on the selected disulfide bonds.

 ssbonds off/false
Turns off the selected disulfide bonds.

 ssbonds &lt;radius&gt;
Turns on the selected disulfide bonds with the specified raidus (angstrom or Rasmol unit). The maximum parameter value is 2.0. 

== stereo ==
 stereo {on/true}
Enables stereo display. This command without arguments cycles three state; 'stereo off', 'stereo on' in cross-eyed mode and 'stereo on' in parallel-eyed mode.

 stereo off/false
Disables stereo display.

 stereo &lt;angle&gt;
Enables stereo display with the specified separation angle. Positive and negative values represent cross-eyed and parallel-eyed viewing, respectively.


== structure ==
 structure
Estimates the secondary structure using Kabsch and Sander's DSSP algorithm. 

== trace ==
 trace {on/true}
Turns on a tube representation for the selected residues.

 trace off/false
Turns off a tube representation for the selected residues.

 trace &lt;radius&gt;
Turns on a tube representation for the selected residues with the specified radius (angstrom or Rasmol unit). The maximum parameter value is 2.0.


== translate ==
 translate x/y/z &lt;value&gt;
Moves images along the specified axis by the specified amount (angstrom). 

== wireframe ==
 wireframe {on/true}
Turns on the selected bonds.

 wireframe off/false
Turns off the selected bonds.

 wireframe &lt;radius&gt;
Turns on the selected bonds with the specified raidus (angstrom or Rasmol unit). The maximum parameter value is 2.0. 

== write ==
 write
A synonym of the [[#save|save]] command.

== zap ==
 zap {&lt;file_IDs&gt;}
Closes the specified files. More than one file IDs can be specified by putting commas as the delimiter. When the paraneter is absent, all files are closed. 

== zoom ==
 zoom {&lt;value&gt;}
Sets the magnification of the image as a whole. The value stands for the magnification as a percentage of the current scale. The minimum parameter value is 10.0.</text>
    <sha1>70baab0cbe32ff4d970e2d80b223875fa0892c94</sha1>
  </revision>
  <revision>
    <id>361</id>
    <parentid>360</parentid>
    <timestamp>2009-12-03T04:37:54Z</timestamp>
    <contributor>
      <username>Cudo29</username>
      <id>5</id>
    </contributor>
    <minor/>
    <comment>/* stereo */ The link to the stereo section was corrected.</comment>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="18761" xml:space="preserve"> {| style="float:right"
  |__TOC__
  |}
Command usage of jV follows that of [http://www.rasmol.org/ Rasmol] with some modifications. In the following part, command arguments that can take an arbitrary value are denoted as &lt;value&gt; for example, arguments restricted to several possible values are listed with / as a delimiter, and arguments that can be omitted are put in brackets {}. Commands, [[#exit|exit]], [[#load|load]], [[#quit|quit]], [[#save|save]], [[#script|script]], and [[#write|write]], are not available in applet circumstance.

== anim ==
 anim forward {&lt;value&gt;}
Starts animation forward. If the &lt;value&gt; is given, just move frames forward by the specified amount.

 anim backward {&lt;value&gt;}
Starts animation backward. If the &lt;value&gt; is given, just move frames backward by the specified amount.

 anim stop
Stops animation.

== animframe ==
 animframe &lt;frame&gt; {&lt;file_ID&gt;}
Sets the frame of all animation files for the specified value. When &lt;file_ID&gt; is given, only the specified file is processed.

== animmode ==
 animmode once
Sets the behavior of animation for 'once'. When the frame reaches the last one, animation is stopped.

 animmode loop
Sets the behavior of animation for 'loop'. When the frame reaches the last one, animation is reset to the first frame and continues playing.

 animmode swing
Sets the behavior of animation for 'swing'. When the frame reaches the last one, the direction of animation is reversed.

== animrange ==
 animrange &lt;init_frame&gt;-&lt;term_frame&gt; {&lt;file_IDs&gt;}
Sets the range of all animation files. When is given, only the specified file is processed.

== animselect ==
 animselect {-a/-r} &lt;file_IDs&gt;
Selects the specified files and makes the others not selected. More than one file IDs can be specified by putting commas as the delimiter. When the option -a or -r is specified, only the selection status of the specified files are modified, selected or not selected, respectively, and the others remain unchanged.

== animspeed ==
 animspeed &lt;speed&gt;
Sets the animation speed. The argument should be an integer value from 1 to 20.

== animstep ==
 animstep &lt;step&gt; {&lt;file_ID&gt;}
Sets the step of all animation files for the specified value. When &lt;file_ID&gt; is given, only the specified file is processed.

== backbone ==
 backbone {on/true}
Turns on the selected backbone bonds.

 backbone off/false
Turns off the selected backbone bonds.

 backbone &lt;radius&gt;
Turns on the selected backbone bonds with the specified raidus (angstrom or Rasmol unit). The maximum parameter value is 2.0.

== background ==
 background &lt;color&gt;
Changes the background color. The color may be given as RGB values [r,g,b], or predefined color names.

== cartoon ==
 cartoon {on/true}
Turns on the thick ribbons for the selected residues.

 cartoon off/false
Turns off the thick ribbons for the selected residues.

 cartoon &lt;half_width&gt;
Turns on the thick ribbons for the selected residues with the specified half width (angstrom or Rasmol unit). The maximum parameter value is 4.0.

== center ==
 center {-r/-s} {&lt;atom_expression&gt;}
Sets the center of rotation and the center of the screen to the center of a group of atoms specified by the atom expression. When the option -r or -s is specified, only the center of rotation or the center of the screen is modified, respectively.

 center {-r} [x, y, z]
Moves the center of rotation and the center of the screen from the current position by the specified amount. When the option -r is specified, only the center of rotation is modified.

 center {-r} {x, y, z}
Sets the center of rotation and the center of the screen to the specified coordinates. When the option -r is specified, only the center of rotation is modified.

 center -s [x, y]
Moves the center of the screen from the current position by the specified amount.

 center -s {x, y}
Sets the center of the screen to the specified coordinates.

== color ==
 color {atoms} &lt;color&gt;
Sets the color of the selected atoms. The color may be given as RGB values [r,g,b], predefined color names, or predefined color schemes; amino, chain, charge, cpk, group, shapely, structure, and temperature.

 color bonds/backbone/ribbons/hbonds/ssbonds &lt;color&gt;
Sets the color of the specified object. The color may be given as RGB values [r,g,b] or predefined color names. For hydrogen bonds, color scheme 'type' can be specified.

 color bonds/backbone/ribbons/hbonds/ssbonds none
Resets the color of the specified object.

== colorvertex ==
 colorvertex &lt;color&gt;
Sets the color of the selected vertices. The color may be given as RGB values [r,g,b] or predefined color names.

 colorvertex none
Resets the color of the selected vertices.

== cpk ==
 cpk
A synonym of the [[#spacefill|spacefill]] command.

== define ==
 define &lt;name&gt; &lt;atom_expression&gt;
Associates an arbitrary set of atoms with a unique name.

== display ==
 display all
Displays the image of all files.

 display none
Turns off the image of all files.

 display {-a/-r} &lt;file_IDs&gt;
Displays the image of the specified files and turns off the others. More than one file IDs can be specified by putting commas as the delimiter. When the option -a or -r is specified, turns the image of the specified files on or off, respectively, and the others remain unchanged.

== displayvertex ==
 displayvertex {on/true}
Displays the selected vertices.

 displayvertex off/false
Turns off the selected vertices.

== echo ==
 echo &lt;string&gt;
Echoes the specified message back to the message area.

== exit ==
 exit
Terminates the application.

== fit ==
 fit &lt;file1_ID&gt; &lt;file2_ID&gt;
Sets the transform matrix of file1 identical to that of file2. 

== fselect ==
 fselect all
Selects all files.

 fselect none
Selects no files.

 fselect {-a/-r} &lt;file_IDs&gt;
Selects the specified files and makes the others not selected. More than one file IDs can be specified by putting commas as the delimiter. When the option -a or -r is specified, only the selection status of the specified files are modified, selected or not selected, respectively, and the others remain unchanged.

== hbonds ==
 hbonds {on/true}
Turns on the selected hydrogen bonds.

 hbonds off/false
Turns off the selected hydrogen bonds.

 hbonds &lt;radius&gt;
Turns on the selected hydrogen bonds with the specified raidus (angstrom or Rasmol unit). The maximum parameter value is 2.0. 

== load ==
 load {pdbml} &lt;filename&gt; {fit &lt;file_ID&gt;}
Opens a PDBML file. URL can be used to open a remote file. On loading, the transform matrix can be set identical to that of the specified file.

 load pdb &lt;filename&gt; {fit &lt;file_ID&gt;}
Opens a PDB file. URL can be used to open a remote file. On loading, the transform matrix can be set identical to that of the specified file.

 load polygon &lt;filename&gt; {fit &lt;file_ID&gt;}
Opens a polygon file. URL can be used to open a remote file. On loading, the transform matrix can be set identical to that of the specified file.

 load animation &lt;filename&gt; {fit &lt;file_ID&gt;}
Opens an animation file. URL can be used to open a remote file. On loading, the transform matrix can be set identical to that of the specified file.

 load ftp &lt;PDB_code&gt; {fit &lt;file_ID&gt;}
Retrieves a PDBML file from the PDBj FTP site and opens it. On loading, the transform matrix can be set identical to that of the specified file. 

== pause ==
 pause
Stops the execution of a script file until any key is pressed to restart. 

== quit ==
 quit
A synonym of the [[#exit|exit]] command.

== refresh ==
 refresh
Redraws all images. 

== reset ==
=== default ===
 reset
Restores the original viewing transformation of all images, the center of rotation, and the view point. 

=== cartoon ===
 reset cartoon
Restores the thickness of the cartoon representation. 

=== line_width ===
 reset line_width
Restores the width of lines in polygon images. 

=== pickradius ===
 reset pickradius
Restores the mouse-pickable region of each atom. 

=== point_size ===
 reset point_size
Restores the size of points in polygon images. 

=== polyline_width ===
 reset polyline_width
Restores the width of polylines in polygon images. 

=== transparency ===
 reset transparency
Restores the transparency of polygon images.

 reset point_transparency
Restores the transparency of points in polygon images.

 reset line_transparency
Restores the transparency of lines in polygon images.

 reset triangle_transparency
Restores the transparency of triangles in polygon images.

 reset quad_transparency
Restores the transparency of quads in polygon images.

 reset polyline_transparency
Restores the transparency of polylines in polygon images. 

== ribbons ==
 ribbons {on/true}
Turns on the ribbon surfaces for the selected residues.

 ribbons off/false
Turns off the ribbon surfaces for the selected residues.

 ribbons &lt;half_width&gt;
Turns on the ribbon surfaces for the selected residues with the specified half width (angstrom or Rasmol unit). The maximum parameter value is 4.0. 

== rotate ==
 rotate x/y/z &lt;angle&gt;
Rotates images about the specified axis by the specified angle in degrees. 

== save ==
 save {pdb} &lt;filename&gt;
Saves the currently selected set of atoms in a PDB format file.

 save script &lt;filename&gt;
Creates a script file that reproduces the currently displayed image.

 save png &lt;filename&gt;
Creates a PNG image file of the currently displayed image.

 save jpeg &lt;filename&gt; {&lt;quality&gt;}
Creates a JPEG image file of the currently displayed image. The compression quality can be specified, 0 &lt; quality &lt;= 1, where 'quality = 1' means no compression. 

== script ==
 script &lt;filename&gt;
Opens and executes the specified script file. URL can be used to open a remote file. 

== select ==
 select
Selects all atoms. Whether hetero atoms and hydrogens are selected or not depends on the internal parameters, hetero and hydrogen, respectively.

 select all
Selects all atoms including hetero atoms and hydrogens.

 select none
Selects no atoms.

 select &lt;atom_expression&gt;
Selects a group of atoms specified by the atom expression. 

== selectvertex ==
 selectvertex {all}
Selects all vertices.

 selectvertex none
Selects no vertices.

 selectvertex &lt;vertex_expression&gt;
Selects a group of vertices specified by the vertex expression. 

== set ==
=== adjustview ===
 set adjustview on
The view point is automatically adjusted when a new file is loaded.

 set adjustview off
The view point is kept unchanged when a new file is loaded. 

=== background ===
 set background &lt;color&gt;
Changes the background color. The color may be given as RGB values [r,g,b], or predefined color names. 

=== bondmode ===
 set bondmode and
Specifies how to select an individual bonds. A bond is selected when both atoms connected by the bond are selected.

 set bondmode or
Specifies how to select an individual bonds. A bond is selected when either of the connected atoms is selected. 

=== cartoon ===
 set cartoon {&lt;value&gt;}
Specifies the thickness of the cartoon representation (angstrom or Rasmol unit). The maximum parameter value is 2.0. When the parameter is not specified, it is restored to the default value. 

=== center ===
 set center &lt;atom_expression&gt;
Sets the default center of the selected files to the center of the specified atoms.

 set center [x, y, z]
Sets the default center of the selected files to the specified coordinates. 

=== drawlevel ===
 set drawlevel &lt;value&gt;
Specifies precision of the rendering of spheres and cylinders. The value may be given as an integer (minimum 5) that stands for the number of straight line segments to represent an arc of 180 degrees. 

=== hbonds ===
 set hbonds backbone
Hydrogen bonds are displayed between backbones.

 set hbonds sidechain
Hydrogen bonds are displayed between sidechains. 

=== hetero ===
 set hetero on
Sets the default behavior of the select command such that hetero atoms are selected.

 set hetero off
Sets the default behavior of the select command such that hetero atoms are not selected. 

=== hydrogen ===
 set hydrogen on
Sets the default behavior of the select command such that hydrogens are selected.

 set hydrogen off
Sets the default behavior of the select command such that hydrogens are not selected. 

=== imagesize ===
 set imagesize &lt;width&gt; &lt;height&gt;
Sets the size of the 3D-rendering panel in pixels. The size will be set within the screen size with the width being an even integer. 

=== line_width ===
 set line_width &lt;value&gt;
Sets the width of lines in polygon images. The &lt;value&gt; should be larger than 0. 

=== loadcenter ===
 set loadcenter on
When a file is opened, sets the default center of that file to the center of all files that have already opened.

 set loadcenter off
When a file is opened, sets the default center of that file according to its own coordiantes. 

=== picking ===
 set picking off
Turns off the mouse picking.

 set picking ident
Sets the mouse picking behavior to show atom identification.

 set picking coord
Sets the mouse picking behavior to show atom coordinates with identification.

 set picking distance
Sets the mouse picking behavior to show the distance between atoms successively picked.

 set picking center
Sets the mouse picking behavior to specify the center of rotation and center of the screen.

 set picking select
Sets the mouse picking behavior to select the file that contains the atom picked. 

=== pickradius ===
 set pickradius &lt;value&gt;
Sets the mouse-pickable region of each atom to be the sphere centered to each atom with the specified radius (angstrom or Rasmol unit). 

=== point_size ===
 set point_size &lt;value&gt;
Sets the size of points in polygon images. The &lt;value&gt; should be larger than 0. 

=== polyline_width ===
 set polyline_width &lt;value&gt;
Sets the width of polylines in polygon images. The &lt;value&gt; should be larger than 0. 

=== projection ===
 set projection perspective
Sets the projection mode for a perspective projection.

 set projection parallel {&lt;size&gt;}
Sets the projection mode for a parallel projection. The size of image (fit to the height of the screen) can be specified (angstrom or Rasmol unit). 

=== specular ===
 set specular on/true
Enables the display of specular highlights on solid objects.

 set specular off/false
Disables the display of specular highlights on solid objects.

 set specular &lt;value&gt;
Enables the display of specular highlights on solid objects. The value between 0 and 100 specifies the specular color in gray scale with 0 and 100 being black and white, respectively. The default value is 50.0. 

=== specpower ===
 set specpower &lt;value&gt;
Sets the shininess of solid objects. The value between 0 and 100 specifies a material reflection coefficient with 0 being diffuse surfaces and 100 being shiny surfaces. 

=== ssbonds ===
 set ssbonds backbone
Disulfide bonds are displayed between backbones.

 set ssbonds sidechain
Disulfide bonds are displayed between sidechains. 

=== stereo ===
 set stereo
A synonym of the [[#stereo_2|stereo]] command.

=== transparency ===
 set transparency &lt;value&gt;
Sets the transparency of polygon images.

 set point_transparency &lt;value&gt;
Sets the transparency of points in polygon images.

 set line_transparency &lt;value&gt;
Sets the transparency of lines in polygon images.

 set triangle_transparency &lt;value&gt;
Sets the transparency of triangles in polygon images.

 set quad_transparency &lt;value&gt;
Sets the transparency of quads in polygon images.

 set polyline_transparency &lt;value&gt;
Sets the transparency of polylines in polygon images. 

=== viewpoint ===
 set viewpoint {x, y, z}
Sets the viewpoint to the specified coordinates. 

== show ==
 show godata
Displays gene ontology data of molecules.

 show imagesize
Displays the size of the 3D-rendering panel.

 show information
Displays a detail discription of molecules.

 show site {&lt;prefix&gt;:&lt;db&gt;:&lt;category&gt;}
Displays site information in an external database.

 show transform
Displays the transform matrix of molecules.

 show viewpoint
Displays the current viewpoint.

 show xps3
Displays keywords available in xps3 selection. 

== slab ==
 slab {on/true}
Enables the z-clipping plane of molecules and polygons.

 slab off/false
Disables the z-clipping plane of molecules and polygons.

 slab &lt;ratio&gt;
Sets the position of the z-clipping plane of molecules and polygons. The parameter may be given as a number from 0 to 100. The values 0 and 100 represent that image as a whole is completely invisible and visible, respectively.

 slab -v &lt;value&gt;
Sets the position of the z-clipping plane of molecules and polygons by specifying the z coordinate value. 

== spacefill ==
 spacefill {on/true}
Turns on the ball image of the selected atoms.

 spacefill off/false
Turns off the ball image of the selected atoms.

 spacefill &lt;radius&gt;
Turns on the ball image of the selected atoms with the specified radius (angstrom or Rasmol unit). The maximum parameter value is 3.0.

 spacefill temperature
Turns on the ball image of the selected atoms using the temperature factor as radius. 

== ssbonds ==
 ssbonds {on/true}
Turns on the selected disulfide bonds.

 ssbonds off/false
Turns off the selected disulfide bonds.

 ssbonds &lt;radius&gt;
Turns on the selected disulfide bonds with the specified raidus (angstrom or Rasmol unit). The maximum parameter value is 2.0. 

== stereo ==
 stereo {on/true}
Enables stereo display. This command without arguments cycles three state; 'stereo off', 'stereo on' in cross-eyed mode and 'stereo on' in parallel-eyed mode.

 stereo off/false
Disables stereo display.

 stereo &lt;angle&gt;
Enables stereo display with the specified separation angle. Positive and negative values represent cross-eyed and parallel-eyed viewing, respectively.


== structure ==
 structure
Estimates the secondary structure using Kabsch and Sander's DSSP algorithm. 

== trace ==
 trace {on/true}
Turns on a tube representation for the selected residues.

 trace off/false
Turns off a tube representation for the selected residues.

 trace &lt;radius&gt;
Turns on a tube representation for the selected residues with the specified radius (angstrom or Rasmol unit). The maximum parameter value is 2.0.


== translate ==
 translate x/y/z &lt;value&gt;
Moves images along the specified axis by the specified amount (angstrom). 

== wireframe ==
 wireframe {on/true}
Turns on the selected bonds.

 wireframe off/false
Turns off the selected bonds.

 wireframe &lt;radius&gt;
Turns on the selected bonds with the specified raidus (angstrom or Rasmol unit). The maximum parameter value is 2.0. 

== write ==
 write
A synonym of the [[#save|save]] command.

== zap ==
 zap {&lt;file_IDs&gt;}
Closes the specified files. More than one file IDs can be specified by putting commas as the delimiter. When the paraneter is absent, all files are closed. 

== zoom ==
 zoom {&lt;value&gt;}
Sets the magnification of the image as a whole. The value stands for the magnification as a percentage of the current scale. The minimum parameter value is 10.0.</text>
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  <revision>
    <id>377</id>
    <parentid>361</parentid>
    <timestamp>2010-07-13T04:01:29Z</timestamp>
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      <username>IMSsato</username>
      <id>4</id>
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  |}
Command usage of jV follows that of [http://www.rasmol.org/ Rasmol] with some modifications. In the following part, command arguments that can take an arbitrary value are denoted as &lt;value&gt; for example, arguments restricted to several possible values are listed with / as a delimiter, and arguments that can be omitted are put in brackets {}. Commands, [[#exit|exit]], [[#load|load]], [[#quit|quit]], [[#save|save]], [[#script|script]], and [[#write|write]], are not available in applet circumstance.

== anim ==
 anim forward {&lt;value&gt;}
Starts animation forward. If the &lt;value&gt; is given, just move frames forward by the specified amount.

 anim backward {&lt;value&gt;}
Starts animation backward. If the &lt;value&gt; is given, just move frames backward by the specified amount.

 anim stop
Stops animation.

== animframe ==
 animframe &lt;frame&gt; {&lt;file_ID&gt;}
Sets the frame of all animation files for the specified value. When &lt;file_ID&gt; is given, only the specified file is processed.

== animmode ==
 animmode once
Sets the behavior of animation for 'once'. When the frame reaches the last one, animation is stopped.

 animmode loop
Sets the behavior of animation for 'loop'. When the frame reaches the last one, animation is reset to the first frame and continues playing.

 animmode swing
Sets the behavior of animation for 'swing'. When the frame reaches the last one, the direction of animation is reversed.

== animrange ==
 animrange &lt;init_frame&gt;-&lt;term_frame&gt; {&lt;file_IDs&gt;}
Sets the range of all animation files. When is given, only the specified file is processed.

== animselect ==
 animselect {-a/-r} &lt;file_IDs&gt;
Selects the specified files and makes the others not selected. More than one file IDs can be specified by putting commas as the delimiter. When the option -a or -r is specified, only the selection status of the specified files are modified, selected or not selected, respectively, and the others remain unchanged.

== animspeed ==
 animspeed &lt;speed&gt;
Sets the animation speed. The argument should be an integer value from 1 to 20.

== animstep ==
 animstep &lt;step&gt; {&lt;file_ID&gt;}
Sets the step of all animation files for the specified value. When &lt;file_ID&gt; is given, only the specified file is processed.

== backbone ==
 backbone {on/true}
Turns on the selected backbone bonds.

 backbone off/false
Turns off the selected backbone bonds.

 backbone &lt;radius&gt;
Turns on the selected backbone bonds with the specified raidus (angstrom or Rasmol unit). The maximum parameter value is 2.0.

== background ==
 background &lt;color&gt;
Changes the background color. The color may be given as RGB values [r,g,b], or predefined color names.

== cartoon ==
 cartoon {on/true}
Turns on the thick ribbons for the selected residues.

 cartoon off/false
Turns off the thick ribbons for the selected residues.

 cartoon &lt;half_width&gt;
Turns on the thick ribbons for the selected residues with the specified half width (angstrom or Rasmol unit). The maximum parameter value is 4.0.

== center ==
 center {-r/-s} {&lt;atom_expression&gt;}
Sets the center of rotation and the center of the screen to the center of a group of atoms specified by the atom expression. When the option -r or -s is specified, only the center of rotation or the center of the screen is modified, respectively.

 center {-r} [x, y, z]
Moves the center of rotation and the center of the screen from the current position by the specified amount. When the option -r is specified, only the center of rotation is modified.

 center {-r} {x, y, z}
Sets the center of rotation and the center of the screen to the specified coordinates. When the option -r is specified, only the center of rotation is modified.

 center -s [x, y]
Moves the center of the screen from the current position by the specified amount.

 center -s {x, y}
Sets the center of the screen to the specified coordinates.

== color ==
 color {atoms} &lt;color&gt;
Sets the color of the selected atoms. The color may be given as RGB values [r,g,b], predefined color names, or predefined color schemes; amino, chain, charge, cpk, group, shapely, structure, and temperature.

 color bonds/backbone/ribbons/hbonds/ssbonds &lt;color&gt;
Sets the color of the specified object. The color may be given as RGB values [r,g,b] or predefined color names. For hydrogen bonds, color scheme 'type' can be specified.

 color bonds/backbone/ribbons/hbonds/ssbonds none
Resets the color of the specified object.

== colorvertex ==
 colorvertex &lt;color&gt;
Sets the color of the selected vertices. The color may be given as RGB values [r,g,b] or predefined color names.

 colorvertex none
Resets the color of the selected vertices.

== cpk ==
 cpk
A synonym of the [[#spacefill|spacefill]] command.

== define ==
 define &lt;name&gt; &lt;atom_expression&gt;
Associates an arbitrary set of atoms with a unique name.

== display ==
 display all
Displays the image of all files.

 display none
Turns off the image of all files.

 display {-a/-r} &lt;file_IDs&gt;
Displays the image of the specified files and turns off the others. More than one file IDs can be specified by putting commas as the delimiter. When the option -a or -r is specified, turns the image of the specified files on or off, respectively, and the others remain unchanged.

== displayatom ==
 displayatom {on/true}
Displays the selected atoms.

 displayatom off/false
Turns off the selected atoms.

== displayvertex ==
 displayvertex {on/true}
Displays the selected vertices.

 displayvertex off/false
Turns off the selected vertices.

== echo ==
 echo &lt;string&gt;
Echoes the specified message back to the message area.

== exit ==
 exit
Terminates the application.

== fit ==
 fit &lt;file1_ID&gt; &lt;file2_ID&gt;
Sets the transform matrix of file1 identical to that of file2. 

== fselect ==
 fselect all
Selects all files.

 fselect none
Selects no files.

 fselect {-a/-r} &lt;file_IDs&gt;
Selects the specified files and makes the others not selected. More than one file IDs can be specified by putting commas as the delimiter. When the option -a or -r is specified, only the selection status of the specified files are modified, selected or not selected, respectively, and the others remain unchanged.

== hbonds ==
 hbonds {on/true}
Turns on the selected hydrogen bonds.

 hbonds off/false
Turns off the selected hydrogen bonds.

 hbonds &lt;radius&gt;
Turns on the selected hydrogen bonds with the specified raidus (angstrom or Rasmol unit). The maximum parameter value is 2.0. 

== load ==
 load {pdbml} &lt;filename&gt; {fit &lt;file_ID&gt;}
Opens a PDBML file. URL can be used to open a remote file. On loading, the transform matrix can be set identical to that of the specified file.

 load pdb &lt;filename&gt; {fit &lt;file_ID&gt;}
Opens a PDB file. URL can be used to open a remote file. On loading, the transform matrix can be set identical to that of the specified file.

 load polygon &lt;filename&gt; {fit &lt;file_ID&gt;}
Opens a polygon file. URL can be used to open a remote file. On loading, the transform matrix can be set identical to that of the specified file.

 load animation &lt;filename&gt; {fit &lt;file_ID&gt;}
Opens an animation file. URL can be used to open a remote file. On loading, the transform matrix can be set identical to that of the specified file.

 load ftp &lt;PDB_code&gt; {fit &lt;file_ID&gt;}
Retrieves a PDBML file from the PDBj FTP site and opens it. On loading, the transform matrix can be set identical to that of the specified file. 

== pause ==
 pause
Stops the execution of a script file until any key is pressed to restart. 

== quit ==
 quit
A synonym of the [[#exit|exit]] command.

== refresh ==
 refresh
Redraws all images. 

== reset ==
=== default ===
 reset
Restores the original viewing transformation of all images, the center of rotation, and the view point. 

=== cartoon ===
 reset cartoon
Restores the thickness of the cartoon representation. 

=== line_width ===
 reset line_width
Restores the width of lines in polygon images. 

=== pickradius ===
 reset pickradius
Restores the mouse-pickable region of each atom. 

=== point_size ===
 reset point_size
Restores the size of points in polygon images. 

=== polyline_width ===
 reset polyline_width
Restores the width of polylines in polygon images. 

=== transparency ===
 reset transparency
Restores the transparency of polygon images.

 reset point_transparency
Restores the transparency of points in polygon images.

 reset line_transparency
Restores the transparency of lines in polygon images.

 reset triangle_transparency
Restores the transparency of triangles in polygon images.

 reset quad_transparency
Restores the transparency of quads in polygon images.

 reset polyline_transparency
Restores the transparency of polylines in polygon images. 

== ribbons ==
 ribbons {on/true}
Turns on the ribbon surfaces for the selected residues.

 ribbons off/false
Turns off the ribbon surfaces for the selected residues.

 ribbons &lt;half_width&gt;
Turns on the ribbon surfaces for the selected residues with the specified half width (angstrom or Rasmol unit). The maximum parameter value is 4.0. 

== rotate ==
 rotate x/y/z &lt;angle&gt;
Rotates images about the specified axis by the specified angle in degrees. 

== save ==
 save {pdb} &lt;filename&gt;
Saves the currently selected set of atoms in a PDB format file.

 save script &lt;filename&gt;
Creates a script file that reproduces the currently displayed image.

 save png &lt;filename&gt;
Creates a PNG image file of the currently displayed image.

 save jpeg &lt;filename&gt; {&lt;quality&gt;}
Creates a JPEG image file of the currently displayed image. The compression quality can be specified, 0 &lt; quality &lt;= 1, where 'quality = 1' means no compression. 

== script ==
 script &lt;filename&gt;
Opens and executes the specified script file. URL can be used to open a remote file. 

== select ==
 select
Selects all atoms. Whether hetero atoms and hydrogens are selected or not depends on the internal parameters, hetero and hydrogen, respectively.

 select all
Selects all atoms including hetero atoms and hydrogens.

 select none
Selects no atoms.

 select &lt;atom_expression&gt;
Selects a group of atoms specified by the atom expression. 

== selectvertex ==
 selectvertex {all}
Selects all vertices.

 selectvertex none
Selects no vertices.

 selectvertex &lt;vertex_expression&gt;
Selects a group of vertices specified by the vertex expression. 

== set ==
=== adjustview ===
 set adjustview on
The view point is automatically adjusted when a new file is loaded.

 set adjustview off
The view point is kept unchanged when a new file is loaded. 

=== background ===
 set background &lt;color&gt;
Changes the background color. The color may be given as RGB values [r,g,b], or predefined color names. 

=== bondmode ===
 set bondmode and
Specifies how to select an individual bonds. A bond is selected when both atoms connected by the bond are selected.

 set bondmode or
Specifies how to select an individual bonds. A bond is selected when either of the connected atoms is selected. 

=== cartoon ===
 set cartoon {&lt;value&gt;}
Specifies the thickness of the cartoon representation (angstrom or Rasmol unit). The maximum parameter value is 2.0. When the parameter is not specified, it is restored to the default value. 

=== center ===
 set center &lt;atom_expression&gt;
Sets the default center of the selected files to the center of the specified atoms.

 set center [x, y, z]
Sets the default center of the selected files to the specified coordinates. 

=== drawlevel ===
 set drawlevel &lt;value&gt;
Specifies precision of the rendering of spheres and cylinders. The value may be given as an integer (minimum 5) that stands for the number of straight line segments to represent an arc of 180 degrees. 

=== hbonds ===
 set hbonds backbone
Hydrogen bonds are displayed between backbones.

 set hbonds sidechain
Hydrogen bonds are displayed between sidechains. 

=== hetero ===
 set hetero on
Sets the default behavior of the select command such that hetero atoms are selected.

 set hetero off
Sets the default behavior of the select command such that hetero atoms are not selected. 

=== hydrogen ===
 set hydrogen on
Sets the default behavior of the select command such that hydrogens are selected.

 set hydrogen off
Sets the default behavior of the select command such that hydrogens are not selected. 

=== imagesize ===
 set imagesize &lt;width&gt; &lt;height&gt;
Sets the size of the 3D-rendering panel in pixels. The size will be set within the screen size with the width being an even integer. 

=== line_width ===
 set line_width &lt;value&gt;
Sets the width of lines in polygon images. The &lt;value&gt; should be larger than 0. 

=== loadcenter ===
 set loadcenter on
When a file is opened, sets the default center of that file to the center of all files that have already opened.

 set loadcenter off
When a file is opened, sets the default center of that file according to its own coordiantes. 

=== picking ===
 set picking off
Turns off the mouse picking.

 set picking ident
Sets the mouse picking behavior to show atom identification.

 set picking coord
Sets the mouse picking behavior to show atom coordinates with identification.

 set picking distance
Sets the mouse picking behavior to show the distance between atoms successively picked.

 set picking center
Sets the mouse picking behavior to specify the center of rotation and center of the screen.

 set picking select
Sets the mouse picking behavior to select the file that contains the atom picked. 

=== pickradius ===
 set pickradius &lt;value&gt;
Sets the mouse-pickable region of each atom to be the sphere centered to each atom with the specified radius (angstrom or Rasmol unit). 

=== point_size ===
 set point_size &lt;value&gt;
Sets the size of points in polygon images. The &lt;value&gt; should be larger than 0. 

=== polyline_width ===
 set polyline_width &lt;value&gt;
Sets the width of polylines in polygon images. The &lt;value&gt; should be larger than 0. 

=== projection ===
 set projection perspective
Sets the projection mode for a perspective projection.

 set projection parallel {&lt;size&gt;}
Sets the projection mode for a parallel projection. The size of image (fit to the height of the screen) can be specified (angstrom or Rasmol unit). 

=== specular ===
 set specular on/true
Enables the display of specular highlights on solid objects.

 set specular off/false
Disables the display of specular highlights on solid objects.

 set specular &lt;value&gt;
Enables the display of specular highlights on solid objects. The value between 0 and 100 specifies the specular color in gray scale with 0 and 100 being black and white, respectively. The default value is 50.0. 

=== specpower ===
 set specpower &lt;value&gt;
Sets the shininess of solid objects. The value between 0 and 100 specifies a material reflection coefficient with 0 being diffuse surfaces and 100 being shiny surfaces. 

=== ssbonds ===
 set ssbonds backbone
Disulfide bonds are displayed between backbones.

 set ssbonds sidechain
Disulfide bonds are displayed between sidechains. 

=== stereo ===
 set stereo
A synonym of the [[#stereo_2|stereo]] command.

=== transparency ===
 set transparency &lt;value&gt;
Sets the transparency of polygon images.

 set point_transparency &lt;value&gt;
Sets the transparency of points in polygon images.

 set line_transparency &lt;value&gt;
Sets the transparency of lines in polygon images.

 set triangle_transparency &lt;value&gt;
Sets the transparency of triangles in polygon images.

 set quad_transparency &lt;value&gt;
Sets the transparency of quads in polygon images.

 set polyline_transparency &lt;value&gt;
Sets the transparency of polylines in polygon images. 

=== viewpoint ===
 set viewpoint {x, y, z}
Sets the viewpoint to the specified coordinates. 

== show ==
 show godata
Displays gene ontology data of molecules.

 show imagesize
Displays the size of the 3D-rendering panel.

 show information
Displays a detail discription of molecules.

 show site {&lt;prefix&gt;:&lt;db&gt;:&lt;category&gt;}
Displays site information in an external database.

 show transform
Displays the transform matrix of molecules.

 show viewpoint
Displays the current viewpoint.

 show xps3
Displays keywords available in xps3 selection. 

== slab ==
 slab {on/true}
Enables the z-clipping plane of molecules and polygons.

 slab off/false
Disables the z-clipping plane of molecules and polygons.

 slab &lt;ratio&gt;
Sets the position of the z-clipping plane of molecules and polygons. The parameter may be given as a number from 0 to 100. The values 0 and 100 represent that image as a whole is completely invisible and visible, respectively.

 slab -v &lt;value&gt;
Sets the position of the z-clipping plane of molecules and polygons by specifying the z coordinate value. 

== spacefill ==
 spacefill {on/true}
Turns on the ball image of the selected atoms.

 spacefill off/false
Turns off the ball image of the selected atoms.

 spacefill &lt;radius&gt;
Turns on the ball image of the selected atoms with the specified radius (angstrom or Rasmol unit). The maximum parameter value is 3.0.

 spacefill temperature
Turns on the ball image of the selected atoms using the temperature factor as radius. 

== ssbonds ==
 ssbonds {on/true}
Turns on the selected disulfide bonds.

 ssbonds off/false
Turns off the selected disulfide bonds.

 ssbonds &lt;radius&gt;
Turns on the selected disulfide bonds with the specified raidus (angstrom or Rasmol unit). The maximum parameter value is 2.0. 

== stereo ==
 stereo {on/true}
Enables stereo display. This command without arguments cycles three state; 'stereo off', 'stereo on' in cross-eyed mode and 'stereo on' in parallel-eyed mode.

 stereo off/false
Disables stereo display.

 stereo &lt;angle&gt;
Enables stereo display with the specified separation angle. Positive and negative values represent cross-eyed and parallel-eyed viewing, respectively.


== structure ==
 structure
Estimates the secondary structure using Kabsch and Sander's DSSP algorithm. 

== trace ==
 trace {on/true}
Turns on a tube representation for the selected residues.

 trace off/false
Turns off a tube representation for the selected residues.

 trace &lt;radius&gt;
Turns on a tube representation for the selected residues with the specified radius (angstrom or Rasmol unit). The maximum parameter value is 2.0.


== translate ==
 translate x/y/z &lt;value&gt;
Moves images along the specified axis by the specified amount (angstrom). 

== wireframe ==
 wireframe {on/true}
Turns on the selected bonds.

 wireframe off/false
Turns off the selected bonds.

 wireframe &lt;radius&gt;
Turns on the selected bonds with the specified raidus (angstrom or Rasmol unit). The maximum parameter value is 2.0. 

== write ==
 write
A synonym of the [[#save|save]] command.

== zap ==
 zap {&lt;file_IDs&gt;}
Closes the specified files. More than one file IDs can be specified by putting commas as the delimiter. When the paraneter is absent, all files are closed. 

== zoom ==
 zoom {&lt;value&gt;}
Sets the magnification of the image as a whole. The value stands for the magnification as a percentage of the current scale. The minimum parameter value is 10.0.</text>
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  </revision>
  <revision>
    <id>378</id>
    <parentid>377</parentid>
    <timestamp>2010-07-13T04:20:49Z</timestamp>
    <contributor>
      <username>IMSsato</username>
      <id>4</id>
    </contributor>
    <model>wikitext</model>
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  |__TOC__
  |}
Command usage of jV follows that of [http://www.rasmol.org/ Rasmol] with some modifications. In the following part, command arguments that can take an arbitrary value are denoted as &lt;value&gt; for example, arguments restricted to several possible values are listed with / as a delimiter, and arguments that can be omitted are put in brackets {}. Commands, [[#exit|exit]], [[#load|load]], [[#quit|quit]], [[#save|save]], [[#script|script]], and [[#write|write]], are not available in applet circumstance.

== anim ==
 anim forward {&lt;value&gt;}
Starts animation forward. If the &lt;value&gt; is given, just move frames forward by the specified amount.

 anim backward {&lt;value&gt;}
Starts animation backward. If the &lt;value&gt; is given, just move frames backward by the specified amount.

 anim stop
Stops animation.

== animframe ==
 animframe &lt;frame&gt; {&lt;file_ID&gt;}
Sets the frame of all animation files for the specified value. When &lt;file_ID&gt; is given, only the specified file is processed.

== animmode ==
 animmode once
Sets the behavior of animation for 'once'. When the frame reaches the last one, animation is stopped.

 animmode loop
Sets the behavior of animation for 'loop'. When the frame reaches the last one, animation is reset to the first frame and continues playing.

 animmode swing
Sets the behavior of animation for 'swing'. When the frame reaches the last one, the direction of animation is reversed.

== animrange ==
 animrange &lt;init_frame&gt;-&lt;term_frame&gt; {&lt;file_IDs&gt;}
Sets the range of all animation files. When is given, only the specified file is processed.

== animselect ==
 animselect {-a/-r} &lt;file_IDs&gt;
Selects the specified files and makes the others not selected. More than one file IDs can be specified by putting commas as the delimiter. When the option -a or -r is specified, only the selection status of the specified files are modified, selected or not selected, respectively, and the others remain unchanged.

== animspeed ==
 animspeed &lt;speed&gt;
Sets the animation speed. The argument should be an integer value from 1 to 20.

== animstep ==
 animstep &lt;step&gt; {&lt;file_ID&gt;}
Sets the step of all animation files for the specified value. When &lt;file_ID&gt; is given, only the specified file is processed.

== backbone ==
 backbone {on/true}
Turns on the selected backbone bonds.

 backbone off/false
Turns off the selected backbone bonds.

 backbone &lt;radius&gt;
Turns on the selected backbone bonds with the specified raidus (angstrom or Rasmol unit). The maximum parameter value is 2.0.

== background ==
 background &lt;color&gt;
Changes the background color. The color may be given as RGB values [r,g,b], or predefined color names.

== cartoon ==
 cartoon {on/true}
Turns on the thick ribbons for the selected residues.

 cartoon off/false
Turns off the thick ribbons for the selected residues.

 cartoon &lt;half_width&gt;
Turns on the thick ribbons for the selected residues with the specified half width (angstrom or Rasmol unit). The maximum parameter value is 4.0.

== center ==
 center {-r/-s} {&lt;atom_expression&gt;}
Sets the center of rotation and the center of the screen to the center of a group of atoms specified by the atom expression. When the option -r or -s is specified, only the center of rotation or the center of the screen is modified, respectively.

 center {-r} [x, y, z]
Moves the center of rotation and the center of the screen from the current position by the specified amount. When the option -r is specified, only the center of rotation is modified.

 center {-r} {x, y, z}
Sets the center of rotation and the center of the screen to the specified coordinates. When the option -r is specified, only the center of rotation is modified.

 center -s [x, y]
Moves the center of the screen from the current position by the specified amount.

 center -s {x, y}
Sets the center of the screen to the specified coordinates.

== color ==
 color {atoms} &lt;color&gt;
Sets the color of the selected atoms. The color may be given as RGB values [r,g,b], predefined color names, or predefined color schemes; amino, chain, charge, cpk, group, shapely, structure, and temperature.

 color bonds/backbone/ribbons/hbonds/ssbonds &lt;color&gt;
Sets the color of the specified object. The color may be given as RGB values [r,g,b] or predefined color names. For hydrogen bonds, color scheme 'type' can be specified.

 color bonds/backbone/ribbons/hbonds/ssbonds none
Resets the color of the specified object.

== colorvertex ==
 colorvertex &lt;color&gt;
Sets the color of the selected vertices. The color may be given as RGB values [r,g,b] or predefined color names.

 colorvertex none
Resets the color of the selected vertices.

== cpk ==
 cpk
A synonym of the [[#spacefill|spacefill]] command.

== define ==
 define &lt;name&gt; &lt;atom_expression&gt;
Associates an arbitrary set of atoms with a unique name.

== display ==
 display all
Displays the image of all files.

 display none
Turns off the image of all files.

 display {-a/-r} &lt;file_IDs&gt;
Displays the image of the specified files and turns off the others. More than one file IDs can be specified by putting commas as the delimiter. When the option -a or -r is specified, turns the image of the specified files on or off, respectively, and the others remain unchanged.

== displayatom ==
 displayatom {on/true}
Displays the selected atoms.

 displayatom off/false
Turns off the selected atoms.

== displayvertex ==
 displayvertex {on/true}
Displays the selected vertices.

 displayvertex off/false
Turns off the selected vertices.

== echo ==
 echo &lt;string&gt;
Echoes the specified message back to the message area.

== exit ==
 exit
Terminates the application.

== fit ==
 fit &lt;file1_ID&gt; &lt;file2_ID&gt;
Sets the transform matrix of file1 identical to that of file2. 

== fselect ==
 fselect all
Selects all files.

 fselect none
Selects no files.

 fselect {-a/-r} &lt;file_IDs&gt;
Selects the specified files and makes the others not selected. More than one file IDs can be specified by putting commas as the delimiter. When the option -a or -r is specified, only the selection status of the specified files are modified, selected or not selected, respectively, and the others remain unchanged.

== hbonds ==
 hbonds {on/true}
Turns on the selected hydrogen bonds.

 hbonds off/false
Turns off the selected hydrogen bonds.

 hbonds &lt;radius&gt;
Turns on the selected hydrogen bonds with the specified raidus (angstrom or Rasmol unit). The maximum parameter value is 2.0. 

== load ==
 load {pdbml} &lt;filename&gt; {fit &lt;file_ID&gt;}
Opens a PDBML file. URL can be used to open a remote file. On loading, the transform matrix can be set identical to that of the specified file.

 load pdb &lt;filename&gt; {fit &lt;file_ID&gt;}
Opens a PDB file. URL can be used to open a remote file. On loading, the transform matrix can be set identical to that of the specified file.

 load polygon &lt;filename&gt; {fit &lt;file_ID&gt;}
Opens a polygon file. URL can be used to open a remote file. On loading, the transform matrix can be set identical to that of the specified file.

 load animation &lt;filename&gt; {fit &lt;file_ID&gt;}
Opens an animation file. URL can be used to open a remote file. On loading, the transform matrix can be set identical to that of the specified file.

 load ftp &lt;PDB_code&gt; {fit &lt;file_ID&gt;}
Retrieves a PDBML file from the PDBj FTP site and opens it. On loading, the transform matrix can be set identical to that of the specified file. 

== pause ==
 pause
Stops the execution of a script file until any key is pressed to restart. 

== pdbj_describe ==
 pdbj_describe &lt;file_id&gt; {&lt;name&gt;} 
Shows the document for the jV_command in PDBMLplus specified by file ID and name. When the name is not specified, all available names are listed.

== pdbj_execute ==
 pdbj_execute &lt;file_id&gt; &lt;name&gt; 
Executes the jV_command in PDBMLplus specified by file ID and name.

== quit ==
 quit
A synonym of the [[#exit|exit]] command.

== refresh ==
 refresh
Redraws all images. 

== reset ==
=== default ===
 reset
Restores the original viewing transformation of all images, the center of rotation, and the view point. 

=== cartoon ===
 reset cartoon
Restores the thickness of the cartoon representation. 

=== line_width ===
 reset line_width
Restores the width of lines in polygon images. 

=== pickradius ===
 reset pickradius
Restores the mouse-pickable region of each atom. 

=== point_size ===
 reset point_size
Restores the size of points in polygon images. 

=== polyline_width ===
 reset polyline_width
Restores the width of polylines in polygon images. 

=== transparency ===
 reset transparency
Restores the transparency of polygon images.

 reset point_transparency
Restores the transparency of points in polygon images.

 reset line_transparency
Restores the transparency of lines in polygon images.

 reset triangle_transparency
Restores the transparency of triangles in polygon images.

 reset quad_transparency
Restores the transparency of quads in polygon images.

 reset polyline_transparency
Restores the transparency of polylines in polygon images. 

== ribbons ==
 ribbons {on/true}
Turns on the ribbon surfaces for the selected residues.

 ribbons off/false
Turns off the ribbon surfaces for the selected residues.

 ribbons &lt;half_width&gt;
Turns on the ribbon surfaces for the selected residues with the specified half width (angstrom or Rasmol unit). The maximum parameter value is 4.0. 

== rotate ==
 rotate x/y/z &lt;angle&gt;
Rotates images about the specified axis by the specified angle in degrees. 

== save ==
 save {pdb} &lt;filename&gt;
Saves the currently selected set of atoms in a PDB format file.

 save script &lt;filename&gt;
Creates a script file that reproduces the currently displayed image.

 save png &lt;filename&gt;
Creates a PNG image file of the currently displayed image.

 save jpeg &lt;filename&gt; {&lt;quality&gt;}
Creates a JPEG image file of the currently displayed image. The compression quality can be specified, 0 &lt; quality &lt;= 1, where 'quality = 1' means no compression. 

== script ==
 script &lt;filename&gt;
Opens and executes the specified script file. URL can be used to open a remote file. 

== select ==
 select
Selects all atoms. Whether hetero atoms and hydrogens are selected or not depends on the internal parameters, hetero and hydrogen, respectively.

 select all
Selects all atoms including hetero atoms and hydrogens.

 select none
Selects no atoms.

 select &lt;atom_expression&gt;
Selects a group of atoms specified by the atom expression. 

== selectvertex ==
 selectvertex {all}
Selects all vertices.

 selectvertex none
Selects no vertices.

 selectvertex &lt;vertex_expression&gt;
Selects a group of vertices specified by the vertex expression. 

== set ==
=== ambient ===
 set ambient {&lt;value&gt;}
Sets the amount of ambient light. The value must be between 0 and 100. When the parameter is not specified, it is restored to the default value 33.

=== adjustview ===
 set adjustview on
The view point is automatically adjusted when a new file is loaded.

 set adjustview off
The view point is kept unchanged when a new file is loaded. 

=== background ===
 set background &lt;color&gt;
Changes the background color. The color may be given as RGB values [r,g,b], or predefined color names. 

=== bondmode ===
 set bondmode and
Specifies how to select an individual bonds. A bond is selected when both atoms connected by the bond are selected.

 set bondmode or
Specifies how to select an individual bonds. A bond is selected when either of the connected atoms is selected. 

=== cartoon ===
 set cartoon {&lt;value&gt;}
Specifies the thickness of the cartoon representation (angstrom or Rasmol unit). The maximum parameter value is 2.0. When the parameter is not specified, it is restored to the default value. 

=== cartoon_loop_tube ===
 set cartoon_loop_tube on
The loop region is drawn as tube in the cartoon representation.

 set cartoon_loop_tube off
The loop region is drawn as square pillar in the cartoon representation.

=== cartoon_round ===
 set cartoon_round on
Square pillar with round edge is drawn in the cartoon representation (except beta strands). 

 set cartoon_round off
Square pillar is drawn in the cartoon representation.

=== center ===
 set center &lt;atom_expression&gt;
Sets the default center of the selected files to the center of the specified atoms.

 set center [x, y, z]
Sets the default center of the selected files to the specified coordinates. 

=== diffuse1 ===
 set diffuse1 {&lt;value&gt;}
Sets the amount of the first diffuse light. The value must be between 0 and 100. When the parameter is not specified, it is restored to the default value 50.

=== diffuse1_direction ===
 set diffuse1_direction {[x, y, z]}
Sets the direction of the first diffuse light. When the parameter is not specified, it is restored to the default value [-1, -1, -1].

=== diffuse2 ===
 set diffuse2 {&lt;value&gt;}
Sets the amount of the second diffuse light. The value must be between 0 and 100. When the parameter is not specified, it is restored to the default value 50.

=== diffuse2_direction ===
 set diffuse2_direction {[x, y, z]}
Sets the direction of the second diffuse light. When the parameter is not specified, it is restored to the default value [-1, -1, -1].

=== drawlevel ===
 set drawlevel &lt;value&gt;
Specifies precision of the rendering of spheres and cylinders. The value may be given as an integer (minimum 5) that stands for the number of straight line segments to represent an arc of 180 degrees. 

=== efsite_url ===
 set efsite_url &lt;URL&gt;
Sets the URL for eF-site.

=== ext_site_url ===
 set ext_site_url &lt;prefix&gt; &lt;URL&gt;
Sets the URL for an external database site.

=== hbonds ===
 set hbonds backbone
Hydrogen bonds are displayed between backbones.

 set hbonds sidechain
Hydrogen bonds are displayed between sidechains. 

=== hetero ===
 set hetero on
Sets the default behavior of the select command such that hetero atoms are selected.

 set hetero off
Sets the default behavior of the select command such that hetero atoms are not selected. 

=== hydrogen ===
 set hydrogen on
Sets the default behavior of the select command such that hydrogens are selected.

 set hydrogen off
Sets the default behavior of the select command such that hydrogens are not selected. 

=== imagesize ===
 set imagesize &lt;width&gt; &lt;height&gt;
Sets the size of the 3D-rendering panel in pixels. The size will be set within the screen size with the width being an even integer. 

=== line_width ===
 set line_width &lt;value&gt;
Sets the width of lines in polygon images. The &lt;value&gt; should be larger than 0. 

=== loadcenter ===
 set loadcenter on
When a file is opened, sets the default center of that file to the center of all files that have already opened.

 set loadcenter off
When a file is opened, sets the default center of that file according to its own coordiantes. 

=== pdbml_noatom_url ===
 set pdbml_noatom_url &lt;URL&gt;
Sets the URL for PDBML noatom files.

=== pdbml_extatom_url ===
 set pdbml_extatom_url &lt;URL&gt;
Sets the URL for PDBML extatom files.

=== pdbml_plus_url ===
 set pdbml_plus_url &lt;URL&gt;
Sets the URL for PDBMLplus files.

=== picking ===
 set picking off
Turns off the mouse picking.

 set picking ident
Sets the mouse picking behavior to show atom identification.

 set picking coord
Sets the mouse picking behavior to show atom coordinates with identification.

 set picking distance
Sets the mouse picking behavior to show the distance between atoms successively picked.

 set picking center
Sets the mouse picking behavior to specify the center of rotation and center of the screen.

 set picking select
Sets the mouse picking behavior to select the file that contains the atom picked. 

=== pickradius ===
 set pickradius &lt;value&gt;
Sets the mouse-pickable region of each atom to be the sphere centered to each atom with the specified radius (angstrom or Rasmol unit). 

=== point_size ===
 set point_size &lt;value&gt;
Sets the size of points in polygon images. The &lt;value&gt; should be larger than 0. 

=== polyline_width ===
 set polyline_width &lt;value&gt;
Sets the width of polylines in polygon images. The &lt;value&gt; should be larger than 0. 

=== projection ===
 set projection perspective
Sets the projection mode for a perspective projection.

 set projection parallel {&lt;size&gt;}
Sets the projection mode for a parallel projection. The size of image (fit to the height of the screen) can be specified (angstrom or Rasmol unit). 

=== ribbonback ===
 set ribbonback &lt;color&gt;
Sets the color of the back of ribbon models. The color may be given as RGB values [r,g,b] or predefined color names.

 set ribbonback none
Resets the color of the back of ribbon models.

=== specular ===
 set specular on/true
Enables the display of specular highlights on solid objects.

 set specular off/false
Disables the display of specular highlights on solid objects.

 set specular &lt;value&gt;
Enables the display of specular highlights on solid objects. The value between 0 and 100 specifies the specular color in gray scale with 0 and 100 being black and white, respectively. The default value is 50.0. 

=== specpower ===
 set specpower &lt;value&gt;
Sets the shininess of solid objects. The value between 0 and 100 specifies a material reflection coefficient with 0 being diffuse surfaces and 100 being shiny surfaces. 

=== ssbonds ===
 set ssbonds backbone
Disulfide bonds are displayed between backbones.

 set ssbonds sidechain
Disulfide bonds are displayed between sidechains. 

=== stereo ===
 set stereo
A synonym of the [[#stereo_2|stereo]] command.

=== transparency ===
 set transparency &lt;value&gt;
Sets the transparency of polygon images.

 set point_transparency &lt;value&gt;
Sets the transparency of points in polygon images.

 set line_transparency &lt;value&gt;
Sets the transparency of lines in polygon images.

 set triangle_transparency &lt;value&gt;
Sets the transparency of triangles in polygon images.

 set quad_transparency &lt;value&gt;
Sets the transparency of quads in polygon images.

 set polyline_transparency &lt;value&gt;
Sets the transparency of polylines in polygon images. 

=== viewpoint ===
 set viewpoint {x, y, z}
Sets the viewpoint to the specified coordinates. 

== show ==
 show godata
Displays gene ontology data of molecules.

 show imagesize
Displays the size of the 3D-rendering panel.

 show information
Displays a detail discription of molecules.

 show site {&lt;prefix&gt;:&lt;db&gt;:&lt;category&gt;}
Displays site information in an external database.

 show transform
Displays the transform matrix of molecules.

 show viewpoint
Displays the current viewpoint.

 show xps3
Displays keywords available in xps3 selection. 

== slab ==
 slab {on/true}
Enables the z-clipping plane of molecules and polygons.

 slab off/false
Disables the z-clipping plane of molecules and polygons.

 slab &lt;ratio&gt;
Sets the position of the z-clipping plane of molecules and polygons. The parameter may be given as a number from 0 to 100. The values 0 and 100 represent that image as a whole is completely invisible and visible, respectively.

 slab -v &lt;value&gt;
Sets the position of the z-clipping plane of molecules and polygons by specifying the z coordinate value. 

== spacefill ==
 spacefill {on/true}
Turns on the ball image of the selected atoms.

 spacefill off/false
Turns off the ball image of the selected atoms.

 spacefill &lt;radius&gt;
Turns on the ball image of the selected atoms with the specified radius (angstrom or Rasmol unit). The maximum parameter value is 3.0.

 spacefill temperature
Turns on the ball image of the selected atoms using the temperature factor as radius. 

== ssbonds ==
 ssbonds {on/true}
Turns on the selected disulfide bonds.

 ssbonds off/false
Turns off the selected disulfide bonds.

 ssbonds &lt;radius&gt;
Turns on the selected disulfide bonds with the specified raidus (angstrom or Rasmol unit). The maximum parameter value is 2.0. 

== stereo ==
 stereo {on/true}
Enables stereo display. This command without arguments cycles three state; 'stereo off', 'stereo on' in cross-eyed mode and 'stereo on' in parallel-eyed mode.

 stereo off/false
Disables stereo display.

 stereo &lt;angle&gt;
Enables stereo display with the specified separation angle. Positive and negative values represent cross-eyed and parallel-eyed viewing, respectively.


== structure ==
 structure
Estimates the secondary structure using Kabsch and Sander's DSSP algorithm. 

== trace ==
 trace {on/true}
Turns on a tube representation for the selected residues.

 trace off/false
Turns off a tube representation for the selected residues.

 trace &lt;radius&gt;
Turns on a tube representation for the selected residues with the specified radius (angstrom or Rasmol unit). The maximum parameter value is 2.0.


== translate ==
 translate x/y/z &lt;value&gt;
Moves images along the specified axis by the specified amount (angstrom). 

== wireframe ==
 wireframe {on/true}
Turns on the selected bonds.

 wireframe off/false
Turns off the selected bonds.

 wireframe &lt;radius&gt;
Turns on the selected bonds with the specified raidus (angstrom or Rasmol unit). The maximum parameter value is 2.0. 

== write ==
 write
A synonym of the [[#save|save]] command.

== zap ==
 zap {&lt;file_IDs&gt;}
Closes the specified files. More than one file IDs can be specified by putting commas as the delimiter. When the paraneter is absent, all files are closed. 

== zoom ==
 zoom {&lt;value&gt;}
Sets the magnification of the image as a whole. The value stands for the magnification as a percentage of the current scale. The minimum parameter value is 10.0.</text>
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  </revision>
  <revision>
    <id>379</id>
    <parentid>378</parentid>
    <timestamp>2010-07-13T04:22:16Z</timestamp>
    <contributor>
      <username>IMSsato</username>
      <id>4</id>
    </contributor>
    <comment>/* show */</comment>
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  |__TOC__
  |}
Command usage of jV follows that of [http://www.rasmol.org/ Rasmol] with some modifications. In the following part, command arguments that can take an arbitrary value are denoted as &lt;value&gt; for example, arguments restricted to several possible values are listed with / as a delimiter, and arguments that can be omitted are put in brackets {}. Commands, [[#exit|exit]], [[#load|load]], [[#quit|quit]], [[#save|save]], [[#script|script]], and [[#write|write]], are not available in applet circumstance.

== anim ==
 anim forward {&lt;value&gt;}
Starts animation forward. If the &lt;value&gt; is given, just move frames forward by the specified amount.

 anim backward {&lt;value&gt;}
Starts animation backward. If the &lt;value&gt; is given, just move frames backward by the specified amount.

 anim stop
Stops animation.

== animframe ==
 animframe &lt;frame&gt; {&lt;file_ID&gt;}
Sets the frame of all animation files for the specified value. When &lt;file_ID&gt; is given, only the specified file is processed.

== animmode ==
 animmode once
Sets the behavior of animation for 'once'. When the frame reaches the last one, animation is stopped.

 animmode loop
Sets the behavior of animation for 'loop'. When the frame reaches the last one, animation is reset to the first frame and continues playing.

 animmode swing
Sets the behavior of animation for 'swing'. When the frame reaches the last one, the direction of animation is reversed.

== animrange ==
 animrange &lt;init_frame&gt;-&lt;term_frame&gt; {&lt;file_IDs&gt;}
Sets the range of all animation files. When is given, only the specified file is processed.

== animselect ==
 animselect {-a/-r} &lt;file_IDs&gt;
Selects the specified files and makes the others not selected. More than one file IDs can be specified by putting commas as the delimiter. When the option -a or -r is specified, only the selection status of the specified files are modified, selected or not selected, respectively, and the others remain unchanged.

== animspeed ==
 animspeed &lt;speed&gt;
Sets the animation speed. The argument should be an integer value from 1 to 20.

== animstep ==
 animstep &lt;step&gt; {&lt;file_ID&gt;}
Sets the step of all animation files for the specified value. When &lt;file_ID&gt; is given, only the specified file is processed.

== backbone ==
 backbone {on/true}
Turns on the selected backbone bonds.

 backbone off/false
Turns off the selected backbone bonds.

 backbone &lt;radius&gt;
Turns on the selected backbone bonds with the specified raidus (angstrom or Rasmol unit). The maximum parameter value is 2.0.

== background ==
 background &lt;color&gt;
Changes the background color. The color may be given as RGB values [r,g,b], or predefined color names.

== cartoon ==
 cartoon {on/true}
Turns on the thick ribbons for the selected residues.

 cartoon off/false
Turns off the thick ribbons for the selected residues.

 cartoon &lt;half_width&gt;
Turns on the thick ribbons for the selected residues with the specified half width (angstrom or Rasmol unit). The maximum parameter value is 4.0.

== center ==
 center {-r/-s} {&lt;atom_expression&gt;}
Sets the center of rotation and the center of the screen to the center of a group of atoms specified by the atom expression. When the option -r or -s is specified, only the center of rotation or the center of the screen is modified, respectively.

 center {-r} [x, y, z]
Moves the center of rotation and the center of the screen from the current position by the specified amount. When the option -r is specified, only the center of rotation is modified.

 center {-r} {x, y, z}
Sets the center of rotation and the center of the screen to the specified coordinates. When the option -r is specified, only the center of rotation is modified.

 center -s [x, y]
Moves the center of the screen from the current position by the specified amount.

 center -s {x, y}
Sets the center of the screen to the specified coordinates.

== color ==
 color {atoms} &lt;color&gt;
Sets the color of the selected atoms. The color may be given as RGB values [r,g,b], predefined color names, or predefined color schemes; amino, chain, charge, cpk, group, shapely, structure, and temperature.

 color bonds/backbone/ribbons/hbonds/ssbonds &lt;color&gt;
Sets the color of the specified object. The color may be given as RGB values [r,g,b] or predefined color names. For hydrogen bonds, color scheme 'type' can be specified.

 color bonds/backbone/ribbons/hbonds/ssbonds none
Resets the color of the specified object.

== colorvertex ==
 colorvertex &lt;color&gt;
Sets the color of the selected vertices. The color may be given as RGB values [r,g,b] or predefined color names.

 colorvertex none
Resets the color of the selected vertices.

== cpk ==
 cpk
A synonym of the [[#spacefill|spacefill]] command.

== define ==
 define &lt;name&gt; &lt;atom_expression&gt;
Associates an arbitrary set of atoms with a unique name.

== display ==
 display all
Displays the image of all files.

 display none
Turns off the image of all files.

 display {-a/-r} &lt;file_IDs&gt;
Displays the image of the specified files and turns off the others. More than one file IDs can be specified by putting commas as the delimiter. When the option -a or -r is specified, turns the image of the specified files on or off, respectively, and the others remain unchanged.

== displayatom ==
 displayatom {on/true}
Displays the selected atoms.

 displayatom off/false
Turns off the selected atoms.

== displayvertex ==
 displayvertex {on/true}
Displays the selected vertices.

 displayvertex off/false
Turns off the selected vertices.

== echo ==
 echo &lt;string&gt;
Echoes the specified message back to the message area.

== exit ==
 exit
Terminates the application.

== fit ==
 fit &lt;file1_ID&gt; &lt;file2_ID&gt;
Sets the transform matrix of file1 identical to that of file2. 

== fselect ==
 fselect all
Selects all files.

 fselect none
Selects no files.

 fselect {-a/-r} &lt;file_IDs&gt;
Selects the specified files and makes the others not selected. More than one file IDs can be specified by putting commas as the delimiter. When the option -a or -r is specified, only the selection status of the specified files are modified, selected or not selected, respectively, and the others remain unchanged.

== hbonds ==
 hbonds {on/true}
Turns on the selected hydrogen bonds.

 hbonds off/false
Turns off the selected hydrogen bonds.

 hbonds &lt;radius&gt;
Turns on the selected hydrogen bonds with the specified raidus (angstrom or Rasmol unit). The maximum parameter value is 2.0. 

== load ==
 load {pdbml} &lt;filename&gt; {fit &lt;file_ID&gt;}
Opens a PDBML file. URL can be used to open a remote file. On loading, the transform matrix can be set identical to that of the specified file.

 load pdb &lt;filename&gt; {fit &lt;file_ID&gt;}
Opens a PDB file. URL can be used to open a remote file. On loading, the transform matrix can be set identical to that of the specified file.

 load polygon &lt;filename&gt; {fit &lt;file_ID&gt;}
Opens a polygon file. URL can be used to open a remote file. On loading, the transform matrix can be set identical to that of the specified file.

 load animation &lt;filename&gt; {fit &lt;file_ID&gt;}
Opens an animation file. URL can be used to open a remote file. On loading, the transform matrix can be set identical to that of the specified file.

 load ftp &lt;PDB_code&gt; {fit &lt;file_ID&gt;}
Retrieves a PDBML file from the PDBj FTP site and opens it. On loading, the transform matrix can be set identical to that of the specified file. 

== pause ==
 pause
Stops the execution of a script file until any key is pressed to restart. 

== pdbj_describe ==
 pdbj_describe &lt;file_id&gt; {&lt;name&gt;} 
Shows the document for the jV_command in PDBMLplus specified by file ID and name. When the name is not specified, all available names are listed.

== pdbj_execute ==
 pdbj_execute &lt;file_id&gt; &lt;name&gt; 
Executes the jV_command in PDBMLplus specified by file ID and name.

== quit ==
 quit
A synonym of the [[#exit|exit]] command.

== refresh ==
 refresh
Redraws all images. 

== reset ==
=== default ===
 reset
Restores the original viewing transformation of all images, the center of rotation, and the view point. 

=== cartoon ===
 reset cartoon
Restores the thickness of the cartoon representation. 

=== line_width ===
 reset line_width
Restores the width of lines in polygon images. 

=== pickradius ===
 reset pickradius
Restores the mouse-pickable region of each atom. 

=== point_size ===
 reset point_size
Restores the size of points in polygon images. 

=== polyline_width ===
 reset polyline_width
Restores the width of polylines in polygon images. 

=== transparency ===
 reset transparency
Restores the transparency of polygon images.

 reset point_transparency
Restores the transparency of points in polygon images.

 reset line_transparency
Restores the transparency of lines in polygon images.

 reset triangle_transparency
Restores the transparency of triangles in polygon images.

 reset quad_transparency
Restores the transparency of quads in polygon images.

 reset polyline_transparency
Restores the transparency of polylines in polygon images. 

== ribbons ==
 ribbons {on/true}
Turns on the ribbon surfaces for the selected residues.

 ribbons off/false
Turns off the ribbon surfaces for the selected residues.

 ribbons &lt;half_width&gt;
Turns on the ribbon surfaces for the selected residues with the specified half width (angstrom or Rasmol unit). The maximum parameter value is 4.0. 

== rotate ==
 rotate x/y/z &lt;angle&gt;
Rotates images about the specified axis by the specified angle in degrees. 

== save ==
 save {pdb} &lt;filename&gt;
Saves the currently selected set of atoms in a PDB format file.

 save script &lt;filename&gt;
Creates a script file that reproduces the currently displayed image.

 save png &lt;filename&gt;
Creates a PNG image file of the currently displayed image.

 save jpeg &lt;filename&gt; {&lt;quality&gt;}
Creates a JPEG image file of the currently displayed image. The compression quality can be specified, 0 &lt; quality &lt;= 1, where 'quality = 1' means no compression. 

== script ==
 script &lt;filename&gt;
Opens and executes the specified script file. URL can be used to open a remote file. 

== select ==
 select
Selects all atoms. Whether hetero atoms and hydrogens are selected or not depends on the internal parameters, hetero and hydrogen, respectively.

 select all
Selects all atoms including hetero atoms and hydrogens.

 select none
Selects no atoms.

 select &lt;atom_expression&gt;
Selects a group of atoms specified by the atom expression. 

== selectvertex ==
 selectvertex {all}
Selects all vertices.

 selectvertex none
Selects no vertices.

 selectvertex &lt;vertex_expression&gt;
Selects a group of vertices specified by the vertex expression. 

== set ==
=== ambient ===
 set ambient {&lt;value&gt;}
Sets the amount of ambient light. The value must be between 0 and 100. When the parameter is not specified, it is restored to the default value 33.

=== adjustview ===
 set adjustview on
The view point is automatically adjusted when a new file is loaded.

 set adjustview off
The view point is kept unchanged when a new file is loaded. 

=== background ===
 set background &lt;color&gt;
Changes the background color. The color may be given as RGB values [r,g,b], or predefined color names. 

=== bondmode ===
 set bondmode and
Specifies how to select an individual bonds. A bond is selected when both atoms connected by the bond are selected.

 set bondmode or
Specifies how to select an individual bonds. A bond is selected when either of the connected atoms is selected. 

=== cartoon ===
 set cartoon {&lt;value&gt;}
Specifies the thickness of the cartoon representation (angstrom or Rasmol unit). The maximum parameter value is 2.0. When the parameter is not specified, it is restored to the default value. 

=== cartoon_loop_tube ===
 set cartoon_loop_tube on
The loop region is drawn as tube in the cartoon representation.

 set cartoon_loop_tube off
The loop region is drawn as square pillar in the cartoon representation.

=== cartoon_round ===
 set cartoon_round on
Square pillar with round edge is drawn in the cartoon representation (except beta strands). 

 set cartoon_round off
Square pillar is drawn in the cartoon representation.

=== center ===
 set center &lt;atom_expression&gt;
Sets the default center of the selected files to the center of the specified atoms.

 set center [x, y, z]
Sets the default center of the selected files to the specified coordinates. 

=== diffuse1 ===
 set diffuse1 {&lt;value&gt;}
Sets the amount of the first diffuse light. The value must be between 0 and 100. When the parameter is not specified, it is restored to the default value 50.

=== diffuse1_direction ===
 set diffuse1_direction {[x, y, z]}
Sets the direction of the first diffuse light. When the parameter is not specified, it is restored to the default value [-1, -1, -1].

=== diffuse2 ===
 set diffuse2 {&lt;value&gt;}
Sets the amount of the second diffuse light. The value must be between 0 and 100. When the parameter is not specified, it is restored to the default value 50.

=== diffuse2_direction ===
 set diffuse2_direction {[x, y, z]}
Sets the direction of the second diffuse light. When the parameter is not specified, it is restored to the default value [-1, -1, -1].

=== drawlevel ===
 set drawlevel &lt;value&gt;
Specifies precision of the rendering of spheres and cylinders. The value may be given as an integer (minimum 5) that stands for the number of straight line segments to represent an arc of 180 degrees. 

=== efsite_url ===
 set efsite_url &lt;URL&gt;
Sets the URL for eF-site.

=== ext_site_url ===
 set ext_site_url &lt;prefix&gt; &lt;URL&gt;
Sets the URL for an external database site.

=== hbonds ===
 set hbonds backbone
Hydrogen bonds are displayed between backbones.

 set hbonds sidechain
Hydrogen bonds are displayed between sidechains. 

=== hetero ===
 set hetero on
Sets the default behavior of the select command such that hetero atoms are selected.

 set hetero off
Sets the default behavior of the select command such that hetero atoms are not selected. 

=== hydrogen ===
 set hydrogen on
Sets the default behavior of the select command such that hydrogens are selected.

 set hydrogen off
Sets the default behavior of the select command such that hydrogens are not selected. 

=== imagesize ===
 set imagesize &lt;width&gt; &lt;height&gt;
Sets the size of the 3D-rendering panel in pixels. The size will be set within the screen size with the width being an even integer. 

=== line_width ===
 set line_width &lt;value&gt;
Sets the width of lines in polygon images. The &lt;value&gt; should be larger than 0. 

=== loadcenter ===
 set loadcenter on
When a file is opened, sets the default center of that file to the center of all files that have already opened.

 set loadcenter off
When a file is opened, sets the default center of that file according to its own coordiantes. 

=== pdbml_noatom_url ===
 set pdbml_noatom_url &lt;URL&gt;
Sets the URL for PDBML noatom files.

=== pdbml_extatom_url ===
 set pdbml_extatom_url &lt;URL&gt;
Sets the URL for PDBML extatom files.

=== pdbml_plus_url ===
 set pdbml_plus_url &lt;URL&gt;
Sets the URL for PDBMLplus files.

=== picking ===
 set picking off
Turns off the mouse picking.

 set picking ident
Sets the mouse picking behavior to show atom identification.

 set picking coord
Sets the mouse picking behavior to show atom coordinates with identification.

 set picking distance
Sets the mouse picking behavior to show the distance between atoms successively picked.

 set picking center
Sets the mouse picking behavior to specify the center of rotation and center of the screen.

 set picking select
Sets the mouse picking behavior to select the file that contains the atom picked. 

=== pickradius ===
 set pickradius &lt;value&gt;
Sets the mouse-pickable region of each atom to be the sphere centered to each atom with the specified radius (angstrom or Rasmol unit). 

=== point_size ===
 set point_size &lt;value&gt;
Sets the size of points in polygon images. The &lt;value&gt; should be larger than 0. 

=== polyline_width ===
 set polyline_width &lt;value&gt;
Sets the width of polylines in polygon images. The &lt;value&gt; should be larger than 0. 

=== projection ===
 set projection perspective
Sets the projection mode for a perspective projection.

 set projection parallel {&lt;size&gt;}
Sets the projection mode for a parallel projection. The size of image (fit to the height of the screen) can be specified (angstrom or Rasmol unit). 

=== ribbonback ===
 set ribbonback &lt;color&gt;
Sets the color of the back of ribbon models. The color may be given as RGB values [r,g,b] or predefined color names.

 set ribbonback none
Resets the color of the back of ribbon models.

=== specular ===
 set specular on/true
Enables the display of specular highlights on solid objects.

 set specular off/false
Disables the display of specular highlights on solid objects.

 set specular &lt;value&gt;
Enables the display of specular highlights on solid objects. The value between 0 and 100 specifies the specular color in gray scale with 0 and 100 being black and white, respectively. The default value is 50.0. 

=== specpower ===
 set specpower &lt;value&gt;
Sets the shininess of solid objects. The value between 0 and 100 specifies a material reflection coefficient with 0 being diffuse surfaces and 100 being shiny surfaces. 

=== ssbonds ===
 set ssbonds backbone
Disulfide bonds are displayed between backbones.

 set ssbonds sidechain
Disulfide bonds are displayed between sidechains. 

=== stereo ===
 set stereo
A synonym of the [[#stereo_2|stereo]] command.

=== transparency ===
 set transparency &lt;value&gt;
Sets the transparency of polygon images.

 set point_transparency &lt;value&gt;
Sets the transparency of points in polygon images.

 set line_transparency &lt;value&gt;
Sets the transparency of lines in polygon images.

 set triangle_transparency &lt;value&gt;
Sets the transparency of triangles in polygon images.

 set quad_transparency &lt;value&gt;
Sets the transparency of quads in polygon images.

 set polyline_transparency &lt;value&gt;
Sets the transparency of polylines in polygon images. 

=== viewpoint ===
 set viewpoint {x, y, z}
Sets the viewpoint to the specified coordinates. 

== show ==
 show godata
Displays gene ontology data of molecules.

 show imagesize
Displays the size of the 3D-rendering panel.

 show information
Displays a detail discription of molecules.

 show site {&lt;prefix&gt;:&lt;db&gt;:&lt;category&gt;}
Displays site information in an external database.

 show transform
Displays the transform matrix of molecules.

 show viewpoint
Displays the current viewpoint.

 show pdbj
Displays keywords available in PDBj expression.

== slab ==
 slab {on/true}
Enables the z-clipping plane of molecules and polygons.

 slab off/false
Disables the z-clipping plane of molecules and polygons.

 slab &lt;ratio&gt;
Sets the position of the z-clipping plane of molecules and polygons. The parameter may be given as a number from 0 to 100. The values 0 and 100 represent that image as a whole is completely invisible and visible, respectively.

 slab -v &lt;value&gt;
Sets the position of the z-clipping plane of molecules and polygons by specifying the z coordinate value. 

== spacefill ==
 spacefill {on/true}
Turns on the ball image of the selected atoms.

 spacefill off/false
Turns off the ball image of the selected atoms.

 spacefill &lt;radius&gt;
Turns on the ball image of the selected atoms with the specified radius (angstrom or Rasmol unit). The maximum parameter value is 3.0.

 spacefill temperature
Turns on the ball image of the selected atoms using the temperature factor as radius. 

== ssbonds ==
 ssbonds {on/true}
Turns on the selected disulfide bonds.

 ssbonds off/false
Turns off the selected disulfide bonds.

 ssbonds &lt;radius&gt;
Turns on the selected disulfide bonds with the specified raidus (angstrom or Rasmol unit). The maximum parameter value is 2.0. 

== stereo ==
 stereo {on/true}
Enables stereo display. This command without arguments cycles three state; 'stereo off', 'stereo on' in cross-eyed mode and 'stereo on' in parallel-eyed mode.

 stereo off/false
Disables stereo display.

 stereo &lt;angle&gt;
Enables stereo display with the specified separation angle. Positive and negative values represent cross-eyed and parallel-eyed viewing, respectively.


== structure ==
 structure
Estimates the secondary structure using Kabsch and Sander's DSSP algorithm. 

== trace ==
 trace {on/true}
Turns on a tube representation for the selected residues.

 trace off/false
Turns off a tube representation for the selected residues.

 trace &lt;radius&gt;
Turns on a tube representation for the selected residues with the specified radius (angstrom or Rasmol unit). The maximum parameter value is 2.0.


== translate ==
 translate x/y/z &lt;value&gt;
Moves images along the specified axis by the specified amount (angstrom). 

== wireframe ==
 wireframe {on/true}
Turns on the selected bonds.

 wireframe off/false
Turns off the selected bonds.

 wireframe &lt;radius&gt;
Turns on the selected bonds with the specified raidus (angstrom or Rasmol unit). The maximum parameter value is 2.0. 

== write ==
 write
A synonym of the [[#save|save]] command.

== zap ==
 zap {&lt;file_IDs&gt;}
Closes the specified files. More than one file IDs can be specified by putting commas as the delimiter. When the paraneter is absent, all files are closed. 

== zoom ==
 zoom {&lt;value&gt;}
Sets the magnification of the image as a whole. The value stands for the magnification as a percentage of the current scale. The minimum parameter value is 10.0.</text>
    <sha1>b7229251e16508c0fa7c56d493d7f6aa378551e2</sha1>
  </revision>
</page>
<page arvcontinue="20091113083303|354">
  <title>Atom Expression</title>
  <ns>0</ns>
  <id>21</id>
  <revision>
    <id>362</id>
    <parentid>322</parentid>
    <timestamp>2010-01-19T08:03:32Z</timestamp>
    <contributor>
      <username>IMSsato</username>
      <id>4</id>
    </contributor>
    <comment>/* xPSSS expression */</comment>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="9235" xml:space="preserve">{| style="float:right"
 |__TOC__
 |}
In order to specify a group of atoms in a molecule, the following five expressions are available.

The standard boolean connectives 'and', 'or' and 'not', and brackets can be used to construct a complex expression. The boolean connectives may be abbreviated as '&amp;', '|', and '|', respectively. 

== predefined set ==
=== element name ===
Element names, such as carbon or nitrogen, can be used to select atoms. 
=== set based on residue property ===
a) amino acids in protein molecule
&lt;table border="1"&gt;
&lt;tr&gt;
&lt;td&gt;&lt;/td&gt;
&lt;td&gt;ALA&lt;/td&gt;&lt;td&gt;ARG&lt;/td&gt;&lt;td&gt;ASN&lt;/td&gt;&lt;td&gt;ASP&lt;/td&gt;&lt;td&gt;CYS&lt;/td&gt;
&lt;td&gt;GLU&lt;/td&gt;&lt;td&gt;GLN&lt;/td&gt;&lt;td&gt;GLY&lt;/td&gt;&lt;td&gt;HIS&lt;/td&gt;&lt;td&gt;ILE&lt;/td&gt;
&lt;td&gt;LEU&lt;/td&gt;&lt;td&gt;LYS&lt;/td&gt;&lt;td&gt;MET&lt;/td&gt;&lt;td&gt;PHE&lt;/td&gt;&lt;td&gt;PRO&lt;/td&gt;
&lt;td&gt;SER&lt;/td&gt;&lt;td&gt;THR&lt;/td&gt;&lt;td&gt;TRP&lt;/td&gt;&lt;td&gt;TYR&lt;/td&gt;&lt;td&gt;VAL&lt;/td&gt;
&lt;/tr&gt;
&lt;tr&gt;
&lt;td&gt;Acidic&lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;/tr&gt;
&lt;tr&gt;
&lt;td&gt;Acyclic&lt;/td&gt;
&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;
&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;
&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;&lt;/td&gt;&lt;td&gt;&lt;/td&gt;
&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;&lt;/td&gt;&lt;td&gt;&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;
&lt;/tr&gt;
&lt;tr&gt;
&lt;td&gt;Aliphatic&lt;/td&gt;
&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;
&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;
&lt;/tr&gt;
&lt;tr&gt;
&lt;td&gt;Aromatic&lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;/tr&gt;
&lt;tr&gt;
&lt;td&gt;Basic&lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;/tr&gt;
&lt;tr&gt;
&lt;td&gt;Buried&lt;/td&gt;
&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;
&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;
&lt;/tr&gt;
&lt;tr&gt;
&lt;td&gt;Charged&lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;/tr&gt;
&lt;tr&gt;
&lt;td&gt;Cyclic&lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;/tr&gt;
&lt;tr&gt;
&lt;td&gt;Hydrophobic&lt;/td&gt;
&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;
&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;
&lt;/tr&gt;
&lt;tr&gt;
&lt;td&gt;Large&lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;
&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;/tr&gt;
&lt;tr&gt;
&lt;td&gt;Medium&lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;
&lt;/tr&gt;
&lt;tr&gt;
&lt;td&gt;Negative&lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;/tr&gt;
&lt;tr&gt;
&lt;td&gt;Neutral&lt;/td&gt;
&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;
&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;
&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;
&lt;/tr&gt;
&lt;tr&gt;
&lt;td&gt;Polar&lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;
&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;/tr&gt;
&lt;tr&gt;
&lt;td&gt;Positive&lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;/tr&gt;
&lt;tr&gt;
&lt;td&gt;Small&lt;/td&gt;
&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;/tr&gt;
&lt;tr&gt;
&lt;td&gt;Surface&lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;
&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;/tr&gt;
&lt;tr&gt;
&lt;td&gt;Cysteine&lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;/tr&gt;
&lt;tr&gt;
&lt;td&gt;Amino&lt;/td&gt;
&lt;td colspan="20"&gt;above 20 amino acids + ASX, GLX, PCA, HYP&lt;/td&gt;
&lt;/tr&gt;
&lt;tr&gt;
&lt;td&gt;Protein&lt;/td&gt;
&lt;td colspan="20"&gt;above 20 amino acids + ASX, GLX, PCA, HYP, UNK, ACE, FOR&lt;/td&gt;
&lt;/tr&gt;
&lt;/table&gt;

b) nucleotides
&lt;table border="1"&gt;
&lt;tr&gt;
&lt;td&gt;&lt;/td&gt;
&lt;td&gt;  A&lt;/td&gt;&lt;td&gt;  C&lt;/td&gt;&lt;td&gt;  G&lt;/td&gt;&lt;td&gt;  T&lt;/td&gt;&lt;td&gt;  U&lt;/td&gt;
&lt;td&gt; +U&lt;/td&gt;&lt;td&gt;  I&lt;/td&gt;&lt;td&gt;1MA&lt;/td&gt;&lt;td&gt;5MC&lt;/td&gt;&lt;td&gt;OMC&lt;/td&gt;
&lt;td&gt;1MG&lt;/td&gt;&lt;td&gt;2MG&lt;/td&gt;&lt;td&gt;M2G&lt;/td&gt;&lt;td&gt;7MG&lt;/td&gt;&lt;td&gt;OMG&lt;/td&gt;
&lt;td&gt; YG&lt;/td&gt;&lt;td&gt;H2U&lt;/td&gt;&lt;td&gt;5MU&lt;/td&gt;&lt;td&gt;PSU&lt;/td&gt;
&lt;/tr&gt;
&lt;tr&gt;
&lt;td&gt;AT&lt;/td&gt;
&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;/tr&gt;
&lt;tr&gt;
&lt;td&gt;CG&lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;/tr&gt;
&lt;tr&gt;
&lt;td&gt;Purine&lt;/td&gt;
&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;/tr&gt;
&lt;tr&gt;
&lt;td&gt;Pyrimidine&lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;/tr&gt;
&lt;tr&gt;
&lt;td&gt;DNA&lt;/td&gt;
&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;/tr&gt;
&lt;tr&gt;
&lt;td&gt;RNA&lt;/td&gt;
&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;
&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;
&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;
&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;
&lt;/tr&gt;
&lt;tr&gt;
&lt;td&gt;Nucleic&lt;/td&gt;
&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;
&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;
&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;
&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;
&lt;/tr&gt;
&lt;/table&gt;

c) others
&lt;table border="1"&gt;
&lt;tr&gt;
&lt;td&gt;&lt;/td&gt;
&lt;td&gt;HOH&lt;/td&gt;&lt;td&gt;DOD&lt;/td&gt;&lt;td&gt;SO4&lt;/td&gt;&lt;td&gt;PO4&lt;/td&gt;
&lt;/tr&gt;
&lt;tr&gt;
&lt;td&gt;Water&lt;/td&gt;
&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;/tr&gt;
&lt;tr&gt;
&lt;td&gt;Ions&lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;
&lt;/tr&gt;
&lt;tr&gt;
&lt;td&gt;Solvent&lt;/td&gt;
&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;
&lt;/tr&gt;
&lt;/table&gt;

=== others ===


== comparison operators ==
Parts of a molecule can be selected using equality, inequality and ordering operators on their properties. Possible operators are =, ==, &lt;&gt;, !=, /=, &lt;, &lt;=, &gt; and &gt;=, and possible property names are as follows.
{| border="1"
 |-
 | AtomNo || atom ID in PDB files.
 |-
 | ElemNo || atomic number.
 |-
 | ResNo || residue ID in PDB files.
 |-
 | Radius || radius of a ball image of atoms.
 |-
 | Temperature || temperature factor of atoms.
 |-
 | Model || model ID in PDB files.
 |-
 | File || File ID.
 |}

== residue range ==
A group of atoms in a molecule can be selected by the residue ID. For example, command 'select 3' selects atoms whose residue ID is 3, and 'select 3-10' selects atoms whose residue ID is larger than or equal to 3 and smaller than or equal to 10. 
Optionally, the chain ID can be specified after residue range with a colon.
For example, command 'select 3:A' selects atoms
whose residue ID is 3 in the A chain.

== within expression ==
A within expression selects atoms that exist within a specified distance from another set of atoms. For example, 'select within(3.0, backbone) selects atoms within a 3.0 Angstrom radius of any atom in a protein or nucleic acid backbone. 

== xPSSS expression ==
A xPSSS expression selects a group of atoms according to molecule's properties defined in the PDBMLplus file. It takes the following form;
 xps3:keyword
For example, 'select xps3:binding'. The keywords available for each molecule are obtained by the 'show xps3' command.

== primitive expression ==
A primitive expression takes such a form as
 residue name[residue ID][:chain ID][.atom name][;alternate location][/model ID][@file ID]
Here, residue name and atom name are three letter and four letter name, respectively, and terms in square brackets can be omitted. For example, command 'select SER.CA' selects all alpha carbon atoms in serine.</text>
    <sha1>4d70c8b49a8825753fe1dff102f9cf633481da54</sha1>
  </revision>
  <revision>
    <id>380</id>
    <parentid>362</parentid>
    <timestamp>2010-07-13T04:23:32Z</timestamp>
    <contributor>
      <username>IMSsato</username>
      <id>4</id>
    </contributor>
    <comment>/* xPSSS expression */</comment>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="9233" xml:space="preserve">{| style="float:right"
 |__TOC__
 |}
In order to specify a group of atoms in a molecule, the following five expressions are available.

The standard boolean connectives 'and', 'or' and 'not', and brackets can be used to construct a complex expression. The boolean connectives may be abbreviated as '&amp;', '|', and '|', respectively. 

== predefined set ==
=== element name ===
Element names, such as carbon or nitrogen, can be used to select atoms. 
=== set based on residue property ===
a) amino acids in protein molecule
&lt;table border="1"&gt;
&lt;tr&gt;
&lt;td&gt;&lt;/td&gt;
&lt;td&gt;ALA&lt;/td&gt;&lt;td&gt;ARG&lt;/td&gt;&lt;td&gt;ASN&lt;/td&gt;&lt;td&gt;ASP&lt;/td&gt;&lt;td&gt;CYS&lt;/td&gt;
&lt;td&gt;GLU&lt;/td&gt;&lt;td&gt;GLN&lt;/td&gt;&lt;td&gt;GLY&lt;/td&gt;&lt;td&gt;HIS&lt;/td&gt;&lt;td&gt;ILE&lt;/td&gt;
&lt;td&gt;LEU&lt;/td&gt;&lt;td&gt;LYS&lt;/td&gt;&lt;td&gt;MET&lt;/td&gt;&lt;td&gt;PHE&lt;/td&gt;&lt;td&gt;PRO&lt;/td&gt;
&lt;td&gt;SER&lt;/td&gt;&lt;td&gt;THR&lt;/td&gt;&lt;td&gt;TRP&lt;/td&gt;&lt;td&gt;TYR&lt;/td&gt;&lt;td&gt;VAL&lt;/td&gt;
&lt;/tr&gt;
&lt;tr&gt;
&lt;td&gt;Acidic&lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;/tr&gt;
&lt;tr&gt;
&lt;td&gt;Acyclic&lt;/td&gt;
&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;
&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;
&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;&lt;/td&gt;&lt;td&gt;&lt;/td&gt;
&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;&lt;/td&gt;&lt;td&gt;&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;
&lt;/tr&gt;
&lt;tr&gt;
&lt;td&gt;Aliphatic&lt;/td&gt;
&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;
&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;
&lt;/tr&gt;
&lt;tr&gt;
&lt;td&gt;Aromatic&lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;/tr&gt;
&lt;tr&gt;
&lt;td&gt;Basic&lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;/tr&gt;
&lt;tr&gt;
&lt;td&gt;Buried&lt;/td&gt;
&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;
&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;
&lt;/tr&gt;
&lt;tr&gt;
&lt;td&gt;Charged&lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;/tr&gt;
&lt;tr&gt;
&lt;td&gt;Cyclic&lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;/tr&gt;
&lt;tr&gt;
&lt;td&gt;Hydrophobic&lt;/td&gt;
&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;
&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;
&lt;/tr&gt;
&lt;tr&gt;
&lt;td&gt;Large&lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;
&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;/tr&gt;
&lt;tr&gt;
&lt;td&gt;Medium&lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;
&lt;/tr&gt;
&lt;tr&gt;
&lt;td&gt;Negative&lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;/tr&gt;
&lt;tr&gt;
&lt;td&gt;Neutral&lt;/td&gt;
&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;
&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;
&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;
&lt;/tr&gt;
&lt;tr&gt;
&lt;td&gt;Polar&lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;
&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;/tr&gt;
&lt;tr&gt;
&lt;td&gt;Positive&lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;/tr&gt;
&lt;tr&gt;
&lt;td&gt;Small&lt;/td&gt;
&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;/tr&gt;
&lt;tr&gt;
&lt;td&gt;Surface&lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;
&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;/tr&gt;
&lt;tr&gt;
&lt;td&gt;Cysteine&lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;/tr&gt;
&lt;tr&gt;
&lt;td&gt;Amino&lt;/td&gt;
&lt;td colspan="20"&gt;above 20 amino acids + ASX, GLX, PCA, HYP&lt;/td&gt;
&lt;/tr&gt;
&lt;tr&gt;
&lt;td&gt;Protein&lt;/td&gt;
&lt;td colspan="20"&gt;above 20 amino acids + ASX, GLX, PCA, HYP, UNK, ACE, FOR&lt;/td&gt;
&lt;/tr&gt;
&lt;/table&gt;

b) nucleotides
&lt;table border="1"&gt;
&lt;tr&gt;
&lt;td&gt;&lt;/td&gt;
&lt;td&gt;  A&lt;/td&gt;&lt;td&gt;  C&lt;/td&gt;&lt;td&gt;  G&lt;/td&gt;&lt;td&gt;  T&lt;/td&gt;&lt;td&gt;  U&lt;/td&gt;
&lt;td&gt; +U&lt;/td&gt;&lt;td&gt;  I&lt;/td&gt;&lt;td&gt;1MA&lt;/td&gt;&lt;td&gt;5MC&lt;/td&gt;&lt;td&gt;OMC&lt;/td&gt;
&lt;td&gt;1MG&lt;/td&gt;&lt;td&gt;2MG&lt;/td&gt;&lt;td&gt;M2G&lt;/td&gt;&lt;td&gt;7MG&lt;/td&gt;&lt;td&gt;OMG&lt;/td&gt;
&lt;td&gt; YG&lt;/td&gt;&lt;td&gt;H2U&lt;/td&gt;&lt;td&gt;5MU&lt;/td&gt;&lt;td&gt;PSU&lt;/td&gt;
&lt;/tr&gt;
&lt;tr&gt;
&lt;td&gt;AT&lt;/td&gt;
&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;/tr&gt;
&lt;tr&gt;
&lt;td&gt;CG&lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;/tr&gt;
&lt;tr&gt;
&lt;td&gt;Purine&lt;/td&gt;
&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;/tr&gt;
&lt;tr&gt;
&lt;td&gt;Pyrimidine&lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;/tr&gt;
&lt;tr&gt;
&lt;td&gt;DNA&lt;/td&gt;
&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;/tr&gt;
&lt;tr&gt;
&lt;td&gt;RNA&lt;/td&gt;
&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;
&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;
&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;
&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;
&lt;/tr&gt;
&lt;tr&gt;
&lt;td&gt;Nucleic&lt;/td&gt;
&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;
&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;
&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;
&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;
&lt;/tr&gt;
&lt;/table&gt;

c) others
&lt;table border="1"&gt;
&lt;tr&gt;
&lt;td&gt;&lt;/td&gt;
&lt;td&gt;HOH&lt;/td&gt;&lt;td&gt;DOD&lt;/td&gt;&lt;td&gt;SO4&lt;/td&gt;&lt;td&gt;PO4&lt;/td&gt;
&lt;/tr&gt;
&lt;tr&gt;
&lt;td&gt;Water&lt;/td&gt;
&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;/tr&gt;
&lt;tr&gt;
&lt;td&gt;Ions&lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;
&lt;/tr&gt;
&lt;tr&gt;
&lt;td&gt;Solvent&lt;/td&gt;
&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;
&lt;/tr&gt;
&lt;/table&gt;

=== others ===


== comparison operators ==
Parts of a molecule can be selected using equality, inequality and ordering operators on their properties. Possible operators are =, ==, &lt;&gt;, !=, /=, &lt;, &lt;=, &gt; and &gt;=, and possible property names are as follows.
{| border="1"
 |-
 | AtomNo || atom ID in PDB files.
 |-
 | ElemNo || atomic number.
 |-
 | ResNo || residue ID in PDB files.
 |-
 | Radius || radius of a ball image of atoms.
 |-
 | Temperature || temperature factor of atoms.
 |-
 | Model || model ID in PDB files.
 |-
 | File || File ID.
 |}

== residue range ==
A group of atoms in a molecule can be selected by the residue ID. For example, command 'select 3' selects atoms whose residue ID is 3, and 'select 3-10' selects atoms whose residue ID is larger than or equal to 3 and smaller than or equal to 10. 
Optionally, the chain ID can be specified after residue range with a colon.
For example, command 'select 3:A' selects atoms
whose residue ID is 3 in the A chain.

== within expression ==
A within expression selects atoms that exist within a specified distance from another set of atoms. For example, 'select within(3.0, backbone) selects atoms within a 3.0 Angstrom radius of any atom in a protein or nucleic acid backbone. 

== PDBj expression ==
A PDBj expression selects a group of atoms according to molecule's properties defined in the PDBMLplus file. It takes the following form;
 pdbj:keyword
For example, 'select pdbj:binding'. The keywords available for each molecule are obtained by the 'show pdbj' command.

== primitive expression ==
A primitive expression takes such a form as
 residue name[residue ID][:chain ID][.atom name][;alternate location][/model ID][@file ID]
Here, residue name and atom name are three letter and four letter name, respectively, and terms in square brackets can be omitted. For example, command 'select SER.CA' selects all alpha carbon atoms in serine.</text>
    <sha1>e22d692f0926c70483c5cfd598d93c7b9173d29d</sha1>
  </revision>
</page>
<page arvcontinue="20091113083303|354">
  <title>Main Page</title>
  <ns>0</ns>
  <id>1</id>
  <revision>
    <id>363</id>
    <parentid>344</parentid>
    <timestamp>2010-04-28T04:19:36Z</timestamp>
    <contributor>
      <username>IMSsato</username>
      <id>4</id>
    </contributor>
    <comment>/* Download */</comment>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="2528" xml:space="preserve">&lt;big&gt;'''Welcome to jV wiki.'''&lt;/big&gt;

jV version 3 (formerly known as PDBjViewer) is a program to display molecular graphics of protein and nucleic acids. 
jV supports the following features:
* jV can read and display PDBML files, the canonical XML format for the Protein Data Bank.
* Of course, jV can read and display the traditional PDB format files, too.
* RasMol-like usability.
* jV can process more than one molecules.
* jV can display polygons specified by XML. ([http://ef-site.hgc.jp/eF-site/schema/polygon12.xsd XML Schema for polygons] is available.)
* Multiple polygons can be processed simultaneously, and be superimposed onto molecular images.
* Animation can be realized.
* jV runs on the Java Runtime Environment ([http://java.sun.com/javase/index.jsp JRE]) so that it can work as a stand-alone application as well as an applet.
* The graphics of jV is based on OpenGL ([http://kenai.com/projects/jogl JOGL]), thereby producing fairly beautiful pictures.


The program 'jV' has been developed by [http://www.hgc.jp/~kinosita/TOP.html Kengo Kinoshita] ([http://www.hgc.jp/english/ Human Genome Center], [http://www.ims.u-tokyo.ac.jp/imsut/en/ Insutitute for Medical Science],[http://www.u-tokyo.ac.jp/index_e.html University of Tokyo]) and [http://www.protein.osaka-u.ac.jp/rcsfp/pi/ Haruki Nakamura] ([http://www.protein.osaka-u.ac.jp/index_e.php Institute for Protein Research], [http://www.osaka-u.ac.jp/eng/index.html Osaka Univeristy]), with the support from [http://www-bird.jst.go.jp/index_e.html JST-BIRD].


&lt;gallery&gt;
File:Spacefill.jpg
File:Cartoon.jpg
File:Surface.jpg
File:edmap.jpg
&lt;/gallery&gt;


== Start up ==
You can start up jV with Java Web Start technology immediately from here.
* [http://ef-site.hgc.jp/eF-site/servlet/stable/jV.jnlp stable JOGL version] (recommended)
* [http://ef-site.hgc.jp/eF-site/servlet/current/jV.jnlp recent JOGL version]

== Download ==
You can also download the program and start it up locally.
In this case, installing JOGL is required in advance (see [[Installation_of_jV3 | Installation]] page).
The following links take you to the download pages. (latest version is 3.7@2010/4/28)
* [http://ef-site.hgc.jp/eF-site/servlet/DownloadViewerBinary binary] 
* [http://ef-site.hgc.jp/eF-site/servlet/Registration source code] (registration will be required)

== Other resources ==

* PDBj Help page in [http://doc.pdbj.org/help?jV English]/[http://doc.pdbj.org/help_jp.cgi?jV Japanese].
* [http://doc.pdbj.org/jV/manual.html Japanese documents] with some usage samples.</text>
    <sha1>653183b491ff437fad8a0d3b4d770af2ab189550</sha1>
  </revision>
  <revision>
    <id>364</id>
    <parentid>363</parentid>
    <timestamp>2010-05-19T03:48:27Z</timestamp>
    <contributor>
      <username>IMSsato</username>
      <id>4</id>
    </contributor>
    <comment>/* Download */</comment>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="2530" xml:space="preserve">&lt;big&gt;'''Welcome to jV wiki.'''&lt;/big&gt;

jV version 3 (formerly known as PDBjViewer) is a program to display molecular graphics of protein and nucleic acids. 
jV supports the following features:
* jV can read and display PDBML files, the canonical XML format for the Protein Data Bank.
* Of course, jV can read and display the traditional PDB format files, too.
* RasMol-like usability.
* jV can process more than one molecules.
* jV can display polygons specified by XML. ([http://ef-site.hgc.jp/eF-site/schema/polygon12.xsd XML Schema for polygons] is available.)
* Multiple polygons can be processed simultaneously, and be superimposed onto molecular images.
* Animation can be realized.
* jV runs on the Java Runtime Environment ([http://java.sun.com/javase/index.jsp JRE]) so that it can work as a stand-alone application as well as an applet.
* The graphics of jV is based on OpenGL ([http://kenai.com/projects/jogl JOGL]), thereby producing fairly beautiful pictures.


The program 'jV' has been developed by [http://www.hgc.jp/~kinosita/TOP.html Kengo Kinoshita] ([http://www.hgc.jp/english/ Human Genome Center], [http://www.ims.u-tokyo.ac.jp/imsut/en/ Insutitute for Medical Science],[http://www.u-tokyo.ac.jp/index_e.html University of Tokyo]) and [http://www.protein.osaka-u.ac.jp/rcsfp/pi/ Haruki Nakamura] ([http://www.protein.osaka-u.ac.jp/index_e.php Institute for Protein Research], [http://www.osaka-u.ac.jp/eng/index.html Osaka Univeristy]), with the support from [http://www-bird.jst.go.jp/index_e.html JST-BIRD].


&lt;gallery&gt;
File:Spacefill.jpg
File:Cartoon.jpg
File:Surface.jpg
File:edmap.jpg
&lt;/gallery&gt;


== Start up ==
You can start up jV with Java Web Start technology immediately from here.
* [http://ef-site.hgc.jp/eF-site/servlet/stable/jV.jnlp stable JOGL version] (recommended)
* [http://ef-site.hgc.jp/eF-site/servlet/current/jV.jnlp recent JOGL version]

== Download ==
You can also download the program and start it up locally.
In this case, installing JOGL is required in advance (see [[Installation_of_jV3 | Installation]] page).
The following links take you to the download pages. (latest version is 3.7.1@2010/5/19)
* [http://ef-site.hgc.jp/eF-site/servlet/DownloadViewerBinary binary] 
* [http://ef-site.hgc.jp/eF-site/servlet/Registration source code] (registration will be required)

== Other resources ==

* PDBj Help page in [http://doc.pdbj.org/help?jV English]/[http://doc.pdbj.org/help_jp.cgi?jV Japanese].
* [http://doc.pdbj.org/jV/manual.html Japanese documents] with some usage samples.</text>
    <sha1>12b30f36157ac8e1c035388b12baa1804cca785c</sha1>
  </revision>
  <revision>
    <id>365</id>
    <parentid>364</parentid>
    <timestamp>2010-05-26T01:13:30Z</timestamp>
    <contributor>
      <username>Cudo29</username>
      <id>5</id>
    </contributor>
    <comment>/* Other resources */ The URLs were changed.</comment>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="2546" xml:space="preserve">&lt;big&gt;'''Welcome to jV wiki.'''&lt;/big&gt;

jV version 3 (formerly known as PDBjViewer) is a program to display molecular graphics of protein and nucleic acids. 
jV supports the following features:
* jV can read and display PDBML files, the canonical XML format for the Protein Data Bank.
* Of course, jV can read and display the traditional PDB format files, too.
* RasMol-like usability.
* jV can process more than one molecules.
* jV can display polygons specified by XML. ([http://ef-site.hgc.jp/eF-site/schema/polygon12.xsd XML Schema for polygons] is available.)
* Multiple polygons can be processed simultaneously, and be superimposed onto molecular images.
* Animation can be realized.
* jV runs on the Java Runtime Environment ([http://java.sun.com/javase/index.jsp JRE]) so that it can work as a stand-alone application as well as an applet.
* The graphics of jV is based on OpenGL ([http://kenai.com/projects/jogl JOGL]), thereby producing fairly beautiful pictures.


The program 'jV' has been developed by [http://www.hgc.jp/~kinosita/TOP.html Kengo Kinoshita] ([http://www.hgc.jp/english/ Human Genome Center], [http://www.ims.u-tokyo.ac.jp/imsut/en/ Insutitute for Medical Science],[http://www.u-tokyo.ac.jp/index_e.html University of Tokyo]) and [http://www.protein.osaka-u.ac.jp/rcsfp/pi/ Haruki Nakamura] ([http://www.protein.osaka-u.ac.jp/index_e.php Institute for Protein Research], [http://www.osaka-u.ac.jp/eng/index.html Osaka Univeristy]), with the support from [http://www-bird.jst.go.jp/index_e.html JST-BIRD].


&lt;gallery&gt;
File:Spacefill.jpg
File:Cartoon.jpg
File:Surface.jpg
File:edmap.jpg
&lt;/gallery&gt;


== Start up ==
You can start up jV with Java Web Start technology immediately from here.
* [http://ef-site.hgc.jp/eF-site/servlet/stable/jV.jnlp stable JOGL version] (recommended)
* [http://ef-site.hgc.jp/eF-site/servlet/current/jV.jnlp recent JOGL version]

== Download ==
You can also download the program and start it up locally.
In this case, installing JOGL is required in advance (see [[Installation_of_jV3 | Installation]] page).
The following links take you to the download pages. (latest version is 3.7.1@2010/5/19)
* [http://ef-site.hgc.jp/eF-site/servlet/DownloadViewerBinary binary] 
* [http://ef-site.hgc.jp/eF-site/servlet/Registration source code] (registration will be required)

== Other resources ==

* PDBj Help page in [http://www.pdbj.org/doc/help.cgi?jV English]/[http://www.pdbj.org/doc/help_jp.cgi?jV Japanese].
* [http://www.pdbj.org/doc/jV/manual.html Japanese documents] with some usage samples.</text>
    <sha1>5fedb20f54cf0485adec5962a63ee7678642f3f7</sha1>
  </revision>
  <revision>
    <id>369</id>
    <parentid>365</parentid>
    <timestamp>2010-06-10T05:35:38Z</timestamp>
    <contributor>
      <username>IMSsato</username>
      <id>4</id>
    </contributor>
    <comment>/* Download */</comment>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="2546" xml:space="preserve">&lt;big&gt;'''Welcome to jV wiki.'''&lt;/big&gt;

jV version 3 (formerly known as PDBjViewer) is a program to display molecular graphics of protein and nucleic acids. 
jV supports the following features:
* jV can read and display PDBML files, the canonical XML format for the Protein Data Bank.
* Of course, jV can read and display the traditional PDB format files, too.
* RasMol-like usability.
* jV can process more than one molecules.
* jV can display polygons specified by XML. ([http://ef-site.hgc.jp/eF-site/schema/polygon12.xsd XML Schema for polygons] is available.)
* Multiple polygons can be processed simultaneously, and be superimposed onto molecular images.
* Animation can be realized.
* jV runs on the Java Runtime Environment ([http://java.sun.com/javase/index.jsp JRE]) so that it can work as a stand-alone application as well as an applet.
* The graphics of jV is based on OpenGL ([http://kenai.com/projects/jogl JOGL]), thereby producing fairly beautiful pictures.


The program 'jV' has been developed by [http://www.hgc.jp/~kinosita/TOP.html Kengo Kinoshita] ([http://www.hgc.jp/english/ Human Genome Center], [http://www.ims.u-tokyo.ac.jp/imsut/en/ Insutitute for Medical Science],[http://www.u-tokyo.ac.jp/index_e.html University of Tokyo]) and [http://www.protein.osaka-u.ac.jp/rcsfp/pi/ Haruki Nakamura] ([http://www.protein.osaka-u.ac.jp/index_e.php Institute for Protein Research], [http://www.osaka-u.ac.jp/eng/index.html Osaka Univeristy]), with the support from [http://www-bird.jst.go.jp/index_e.html JST-BIRD].


&lt;gallery&gt;
File:Spacefill.jpg
File:Cartoon.jpg
File:Surface.jpg
File:edmap.jpg
&lt;/gallery&gt;


== Start up ==
You can start up jV with Java Web Start technology immediately from here.
* [http://ef-site.hgc.jp/eF-site/servlet/stable/jV.jnlp stable JOGL version] (recommended)
* [http://ef-site.hgc.jp/eF-site/servlet/current/jV.jnlp recent JOGL version]

== Download ==
You can also download the program and start it up locally.
In this case, installing JOGL is required in advance (see [[Installation_of_jV3 | Installation]] page).
The following links take you to the download pages. (latest version is 3.7.2@2010/6/10)
* [http://ef-site.hgc.jp/eF-site/servlet/DownloadViewerBinary binary] 
* [http://ef-site.hgc.jp/eF-site/servlet/Registration source code] (registration will be required)

== Other resources ==

* PDBj Help page in [http://www.pdbj.org/doc/help.cgi?jV English]/[http://www.pdbj.org/doc/help_jp.cgi?jV Japanese].
* [http://www.pdbj.org/doc/jV/manual.html Japanese documents] with some usage samples.</text>
    <sha1>89e983b78a1eb631802ca9492cd4de3cd110159f</sha1>
  </revision>
  <revision>
    <id>370</id>
    <parentid>369</parentid>
    <timestamp>2010-06-18T08:02:06Z</timestamp>
    <contributor>
      <username>IMSsato</username>
      <id>4</id>
    </contributor>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="2500" xml:space="preserve">&lt;big&gt;'''Welcome to jV wiki.'''&lt;/big&gt;

jV version 3 (formerly known as PDBjViewer) is a program to display molecular graphics of protein and nucleic acids. 
jV supports the following features:
* jV can read and display PDBML files, the canonical XML format for the Protein Data Bank.
* Of course, jV can read and display the traditional PDB format files, too.
* RasMol-like usability.
* jV can process more than one molecules.
* jV can display polygons specified by XML. ([http://ef-site.hgc.jp/eF-site/schema/polygon12.xsd XML Schema for polygons] is available.)
* Multiple polygons can be processed simultaneously, and be superimposed onto molecular images.
* Animation can be realized.
* jV runs on the Java Runtime Environment ([http://java.sun.com/javase/index.jsp JRE]) so that it can work as a stand-alone application as well as an applet.
* The graphics of jV is based on OpenGL ([http://kenai.com/projects/jogl JOGL]), thereby producing fairly beautiful pictures.


The program 'jV' has been developed by [http://www.hgc.jp/~kinosita/TOP.html Kengo Kinoshita] ([http://www.is.tohoku.ac.jp/index-e.html Graduate School of Information Sciences], [http://www.tohoku.ac.jp/english/ Tohoku University]) and [http://www.protein.osaka-u.ac.jp/rcsfp/pi/ Haruki Nakamura] ([http://www.protein.osaka-u.ac.jp/index_e.php Institute for Protein Research], [http://www.osaka-u.ac.jp/eng/index.html Osaka Univeristy]), with the support from [http://www-bird.jst.go.jp/index_e.html JST-BIRD].


&lt;gallery&gt;
File:Spacefill.jpg
File:Cartoon.jpg
File:Surface.jpg
File:edmap.jpg
&lt;/gallery&gt;


== Start up ==
You can start up jV with Java Web Start technology immediately from here.
* [http://ef-site.hgc.jp/eF-site/servlet/stable/jV.jnlp stable JOGL version] (recommended)
* [http://ef-site.hgc.jp/eF-site/servlet/current/jV.jnlp recent JOGL version]

== Download ==
You can also download the program and start it up locally.
In this case, installing JOGL is required in advance (see [[Installation_of_jV3 | Installation]] page).
The following links take you to the download pages. (latest version is 3.7.2@2010/6/10)
* [http://ef-site.hgc.jp/eF-site/servlet/DownloadViewerBinary binary] 
* [http://ef-site.hgc.jp/eF-site/servlet/Registration source code] (registration will be required)

== Other resources ==

* PDBj Help page in [http://www.pdbj.org/doc/help.cgi?jV English]/[http://www.pdbj.org/doc/help_jp.cgi?jV Japanese].
* [http://www.pdbj.org/doc/jV/manual.html Japanese documents] with some usage samples.</text>
    <sha1>98334c10684d06dc713c3622490349fac2e0f43d</sha1>
  </revision>
  <revision>
    <id>372</id>
    <parentid>370</parentid>
    <timestamp>2010-07-06T06:58:17Z</timestamp>
    <contributor>
      <username>IMSsato</username>
      <id>4</id>
    </contributor>
    <comment>/* Start up */</comment>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="2508" xml:space="preserve">&lt;big&gt;'''Welcome to jV wiki.'''&lt;/big&gt;

jV version 3 (formerly known as PDBjViewer) is a program to display molecular graphics of protein and nucleic acids. 
jV supports the following features:
* jV can read and display PDBML files, the canonical XML format for the Protein Data Bank.
* Of course, jV can read and display the traditional PDB format files, too.
* RasMol-like usability.
* jV can process more than one molecules.
* jV can display polygons specified by XML. ([http://ef-site.hgc.jp/eF-site/schema/polygon12.xsd XML Schema for polygons] is available.)
* Multiple polygons can be processed simultaneously, and be superimposed onto molecular images.
* Animation can be realized.
* jV runs on the Java Runtime Environment ([http://java.sun.com/javase/index.jsp JRE]) so that it can work as a stand-alone application as well as an applet.
* The graphics of jV is based on OpenGL ([http://kenai.com/projects/jogl JOGL]), thereby producing fairly beautiful pictures.


The program 'jV' has been developed by [http://www.hgc.jp/~kinosita/TOP.html Kengo Kinoshita] ([http://www.is.tohoku.ac.jp/index-e.html Graduate School of Information Sciences], [http://www.tohoku.ac.jp/english/ Tohoku University]) and [http://www.protein.osaka-u.ac.jp/rcsfp/pi/ Haruki Nakamura] ([http://www.protein.osaka-u.ac.jp/index_e.php Institute for Protein Research], [http://www.osaka-u.ac.jp/eng/index.html Osaka Univeristy]), with the support from [http://www-bird.jst.go.jp/index_e.html JST-BIRD].


&lt;gallery&gt;
File:Spacefill.jpg
File:Cartoon.jpg
File:Surface.jpg
File:edmap.jpg
&lt;/gallery&gt;


== Start up ==
You can start up jV (3.7.2) with Java Web Start technology immediately from here.
* [http://ef-site.hgc.jp/eF-site/servlet/stable/jV.jnlp stable JOGL version] (recommended)
* [http://ef-site.hgc.jp/eF-site/servlet/current/jV.jnlp recent JOGL version]

== Download ==
You can also download the program and start it up locally.
In this case, installing JOGL is required in advance (see [[Installation_of_jV3 | Installation]] page).
The following links take you to the download pages. (latest version is 3.7.2@2010/6/10)
* [http://ef-site.hgc.jp/eF-site/servlet/DownloadViewerBinary binary] 
* [http://ef-site.hgc.jp/eF-site/servlet/Registration source code] (registration will be required)

== Other resources ==

* PDBj Help page in [http://www.pdbj.org/doc/help.cgi?jV English]/[http://www.pdbj.org/doc/help_jp.cgi?jV Japanese].
* [http://www.pdbj.org/doc/jV/manual.html Japanese documents] with some usage samples.</text>
    <sha1>83ea344990a58076fae49f8e1cd69a68632ba22a</sha1>
  </revision>
  <revision>
    <id>373</id>
    <parentid>372</parentid>
    <timestamp>2010-07-06T06:59:07Z</timestamp>
    <contributor>
      <username>IMSsato</username>
      <id>4</id>
    </contributor>
    <comment>/* Download */</comment>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="2524" xml:space="preserve">&lt;big&gt;'''Welcome to jV wiki.'''&lt;/big&gt;

jV version 3 (formerly known as PDBjViewer) is a program to display molecular graphics of protein and nucleic acids. 
jV supports the following features:
* jV can read and display PDBML files, the canonical XML format for the Protein Data Bank.
* Of course, jV can read and display the traditional PDB format files, too.
* RasMol-like usability.
* jV can process more than one molecules.
* jV can display polygons specified by XML. ([http://ef-site.hgc.jp/eF-site/schema/polygon12.xsd XML Schema for polygons] is available.)
* Multiple polygons can be processed simultaneously, and be superimposed onto molecular images.
* Animation can be realized.
* jV runs on the Java Runtime Environment ([http://java.sun.com/javase/index.jsp JRE]) so that it can work as a stand-alone application as well as an applet.
* The graphics of jV is based on OpenGL ([http://kenai.com/projects/jogl JOGL]), thereby producing fairly beautiful pictures.


The program 'jV' has been developed by [http://www.hgc.jp/~kinosita/TOP.html Kengo Kinoshita] ([http://www.is.tohoku.ac.jp/index-e.html Graduate School of Information Sciences], [http://www.tohoku.ac.jp/english/ Tohoku University]) and [http://www.protein.osaka-u.ac.jp/rcsfp/pi/ Haruki Nakamura] ([http://www.protein.osaka-u.ac.jp/index_e.php Institute for Protein Research], [http://www.osaka-u.ac.jp/eng/index.html Osaka Univeristy]), with the support from [http://www-bird.jst.go.jp/index_e.html JST-BIRD].


&lt;gallery&gt;
File:Spacefill.jpg
File:Cartoon.jpg
File:Surface.jpg
File:edmap.jpg
&lt;/gallery&gt;


== Start up ==
You can start up jV (3.7.2) with Java Web Start technology immediately from here.
* [http://ef-site.hgc.jp/eF-site/servlet/stable/jV.jnlp stable JOGL version] (recommended)
* [http://ef-site.hgc.jp/eF-site/servlet/current/jV.jnlp recent JOGL version]

== Download ==
You can also download the program and start it up locally.
In this case, installing JOGL is required in advance (see [[Installation_of_jV3 | Installation]] page).
The following links take you to the download pages. (latest version is 3.7.2@2010/6/10)
* [http://ef-site.hgc.jp/eF-site/servlet/DownloadViewerBinary binary (3.7.2)] 
* [http://ef-site.hgc.jp/eF-site/servlet/Registration source code (3.7.2)] (registration will be required)

== Other resources ==

* PDBj Help page in [http://www.pdbj.org/doc/help.cgi?jV English]/[http://www.pdbj.org/doc/help_jp.cgi?jV Japanese].
* [http://www.pdbj.org/doc/jV/manual.html Japanese documents] with some usage samples.</text>
    <sha1>d7be5234fc38249c8237f224412f2f60c80fa44d</sha1>
  </revision>
  <revision>
    <id>374</id>
    <parentid>373</parentid>
    <timestamp>2010-07-07T02:16:24Z</timestamp>
    <contributor>
      <username>Cudo29</username>
      <id>5</id>
    </contributor>
    <comment>/* Other resources */ The URL of Japanese documents was changed.</comment>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="2529" xml:space="preserve">&lt;big&gt;'''Welcome to jV wiki.'''&lt;/big&gt;

jV version 3 (formerly known as PDBjViewer) is a program to display molecular graphics of protein and nucleic acids. 
jV supports the following features:
* jV can read and display PDBML files, the canonical XML format for the Protein Data Bank.
* Of course, jV can read and display the traditional PDB format files, too.
* RasMol-like usability.
* jV can process more than one molecules.
* jV can display polygons specified by XML. ([http://ef-site.hgc.jp/eF-site/schema/polygon12.xsd XML Schema for polygons] is available.)
* Multiple polygons can be processed simultaneously, and be superimposed onto molecular images.
* Animation can be realized.
* jV runs on the Java Runtime Environment ([http://java.sun.com/javase/index.jsp JRE]) so that it can work as a stand-alone application as well as an applet.
* The graphics of jV is based on OpenGL ([http://kenai.com/projects/jogl JOGL]), thereby producing fairly beautiful pictures.


The program 'jV' has been developed by [http://www.hgc.jp/~kinosita/TOP.html Kengo Kinoshita] ([http://www.is.tohoku.ac.jp/index-e.html Graduate School of Information Sciences], [http://www.tohoku.ac.jp/english/ Tohoku University]) and [http://www.protein.osaka-u.ac.jp/rcsfp/pi/ Haruki Nakamura] ([http://www.protein.osaka-u.ac.jp/index_e.php Institute for Protein Research], [http://www.osaka-u.ac.jp/eng/index.html Osaka Univeristy]), with the support from [http://www-bird.jst.go.jp/index_e.html JST-BIRD].


&lt;gallery&gt;
File:Spacefill.jpg
File:Cartoon.jpg
File:Surface.jpg
File:edmap.jpg
&lt;/gallery&gt;


== Start up ==
You can start up jV (3.7.2) with Java Web Start technology immediately from here.
* [http://ef-site.hgc.jp/eF-site/servlet/stable/jV.jnlp stable JOGL version] (recommended)
* [http://ef-site.hgc.jp/eF-site/servlet/current/jV.jnlp recent JOGL version]

== Download ==
You can also download the program and start it up locally.
In this case, installing JOGL is required in advance (see [[Installation_of_jV3 | Installation]] page).
The following links take you to the download pages. (latest version is 3.7.2@2010/6/10)
* [http://ef-site.hgc.jp/eF-site/servlet/DownloadViewerBinary binary (3.7.2)] 
* [http://ef-site.hgc.jp/eF-site/servlet/Registration source code (3.7.2)] (registration will be required)

== Other resources ==

* PDBj Help page in [http://www.pdbj.org/doc/help.cgi?jV English]/[http://www.pdbj.org/doc/help_jp.cgi?jV Japanese].
* [http://www.pdbj.org/jv/manual/index_ja.html Japanese documents] with some usage samples.</text>
    <sha1>bcd0e0ef3dda58b2b430ac12c8819e1e18a2ad82</sha1>
  </revision>
  <revision>
    <id>375</id>
    <parentid>374</parentid>
    <timestamp>2010-07-13T03:38:58Z</timestamp>
    <contributor>
      <username>IMSsato</username>
      <id>4</id>
    </contributor>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="2521" xml:space="preserve">&lt;big&gt;'''Welcome to jV wiki.'''&lt;/big&gt;

jV version 3 (formerly known as PDBjViewer) is a program to display molecular graphics of protein and nucleic acids. 
jV supports the following features:
* jV can read and display PDBML files, the canonical XML format for the Protein Data Bank.
* Of course, jV can read and display the traditional PDB format files, too.
* RasMol-like usability.
* jV can process more than one molecules.
* jV can display polygons specified by XML. ([http://ef-site.hgc.jp/eF-site/schema/polygon12.xsd XML Schema for polygons] is available.)
* Multiple polygons can be processed simultaneously, and be superimposed onto molecular images.
* Animation can be realized.
* jV runs on the Java Runtime Environment ([http://java.sun.com/javase/index.jsp JRE]) so that it can work as a stand-alone application as well as an applet.
* The graphics of jV is based on OpenGL ([http://kenai.com/projects/jogl JOGL]), thereby producing fairly beautiful pictures.


The program 'jV' has been developed by [http://www.hgc.jp/~kinosita/TOP.html Kengo Kinoshita] ([http://www.is.tohoku.ac.jp/index-e.html Graduate School of Information Sciences], [http://www.tohoku.ac.jp/english/ Tohoku University]) and [http://www.protein.osaka-u.ac.jp/rcsfp/pi/ Haruki Nakamura] ([http://www.protein.osaka-u.ac.jp/index_e.php Institute for Protein Research], [http://www.osaka-u.ac.jp/eng/index.html Osaka Univeristy]), with the support from [http://www-bird.jst.go.jp/index_e.html JST-BIRD].


&lt;gallery&gt;
File:Spacefill.jpg
File:Cartoon.jpg
File:Surface.jpg
File:edmap.jpg
&lt;/gallery&gt;


== Start up ==
You can start up jV (3.8) with Java Web Start technology immediately from here.
* [http://ef-site.hgc.jp/eF-site/servlet/stable/jV.jnlp stable JOGL version] (recommended)
* [http://ef-site.hgc.jp/eF-site/servlet/current/jV.jnlp recent JOGL version]

== Download ==
You can also download the program and start it up locally.
In this case, installing JOGL is required in advance (see [[Installation_of_jV3 | Installation]] page).
The following links take you to the download pages. (latest version is 3.8@2010/7/13)
* [http://ef-site.hgc.jp/eF-site/servlet/DownloadViewerBinary binary (3.8)] 
* [http://ef-site.hgc.jp/eF-site/servlet/Registration source code (3.8)] (registration will be required)

== Other resources ==

* PDBj Help page in [http://www.pdbj.org/doc/help.cgi?jV English]/[http://www.pdbj.org/doc/help_jp.cgi?jV Japanese].
* [http://www.pdbj.org/jv/manual/index_ja.html Japanese documents] with some usage samples.</text>
    <sha1>904d61791db933728be98ffdcd1ad6c2dd426597</sha1>
  </revision>
  <revision>
    <id>403</id>
    <parentid>375</parentid>
    <timestamp>2010-07-23T08:11:55Z</timestamp>
    <contributor>
      <username>Cudo29</username>
      <id>5</id>
    </contributor>
    <comment>The section of [[#Basic Usage]] was added. The section [[#Other resources]] was edited.</comment>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="6401" xml:space="preserve">&lt;big&gt;'''Welcome to jV wiki.'''&lt;/big&gt;

jV version 3 (formerly known as PDBjViewer) is a program to display molecular graphics of protein and nucleic acids. 
jV supports the following features:
* jV can read and display PDBML files, the canonical XML format for the Protein Data Bank.
* Of course, jV can read and display the traditional PDB format files, too.
* RasMol-like usability.
* jV can process more than one molecules.
* jV can display polygons specified by XML. ([http://ef-site.hgc.jp/eF-site/schema/polygon12.xsd XML Schema for polygons] is available.)
* Multiple polygons can be processed simultaneously, and be superimposed onto molecular images.
* Animation can be realized.
* jV runs on the Java Runtime Environment ([http://java.sun.com/javase/index.jsp JRE]) so that it can work as a stand-alone application as well as an applet.
* The graphics of jV is based on OpenGL ([http://kenai.com/projects/jogl JOGL]), thereby producing fairly beautiful pictures.


The program 'jV' has been developed by [http://www.hgc.jp/~kinosita/TOP.html Kengo Kinoshita] ([http://www.is.tohoku.ac.jp/index-e.html Graduate School of Information Sciences], [http://www.tohoku.ac.jp/english/ Tohoku University]) and [http://www.protein.osaka-u.ac.jp/rcsfp/pi/ Haruki Nakamura] ([http://www.protein.osaka-u.ac.jp/index_e.php Institute for Protein Research], [http://www.osaka-u.ac.jp/eng/index.html Osaka Univeristy]), with the support from [http://www-bird.jst.go.jp/index_e.html JST-BIRD].


&lt;gallery&gt;
File:Spacefill.jpg
File:Cartoon.jpg
File:Surface.jpg
File:edmap.jpg
&lt;/gallery&gt;


== Start up ==
You can start up jV (3.8) with Java Web Start technology immediately from here.
* [http://ef-site.hgc.jp/eF-site/servlet/stable/jV.jnlp stable JOGL version] (recommended)
* [http://ef-site.hgc.jp/eF-site/servlet/current/jV.jnlp recent JOGL version]

== Basic Usage ==
You can execute basic operations such as rotation and translation with mouse action. Major actions are described in the following table:
{| style="margin:auto;border:1px solid gray"
! rowspan="2" style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap;font-weight:bold" |Action
! colspan="2" style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap;font-weight:bold" |Mouse Operation
|-
! style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap;font-weight:bold" |Windows, Linux
! style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap;font-weight:bold" |Mac OS X
|-
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |rotate around X (horizontal) axis&lt;br /&gt;rotate around Y (vertical) axis
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |left drag
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |drag
|-
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |translate along X axis (holizontally)&lt;br /&gt;translate along Y axis (vertically)
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |right drag
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |Command + drag
|-
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |translate along Z axis (zoom in/out)
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |Shift + left drag
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |Shift + drag
|}

Operations such as changing display models and colors and saving the image, can be executed with a menu. The location of the menu is at the top of the application window in Windows and at the top of screen in Mac as the stand-alone application. As an applet usage, a popup menu appears by clicking the right mouse button on the display screen, or clicking with a "Command" button in case of Mac.

{| style="margin:auto;border:0"
|-
| [[File:Jv_menu_win.png|The location of menu in jV stand-alone version in Windows.|250px]]
| [[File:Jv_menu_mac.png|The location of menu in jV stand-alone version in Mac.|250px]]
| [[File:popupmenu_en.png|The location of menu in applet version.|250px]]
|-
| style="text-align:center" |Stand-alone (Windows)
| style="text-align:center" |Stand-alone (Mac)
| style="text-align:center" |Applet
|}

Basic menu operations are following (see also [[GUI]] for details):

{| style="margin:auto;border:1px solid gray;border-collapse:collapse"
! style="padding:0 0.5em;border:1px solid gray" | Operations
! style="padding:0 0.5em;border:1px solid gray" | Menu location
|-
| style="padding:0 0.5em;border:1px solid gray" | Save a static image
| style="padding:0 0.5em;border:1px solid gray" | [File]-[Save]-[PNG/JPEG]
|-
| style="padding:0 0.5em;border:1px solid gray" | Change the expression format
| style="padding:0 0.5em;border:1px solid gray" | [File]-[Display]-[Wireframe/Backbone/Sticks/Spacefill/Ball&amp;amp;Stick/Ribbons/Cartoon]
|-
| style="padding:0 0.5em;border:1px solid gray" | Change the color
| style="padding:0 0.5em;border:1px solid gray" | [File]-[Colors]-[Monochrome/CPK/Shapely/Group/Chain/Temperature/Structure/Charge/Amino]
|}

To execute more complicated operation such as diplaying some piece of the molecule or changing some part of molecule in another style, use command line operation.

See also [[#Other resources]] for details:


== Download ==
You can also download the program and start it up locally.
In this case, installing JOGL is required in advance (see [[Installation_of_jV3 | Installation]] page).
The following links take you to the download pages. (latest version is 3.8@2010/7/13)
* [http://ef-site.hgc.jp/eF-site/servlet/DownloadViewerBinary binary (3.8)] 
* [http://ef-site.hgc.jp/eF-site/servlet/Registration source code (3.8)] (registration will be required)

== Other resources ==
* [http://ef-site.hgc.jp/eF-site/jV/jV_manual.html Manual] (html in English)
* [[How_to_use]] (in this site in English)
* [http://www.pdbj.org/jv/manual/index_ja.html Manual] (html in Japanese)
* [http://www.pdbj.org/jv/manual/jV_manual.pdf Manual] (pdf in English, for ver. 3.3)
* [http://ef-site.hgc.jp/eF-site/jV/jV3_User'sGuide.pdf User's guide] (for ver. 3.3 in English)</text>
    <sha1>78d26c6cbf27d81590880f5071758c650fa18c65</sha1>
  </revision>
</page>
<page arvcontinue="20091113083303|354">
  <title>Links</title>
  <ns>0</ns>
  <id>4</id>
  <revision>
    <id>366</id>
    <parentid>339</parentid>
    <timestamp>2010-05-26T02:38:23Z</timestamp>
    <contributor>
      <username>Cudo29</username>
      <id>5</id>
    </contributor>
    <comment>/* DBs */ The URL of eProtS was changed</comment>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="1272" xml:space="preserve">== Organization ==
* [http://www-bird.jst.go.jp/index_e.html JST-BIRD]
* [http://www.hgc.jp/english/ Human Genome Center]
* [http://www.protein.osaka-u.ac.jp/home_e/index_e.html Institute for Protein Research]
&lt;br /&gt;

== DBs ==
* [http://ef-site.hgc.jp/eF-site/ eF-site] (DB of electrostatic surface of functional site of proteins)
* [http://ef-site.hgc.jp/eF-seek/ eF-seek] (Prediction of ligand binding site of proteins)
* [http://ef-site.hgc.jp/eF-surf/ eF-surf] (Calculate the molecular surface and electrostatic potential of proteins)
&lt;br /&gt;
* [http://pre-s.protein.osaka-u.ac.jp/~preds/ P&lt;i&gt;re&lt;/i&gt;D&lt;i&gt;s&lt;/i&gt;] (Prediction of DNA-binding site)
* [http://pre-s.protein.osaka-u.ac.jp/~prebi/ PreBI] (Prediction of biological interface of proteins homo-interface)
* [http://pre-s.protein.osaka-u.ac.jp/~preds classPPI] (Classification of homo protein-protein interfaces)
&lt;br /&gt;
* [http://p-cats.hgc.jp/p-cats/ P-cats] (Prediction of Catalytic residues in proteins)
&lt;br /&gt;
* [http://pdbjs3.protein.osaka-u.ac.jp/xPSSS/index.html xPSSS] (xml-based protein structure search service)
* [http://www.pdbj.org/eprots/index.php?l=en eProtS] (Encyclopedia of protein structures)
* [http://cube.socs.waseda.ac.jp/pages/jsp/index.jsp ProMode] (DB of normal mode analysis of proteins)</text>
    <sha1>6e2640dbbec3bfe7195268a69682848fd32d8e60</sha1>
  </revision>
  <revision>
    <id>367</id>
    <parentid>366</parentid>
    <timestamp>2010-05-26T02:38:52Z</timestamp>
    <contributor>
      <username>Cudo29</username>
      <id>5</id>
    </contributor>
    <comment>/* DBs */ The URL of eProtS was changed</comment>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="1270" xml:space="preserve">== Organization ==
* [http://www-bird.jst.go.jp/index_e.html JST-BIRD]
* [http://www.hgc.jp/english/ Human Genome Center]
* [http://www.protein.osaka-u.ac.jp/home_e/index_e.html Institute for Protein Research]
&lt;br /&gt;

== DBs ==
* [http://ef-site.hgc.jp/eF-site/ eF-site] (DB of electrostatic surface of functional site of proteins)
* [http://ef-site.hgc.jp/eF-seek/ eF-seek] (Prediction of ligand binding site of proteins)
* [http://ef-site.hgc.jp/eF-surf/ eF-surf] (Calculate the molecular surface and electrostatic potential of proteins)
&lt;br /&gt;
* [http://pre-s.protein.osaka-u.ac.jp/~preds/ P&lt;i&gt;re&lt;/i&gt;D&lt;i&gt;s&lt;/i&gt;] (Prediction of DNA-binding site)
* [http://pre-s.protein.osaka-u.ac.jp/~prebi/ PreBI] (Prediction of biological interface of proteins homo-interface)
* [http://pre-s.protein.osaka-u.ac.jp/~preds classPPI] (Classification of homo protein-protein interfaces)
&lt;br /&gt;
* [http://p-cats.hgc.jp/p-cats/ P-cats] (Prediction of Catalytic residues in proteins)
&lt;br /&gt;
* [http://pdbjs3.protein.osaka-u.ac.jp/xPSSS/index.html xPSSS] (xml-based protein structure search service)
* [http://www.pdbj.org/eprots/index_en.cgi eProtS] (Encyclopedia of protein structures)
* [http://cube.socs.waseda.ac.jp/pages/jsp/index.jsp ProMode] (DB of normal mode analysis of proteins)</text>
    <sha1>e12808180d1ad25168ecdfcff54d51caa9bb9e71</sha1>
  </revision>
  <revision>
    <id>368</id>
    <parentid>367</parentid>
    <timestamp>2010-05-26T02:40:25Z</timestamp>
    <contributor>
      <username>Cudo29</username>
      <id>5</id>
    </contributor>
    <comment>/* DBs */ The item of xPSSS was replaced to PDBj Mine.</comment>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="1241" xml:space="preserve">== Organization ==
* [http://www-bird.jst.go.jp/index_e.html JST-BIRD]
* [http://www.hgc.jp/english/ Human Genome Center]
* [http://www.protein.osaka-u.ac.jp/home_e/index_e.html Institute for Protein Research]
&lt;br /&gt;

== DBs ==
* [http://ef-site.hgc.jp/eF-site/ eF-site] (DB of electrostatic surface of functional site of proteins)
* [http://ef-site.hgc.jp/eF-seek/ eF-seek] (Prediction of ligand binding site of proteins)
* [http://ef-site.hgc.jp/eF-surf/ eF-surf] (Calculate the molecular surface and electrostatic potential of proteins)
&lt;br /&gt;
* [http://pre-s.protein.osaka-u.ac.jp/~preds/ P&lt;i&gt;re&lt;/i&gt;D&lt;i&gt;s&lt;/i&gt;] (Prediction of DNA-binding site)
* [http://pre-s.protein.osaka-u.ac.jp/~prebi/ PreBI] (Prediction of biological interface of proteins homo-interface)
* [http://pre-s.protein.osaka-u.ac.jp/~preds classPPI] (Classification of homo protein-protein interfaces)
&lt;br /&gt;
* [http://p-cats.hgc.jp/p-cats/ P-cats] (Prediction of Catalytic residues in proteins)
&lt;br /&gt;
* [http://service.pdbj.org/mine/ PDBj Mine] (protein structure search service)
* [http://www.pdbj.org/eprots/index_en.cgi eProtS] (Encyclopedia of protein structures)
* [http://cube.socs.waseda.ac.jp/pages/jsp/index.jsp ProMode] (DB of normal mode analysis of proteins)</text>
    <sha1>9dfe0ed67e8e058dc3ed49fc32a9676216126ceb</sha1>
  </revision>
</page>
<page arvcontinue="20091113083303|354">
  <title>Release note</title>
  <ns>0</ns>
  <id>17</id>
  <revision>
    <id>371</id>
    <parentid>319</parentid>
    <timestamp>2010-07-06T05:53:46Z</timestamp>
    <contributor>
      <username>IMSsato</username>
      <id>4</id>
    </contributor>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="3412" xml:space="preserve">Changes and improvements have been made as follows.

* version 3.1
** The following commands have been added; 'animrange', 'set adjustview', 'show godata', and 'show xps3'.
** The xPSSS expression has been added in order to select a group of atoms.
** Several public methods have been added to the applet so as to append molecule or polygon files after the applet started.
** The applet can send information about mouse-picked atoms to JavaScript.
* version 3.1.1
** Some problems in GUI menu [Options]-[Hetero Atoms] and [Hydrogens] have been fixed.
** Some problems in 'trace' command have been fixed.
* version 3.1.2
** eF-site ID has been changed to a new format.
* version 3.1.3
** Some problems in xps3 atom selection have been fixed.
* version 3.1.4
** Some problems in finalization process of openGL rendering have been fixed.
* version 3.1.5
** The output of 'show xps3' command has been modified.
** Some problems in 'save png/jpeg' command have been fixed.
* version 3.1.6
** Some problems in loading an empty polygon file have been fixed.
* version 3.1.7
** Some problems in initialization process of the applet have been fixed.
* version 3.2
** 'show site' command has been added.
* version 3.3 beta 1
** Availabe JOGL version is restricted to JSR-231 beta 5 only.
* version 3.3
** Both the previous JOGL (version 1.1.1) and JSR-231 are available.
** The following commands have been added; 'set viewpoint', 'show viewpoint', 'set imagesize', and 'show imagesize'.
* version 3.3.1
** Some problems in reading a pdbMLplus file have been fixed.
* version 3.4
** PDB format version 3 can be processed.
* version 3.5
** Discrimination of DNA and RNA linking nucleotides is based on [http://remediation.wwpdb.org/downloads.html Chemical Component Dictionary] for PDB format version 3.
** The default representation of the cartoon model has been changed. Commands 'set cartoon_loop_tube', 'set cartoon_round' and 'set ribbonback' have been added.
** The default parameters of lighting have been changed. Commands 'set ambient', 'set diffuse1', 'set diffuse1_direction', 'set diffuse2' and 'set diffuse1_direction' have been added.
** Commands 'set pdbml_noatom_url', 'set pdbml_extatom_url', 'set pdbml_plus_url', 'set efsite_url', 'set ext_site_url', 'show pdbml_url', 'show efsite_url' and 'show ext_site_url' have been added.
** The command-line option '-stdin' has been added to receive commands from stdin stream.
* version 3.6
** Users can specify the JavaScript function name used in Applet-to-JavaScript Communication.
** Applet parameter 'file_load_message' has been added.
* version 3.6.1
** Predefined set of residues has been modified.
** Old JOGL API is not supported.
* version 3.6.2
** Latest version of PDBML can be processed.
** Some problems in mouse control on Mac have been fixed.
* version 3.6.3
** Molecule file parsing has been modified to detect chain breaks properly by reading the 'label_asym_id' column in PDBML and the TER line in PDB flat file, respectively.
* version 3.6.4
** Some problems in GUI menu on Mac have been fixed.
* version 3.6.5
** The jV applet can invoke a JavaScript function when it started.
* version 3.7
** Commands 'pdbj_describe' and 'pdbj_execute' have been added.
** Keyword 'xps3' have been replaced by 'pdbj'.
* version 3.7.1
** Default PDBML URLs have been changed.
* version 3.7.2
** Some problems in creating png/jpeg image files have been fixed.</text>
    <sha1>dd149e89eb94b935a1336f5751d06a8dee6ff060</sha1>
  </revision>
  <revision>
    <id>376</id>
    <parentid>371</parentid>
    <timestamp>2010-07-13T04:00:14Z</timestamp>
    <contributor>
      <username>IMSsato</username>
      <id>4</id>
    </contributor>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="3522" xml:space="preserve">Changes and improvements have been made as follows.

* version 3.1
** The following commands have been added; 'animrange', 'set adjustview', 'show godata', and 'show xps3'.
** The xPSSS expression has been added in order to select a group of atoms.
** Several public methods have been added to the applet so as to append molecule or polygon files after the applet started.
** The applet can send information about mouse-picked atoms to JavaScript.
* version 3.1.1
** Some problems in GUI menu [Options]-[Hetero Atoms] and [Hydrogens] have been fixed.
** Some problems in 'trace' command have been fixed.
* version 3.1.2
** eF-site ID has been changed to a new format.
* version 3.1.3
** Some problems in xps3 atom selection have been fixed.
* version 3.1.4
** Some problems in finalization process of openGL rendering have been fixed.
* version 3.1.5
** The output of 'show xps3' command has been modified.
** Some problems in 'save png/jpeg' command have been fixed.
* version 3.1.6
** Some problems in loading an empty polygon file have been fixed.
* version 3.1.7
** Some problems in initialization process of the applet have been fixed.
* version 3.2
** 'show site' command has been added.
* version 3.3 beta 1
** Availabe JOGL version is restricted to JSR-231 beta 5 only.
* version 3.3
** Both the previous JOGL (version 1.1.1) and JSR-231 are available.
** The following commands have been added; 'set viewpoint', 'show viewpoint', 'set imagesize', and 'show imagesize'.
* version 3.3.1
** Some problems in reading a pdbMLplus file have been fixed.
* version 3.4
** PDB format version 3 can be processed.
* version 3.5
** Discrimination of DNA and RNA linking nucleotides is based on [http://remediation.wwpdb.org/downloads.html Chemical Component Dictionary] for PDB format version 3.
** The default representation of the cartoon model has been changed. Commands 'set cartoon_loop_tube', 'set cartoon_round' and 'set ribbonback' have been added.
** The default parameters of lighting have been changed. Commands 'set ambient', 'set diffuse1', 'set diffuse1_direction', 'set diffuse2' and 'set diffuse1_direction' have been added.
** Commands 'set pdbml_noatom_url', 'set pdbml_extatom_url', 'set pdbml_plus_url', 'set efsite_url', 'set ext_site_url', 'show pdbml_url', 'show efsite_url' and 'show ext_site_url' have been added.
** The command-line option '-stdin' has been added to receive commands from stdin stream.
* version 3.6
** Users can specify the JavaScript function name used in Applet-to-JavaScript Communication.
** Applet parameter 'file_load_message' has been added.
* version 3.6.1
** Predefined set of residues has been modified.
** Old JOGL API is not supported.
* version 3.6.2
** Latest version of PDBML can be processed.
** Some problems in mouse control on Mac have been fixed.
* version 3.6.3
** Molecule file parsing has been modified to detect chain breaks properly by reading the 'label_asym_id' column in PDBML and the TER line in PDB flat file, respectively.
* version 3.6.4
** Some problems in GUI menu on Mac have been fixed.
* version 3.6.5
** The jV applet can invoke a JavaScript function when it started.
* version 3.7
** Commands 'pdbj_describe' and 'pdbj_execute' have been added.
** Keyword 'xps3' have been replaced by 'pdbj'.
* version 3.7.1
** Default PDBML URLs have been changed.
* version 3.7.2
** Some problems in creating png/jpeg image files have been fixed.
* version 3.8
** Command 'displayatom' has been added.
** The signed jV applet can save PNG/JPEG image files.</text>
    <sha1>2b1bc389e75ceb3c71c0228856bfdd186cc41b3f</sha1>
  </revision>
</page>
<page arvcontinue="20091113083303|354">
  <title>How to use</title>
  <ns>0</ns>
  <id>11</id>
  <revision>
    <id>381</id>
    <parentid>353</parentid>
    <timestamp>2010-07-14T01:53:44Z</timestamp>
    <contributor>
      <username>Cudo29</username>
      <id>5</id>
    </contributor>
    <minor/>
    <comment>Each item was divided into chapter.</comment>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="1092" xml:space="preserve">The following table shows how to do the minimum things with jV; the mouse controls.
For the detail, see the reference manual and User's guide.&lt;br /&gt;
{| class="wikitable" border="1" style="margin:0 auto" 
 ! Action !! Window, Linux !! Mac OS X 
 |-
 ! style="text-align:left" | rotate around X,Y axes
 | left drag || drag
 |-
 ! style="text-align:left" | rotate around Z axis
 | Shift + right drag || Shift + command + drag
 |-
 ! style="text-align:left" | translate along X,Y axes
 | right drag || command + drag
 |-
 ! style="text-align:left" | translate along Z axis (zoom in/out)
 | Shift + left drag || Shift + drag
 |-
 ! style="text-align:left" | translate slab plane along Z axis
 | (Alt or Ctrl) + left drag || Alt + drag
 |}


== Reference manual ==
# [[Introduction]]
# [[Command List]]
# [[Atom Expression]]
# [[Vertex Expression]]
# [[Color Expression]]
# [[Use as Applet]]


== User's Guide ==
# [[Tutorials]]
# [[GUI]]
# [[Document type of the polygon file]]
# [[Functional site information for molecules]]


== Some examples ==
# [[Animation]]
# [[Use jV with applet launcher]]</text>
    <sha1>0075a9aa6ebdc72d3d48a2583c77a0ac5f4211b3</sha1>
  </revision>
  <revision>
    <id>382</id>
    <parentid>381</parentid>
    <timestamp>2010-07-14T01:59:59Z</timestamp>
    <contributor>
      <username>Cudo29</username>
      <id>5</id>
    </contributor>
    <comment>/* Some examples */ An item [[Basic examples]] was added.</comment>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="1113" xml:space="preserve">The following table shows how to do the minimum things with jV; the mouse controls.
For the detail, see the reference manual and User's guide.&lt;br /&gt;
{| class="wikitable" border="1" style="margin:0 auto" 
 ! Action !! Window, Linux !! Mac OS X 
 |-
 ! style="text-align:left" | rotate around X,Y axes
 | left drag || drag
 |-
 ! style="text-align:left" | rotate around Z axis
 | Shift + right drag || Shift + command + drag
 |-
 ! style="text-align:left" | translate along X,Y axes
 | right drag || command + drag
 |-
 ! style="text-align:left" | translate along Z axis (zoom in/out)
 | Shift + left drag || Shift + drag
 |-
 ! style="text-align:left" | translate slab plane along Z axis
 | (Alt or Ctrl) + left drag || Alt + drag
 |}


== Reference manual ==
# [[Introduction]]
# [[Command List]]
# [[Atom Expression]]
# [[Vertex Expression]]
# [[Color Expression]]
# [[Use as Applet]]


== User's Guide ==
# [[Tutorials]]
# [[GUI]]
# [[Document type of the polygon file]]
# [[Functional site information for molecules]]


== Some examples ==
# [[Basic examples]]
# [[Animation]]
# [[Use jV with applet launcher]]</text>
    <sha1>d01d3e6b256c691a7959f66ccac0129e8ca077d5</sha1>
  </revision>
</page>
<page arvcontinue="20091113083303|354">
  <title>File:1smd backbone01.jpg</title>
  <ns>6</ns>
  <id>49</id>
  <revision>
    <id>383</id>
    <timestamp>2010-07-14T02:21:26Z</timestamp>
    <contributor>
      <username>Cudo29</username>
      <id>5</id>
    </contributor>
    <comment>Amylase from PDB:1smd, expressed in backbone expression. Created with jV.</comment>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="73" xml:space="preserve">Amylase from PDB:1smd, expressed in backbone expression. Created with jV.</text>
    <sha1>b2a8e2db323db905cb966ae3c7f7ff736e92ac82</sha1>
  </revision>
</page>
<page arvcontinue="20091113083303|354">
  <title>File:1smd backbone02.png</title>
  <ns>6</ns>
  <id>50</id>
  <revision>
    <id>384</id>
    <timestamp>2010-07-14T02:26:04Z</timestamp>
    <contributor>
      <username>Cudo29</username>
      <id>5</id>
    </contributor>
    <comment>Amylase from PDB:1smd, expressed in backbone expression. Created with jV. The residues between from 91 to 103 were emphasized.</comment>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="126" xml:space="preserve">Amylase from PDB:1smd, expressed in backbone expression. Created with jV. The residues between from 91 to 103 were emphasized.</text>
    <sha1>bb60e5f86b41d2b502992e6c310621a3b2d88ec6</sha1>
  </revision>
  <revision>
    <id>385</id>
    <parentid>384</parentid>
    <timestamp>2010-07-14T02:42:48Z</timestamp>
    <contributor>
      <username>Cudo29</username>
      <id>5</id>
    </contributor>
    <comment>uploaded a new version of "[[File:1smd backbone02.png]]":&amp;#32;The margin was deleted.</comment>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="126" xml:space="preserve">Amylase from PDB:1smd, expressed in backbone expression. Created with jV. The residues between from 91 to 103 were emphasized.</text>
    <sha1>bb60e5f86b41d2b502992e6c310621a3b2d88ec6</sha1>
  </revision>
</page>
<page arvcontinue="20091113083303|354">
  <title>Basic examples</title>
  <ns>0</ns>
  <id>51</id>
  <revision>
    <id>386</id>
    <timestamp>2010-07-14T02:48:32Z</timestamp>
    <contributor>
      <username>Cudo29</username>
      <id>5</id>
    </contributor>
    <comment>An example was added.</comment>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="1612" xml:space="preserve">== Changing display format ==
{| style="border:0;border-collapse:collapse"
|-
| style="border:0;padding:0 1em 0 0.5em;font-family:monospace" | load ftp 1smd
| style="border:0;padding:0 0.5em 0 1em" | Load the structure file.
|-
| style="border:0;padding:0 1em 0 0.5em;font-family:monospace" | select all
| style="border:0;padding:0 0.5em 0 1em" | Select the whole of the molecule.
|-
| style="border:0;padding:0 1em 0 0.5em" | [Dsiplay]-[Backbone]
| style="border:0;padding:0 0.5em 0 1em" | Change the format to backbone expression.
|-
| style="border:0;padding:0 1em 0 0.5em" | 
| style="border:0;padding:0 0.5em 0 1em" | [[Image:1smd backbone01.jpg|Amylase from PDB:1smd in backbone expression]]
|-
| style="border:0;padding:0 1em 0 0.5em;font-family:monospace" | select 91-103
| style="border:0;padding:0 0.5em 0 1em" | Select the residues from 91 to 103 of each chain (actually this entry has only one chain).
|-
| style="border:0;padding:0 1em 0 0.5em;font-family:monospace" | color red
| style="border:0;padding:0 0.5em 0 1em" | Change the color of the selected atoms to red.
|-
| style="border:0;padding:0 1em 0 0.5em;font-family:monospace" | backbone 1.0
| style="border:0;padding:0 0.5em 0 1em" | Change the backbone thickness (radius) of the selected atoms to 1.0 angstrom.
|-
| style="border:0;padding:0 1em 0 0.5em" | 
| style="border:0;padding:0 0.5em 0 1em" | [[Image:1smd backbone02.png|Amylase from PDB:1smd in backbone expression with the region between 91 and 103 residues are emphasized.]]
|}

* Similar example in Japanese is available from [http://www.pdbj.org/jv/manual/ex001_ja.html here].</text>
    <sha1>e6e1f017792bd5824bb459936f9a9f7491f4264b</sha1>
  </revision>
  <revision>
    <id>391</id>
    <parentid>386</parentid>
    <timestamp>2010-07-14T03:14:46Z</timestamp>
    <contributor>
      <username>Cudo29</username>
      <id>5</id>
    </contributor>
    <comment>An example was added. Some of description such as typo was edited. The index was forced to display.</comment>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="4070" xml:space="preserve">__TOC__
== Changing Display Format ==
{| style="border:0;border-collapse:collapse"
|-
| style="border:0;padding:0 1em 0 0.5em;font-family:monospace" | load ftp 1smd
| style="border:0;padding:0 0.5em 0 1em" | Load the structure file.
|-
| style="border:0;padding:0 1em 0 0.5em;font-family:monospace" | select all
| style="border:0;padding:0 0.5em 0 1em" | Select the whole of the molecule (in fact, this procedure is not necessary, because all the atoms are already selected just after the file is loaded).
|-
| style="border:0;padding:0 1em 0 0.5em" | [Display]-[Backbone]
| style="border:0;padding:0 0.5em 0 1em" | Change the format to backbone expression.
|-
| style="border:0;padding:0 1em 0 0.5em" | 
| style="border:0;padding:0 0.5em 0 1em" | [[Image:1smd backbone01.jpg|Amylase from PDB:1smd in backbone expression]]
|-
| style="border:0;padding:0 1em 0 0.5em;font-family:monospace" | select 91-103
| style="border:0;padding:0 0.5em 0 1em" | Select the residues from 91 to 103 of each chain (actually this entry has only one chain).
|-
| style="border:0;padding:0 1em 0 0.5em;font-family:monospace" | color red
| style="border:0;padding:0 0.5em 0 1em" | Change the color of the selected atoms to red.
|-
| style="border:0;padding:0 1em 0 0.5em;font-family:monospace" | backbone 1.0
| style="border:0;padding:0 0.5em 0 1em" | Change the backbone thickness (radius) of the selected atoms to 1.0 angstrom.
|-
| style="border:0;padding:0 1em 0 0.5em" | 
| style="border:0;padding:0 0.5em 0 1em" | [[Image:1smd backbone02.png|Amylase from PDB:1smd in backbone expression with the region between 91 and 103 residues are emphasized.]]
|}

* Similar example in Japanese is available from [http://www.pdbj.org/jv/manual/ex001_ja.html here].

== Moving the Rotation Center ==
{| style="border:0;border-collapse:collapse"
|-
| style="border:0;padding:0 1em 0 0.5em;font-family:monospace" | load ftp 1zcd
| style="border:0;padding:0 0.5em 0 1em" | Load the structure file.
|-
| style="border:0;padding:0 1em 0 0.5em" | 
| style="border:0;padding:0 0.5em 0 1em" | [[Image:JV_center01.png‎|Na(+)/H(+) antiporter 1 from PDB:1zcd.]]
|-
| style="border:0;padding:0 1em 0 0.5em;font-family:monospace" | select all
| style="border:0;padding:0 0.5em 0 1em" | Select the whole of the molecule (in fact, this procedure is not necessary, because all the atoms are already selected just after the file is loaded).
|-
| style="border:0;padding:0 1em 0 0.5em;font-family:monospace" | wireframe off
| style="border:0;padding:0 0.5em 0 1em" | Turn off the wireframe expression of the selected region.
|-
| style="border:0;padding:0 1em 0 0.5em" | 
| style="border:0;padding:0 0.5em 0 1em" | [[Image:JV_center02.png‎|Na(+)/H(+) antiporter 1 from PDB:1zcd. All display of the atoms are turned off.]]
|-
| style="border:0;padding:0 1em 0 0.5em;font-family:monospace" | select *:a
| style="border:0;padding:0 0.5em 0 1em" | Select all the atoms in chain a.
|-
| style="border:0;padding:0 1em 0 0.5em" | [Display]-[Cartoon]
| style="border:0;padding:0 0.5em 0 1em" | Change the format to cartoon expression.
|-
| style="border:0;padding:0 1em 0 0.5em" | 
| style="border:0;padding:0 0.5em 0 1em" | [[Image:JV_center03.png‎|Na(+)/H(+) antiporter 1 from PDB:1zcd. Only the chain A is displayed.]]
|-
| style="border:0;padding:0 1em 0 0.5em" |
| style="border:0;padding:0 0.5em 0 1em" | * In this state, it is not convenient to move the molecule, because the rotation axis doesn't exist at the center of displayed region. To solve it, the following command should be execute.
|-
| style="border:0;padding:0 1em 0 0.5em;font-family:monospace" | center *:a
| style="border:0;padding:0 0.5em 0 1em" | Move the rotation axis and the position of molecule to the center of display area.
|-
| style="border:0;padding:0 1em 0 0.5em" | 
| style="border:0;padding:0 0.5em 0 1em" | [[Image:JV_center04.png‎|Na(+)/H(+) antiporter 1 from PDB:1zcd. Only the chain A is displayed. Moved to the center.]]
|}

* Similar example in Japanese is available from [http://www.pdbj.org/jv/manual/ex003_ja.html here].</text>
    <sha1>eed5ca588c0de61594a456768f4072bb3e8e690d</sha1>
  </revision>
  <revision>
    <id>396</id>
    <parentid>391</parentid>
    <timestamp>2010-07-14T05:04:30Z</timestamp>
    <contributor>
      <username>Cudo29</username>
      <id>5</id>
    </contributor>
    <comment>An example was added.</comment>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="6310" xml:space="preserve">__TOC__
== Changing Display Format ==
{| style="border:0;border-collapse:collapse"
|-
| style="border:0;padding:0 1em 0 0.5em;font-family:monospace" | load ftp 1smd
| style="border:0;padding:0 0.5em 0 1em" | Load the structure file.
|-
| style="border:0;padding:0 1em 0 0.5em;font-family:monospace" | select all
| style="border:0;padding:0 0.5em 0 1em" | Select the whole of the molecule (in fact, this procedure is not necessary, because all the atoms are already selected just after the file is loaded).
|-
| style="border:0;padding:0 1em 0 0.5em" | [Display]-[Backbone]
| style="border:0;padding:0 0.5em 0 1em" | Change the format to backbone expression.
|-
| style="border:0;padding:0 1em 0 0.5em" | 
| style="border:0;padding:0 0.5em 0 1em" | [[Image:1smd backbone01.jpg|Amylase from PDB:1smd in backbone expression]]
|-
| style="border:0;padding:0 1em 0 0.5em;font-family:monospace" | select 91-103
| style="border:0;padding:0 0.5em 0 1em" | Select the residues from 91 to 103 of each chain (actually this entry has only one chain).
|-
| style="border:0;padding:0 1em 0 0.5em;font-family:monospace" | color red
| style="border:0;padding:0 0.5em 0 1em" | Change the color of the selected atoms to red.
|-
| style="border:0;padding:0 1em 0 0.5em;font-family:monospace" | backbone 1.0
| style="border:0;padding:0 0.5em 0 1em" | Change the backbone thickness (radius) of the selected atoms to 1.0 angstrom.
|-
| style="border:0;padding:0 1em 0 0.5em" | 
| style="border:0;padding:0 0.5em 0 1em" | [[Image:1smd backbone02.png|Amylase from PDB:1smd in backbone expression with the region between 91 and 103 residues are emphasized.]]
|}

* Similar example in Japanese is available from [http://www.pdbj.org/jv/manual/ex001_ja.html here].

== Moving the Rotation Center ==
{| style="border:0;border-collapse:collapse"
|-
| style="border:0;padding:0 1em 0 0.5em;font-family:monospace" | load ftp 1zcd
| style="border:0;padding:0 0.5em 0 1em" | Load the structure file.
|-
| style="border:0;padding:0 1em 0 0.5em" | 
| style="border:0;padding:0 0.5em 0 1em" | [[Image:JV_center01.png‎|Na(+)/H(+) antiporter 1 from PDB:1zcd.]]
|-
| style="border:0;padding:0 1em 0 0.5em;font-family:monospace" | select all
| style="border:0;padding:0 0.5em 0 1em" | Select the whole of the molecule (in fact, this procedure is not necessary, because all the atoms are already selected just after the file is loaded).
|-
| style="border:0;padding:0 1em 0 0.5em;font-family:monospace" | wireframe off
| style="border:0;padding:0 0.5em 0 1em" | Turn off the wireframe expression of the selected region.
|-
| style="border:0;padding:0 1em 0 0.5em" | 
| style="border:0;padding:0 0.5em 0 1em" | [[Image:JV_center02.png‎|Na(+)/H(+) antiporter 1 from PDB:1zcd. All display of the atoms are turned off.]]
|-
| style="border:0;padding:0 1em 0 0.5em;font-family:monospace" | select *:a
| style="border:0;padding:0 0.5em 0 1em" | Select all the atoms in chain a.
|-
| style="border:0;padding:0 1em 0 0.5em" | [Display]-[Cartoon]
| style="border:0;padding:0 0.5em 0 1em" | Change the format to cartoon expression.
|-
| style="border:0;padding:0 1em 0 0.5em" | 
| style="border:0;padding:0 0.5em 0 1em" | [[Image:JV_center03.png‎|Na(+)/H(+) antiporter 1 from PDB:1zcd. Only the chain A is displayed.]]
|-
| style="border:0;padding:0 1em 0 0.5em" |
| style="border:0;padding:0 0.5em 0 1em" | * In this state, it is not convenient to move the molecule, because the rotation axis doesn't exist at the center of displayed region. To solve it, the following command should be execute.
|-
| style="border:0;padding:0 1em 0 0.5em;font-family:monospace" | center *:a
| style="border:0;padding:0 0.5em 0 1em" | Move the rotation axis and the position of molecule to the center of display area.
|-
| style="border:0;padding:0 1em 0 0.5em" | 
| style="border:0;padding:0 0.5em 0 1em" | [[Image:JV_center04.png‎|Na(+)/H(+) antiporter 1 from PDB:1zcd. Only the chain A is displayed. Moved to the center.]]
|}

* Similar example in Japanese is available from [http://www.pdbj.org/jv/manual/ex003_ja.html here].

== Selecting Atom ==
{| style="border:0;border-collapse:collapse"
|-
| style="border:0;padding:0 1em 0 0.5em;font-family:monospace" | load ftp 1mbn
| style="border:0;padding:0 0.5em 0 1em" | Load the structure file.
|-
| style="border:0;padding:0 1em 0 0.5em" | 
| style="border:0;padding:0 0.5em 0 1em" | [[Image:1mbn_01.png‎|Myoglobin from PDB:1mbn.]]
|-
| style="border:0;padding:0 1em 0 0.5em;font-family:monospace" | select hem
| style="border:0;padding:0 0.5em 0 1em" | Select the heme group of this molecule.
|-
| style="border:0;padding:0 1em 0 0.5em" | [Display]-[Ball&amp;Stick]
| style="border:0;padding:0 0.5em 0 1em" | Change the format to ball and stick expression.
|-
| style="border:0;padding:0 1em 0 0.5em" | 
| style="border:0;padding:0 0.5em 0 1em" | [[Image:1mbn_02.png‎|Myoglobin from PDB:1mbn.The expression of the heme group was changed to ball and stick.]]
|-
| style="border:0;padding:0 1em 0 0.5em;font-family:monospace" | select iron
| style="border:0;padding:0 0.5em 0 1em" | Select the iron atom. The same procedure can be execute by the command "&lt;code&gt;select elemno=26&lt;/code&gt;".
|-
| style="border:0;padding:0 1em 0 0.5em;font-family:monospace" | cpk
| style="border:0;padding:0 0.5em 0 1em" | The expression of the selected atom turned to spacefill expression.
|-
| style="border:0;padding:0 1em 0 0.5em" | 
| style="border:0;padding:0 0.5em 0 1em" | [[Image:1mbn_03.png‎|The expression of the heme group was changed to the ball and stick, and that of iron atom was changed to the spacefill.]]
|-
| style="border:0;padding:0 1em 0 0.5em;font-family:monospace" | select atomno=1217
| style="border:0;padding:0 0.5em 0 1em" | Select the atom with its atom number is 1217 (oxygen).
|-
| style="border:0;padding:0 1em 0 0.5em" | 
| style="border:0;padding:0 0.5em 0 1em" | [[Image:1mbn_04.png‎|Myoglobin from PDB:1mbn.The expression of the heme group was changed to the ball and stick, and those of iron atom and the neighbor oxygen atom were changed to the spacefill.]]
|}

* The atom number is included in the value of the id attribute of "PDBx:atom_siteCategory/PDBx:atom_site" element in each PDBML file.
* Similar example in Japanese is available from [http://www.pdbj.org/jv/manual/ex017_ja.html here].</text>
    <sha1>90d28f7f97258cb3dfb6e34088ba91909c8e8755</sha1>
  </revision>
  <revision>
    <id>397</id>
    <parentid>396</parentid>
    <timestamp>2010-07-14T05:14:32Z</timestamp>
    <contributor>
      <username>Cudo29</username>
      <id>5</id>
    </contributor>
    <comment>/* Changing Display Format */ Some links to the command explanation were added.</comment>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="6605" xml:space="preserve">__TOC__
== Changing Display Format ==
{| style="border:0;border-collapse:collapse"
|-
| style="border:0;padding:0 1em 0 0.5em;font-family:monospace" | load ftp 1smd
| style="border:0;padding:0 0.5em 0 1em" | Load the structure file (click [[Command_List#load|here]] to see the detail of "load" command).
|-
| style="border:0;padding:0 1em 0 0.5em;font-family:monospace" | select all
| style="border:0;padding:0 0.5em 0 1em" | Select the whole of the molecule (in fact, this procedure is not necessary, because all the atoms are already selected just after the file is loaded). To see the detail of "select" command, click [[Command_List#select|here]].
|-
| style="border:0;padding:0 1em 0 0.5em" | [Display]-[Backbone]
| style="border:0;padding:0 0.5em 0 1em" | Change the format to backbone expression.
|-
| style="border:0;padding:0 1em 0 0.5em" | 
| style="border:0;padding:0 0.5em 0 1em" | [[Image:1smd backbone01.jpg|Amylase from PDB:1smd in backbone expression]]
|-
| style="border:0;padding:0 1em 0 0.5em;font-family:monospace" | select 91-103
| style="border:0;padding:0 0.5em 0 1em" | Select the residues from 91 to 103 of each chain (actually this entry has only one chain).
|-
| style="border:0;padding:0 1em 0 0.5em;font-family:monospace" | color red
| style="border:0;padding:0 0.5em 0 1em" | Change the color of the selected atoms to red (click [[Command_List#color|here]] to see the detail of "color" command).
|-
| style="border:0;padding:0 1em 0 0.5em;font-family:monospace" | backbone 1.0
| style="border:0;padding:0 0.5em 0 1em" | Change the backbone thickness (radius) of the selected atoms to 1.0 angstrom (click [[Command_List#color|here]] to see the detail of "backbone" command).
|-
| style="border:0;padding:0 1em 0 0.5em" | 
| style="border:0;padding:0 0.5em 0 1em" | [[Image:1smd backbone02.png|Amylase from PDB:1smd in backbone expression with the region between 91 and 103 residues are emphasized.]]
|}

* Similar example in Japanese is available from [http://www.pdbj.org/jv/manual/ex001_ja.html here].

== Moving the Rotation Center ==
{| style="border:0;border-collapse:collapse"
|-
| style="border:0;padding:0 1em 0 0.5em;font-family:monospace" | load ftp 1zcd
| style="border:0;padding:0 0.5em 0 1em" | Load the structure file.
|-
| style="border:0;padding:0 1em 0 0.5em" | 
| style="border:0;padding:0 0.5em 0 1em" | [[Image:JV_center01.png‎|Na(+)/H(+) antiporter 1 from PDB:1zcd.]]
|-
| style="border:0;padding:0 1em 0 0.5em;font-family:monospace" | select all
| style="border:0;padding:0 0.5em 0 1em" | Select the whole of the molecule (in fact, this procedure is not necessary, because all the atoms are already selected just after the file is loaded).
|-
| style="border:0;padding:0 1em 0 0.5em;font-family:monospace" | wireframe off
| style="border:0;padding:0 0.5em 0 1em" | Turn off the wireframe expression of the selected region.
|-
| style="border:0;padding:0 1em 0 0.5em" | 
| style="border:0;padding:0 0.5em 0 1em" | [[Image:JV_center02.png‎|Na(+)/H(+) antiporter 1 from PDB:1zcd. All display of the atoms are turned off.]]
|-
| style="border:0;padding:0 1em 0 0.5em;font-family:monospace" | select *:a
| style="border:0;padding:0 0.5em 0 1em" | Select all the atoms in chain a.
|-
| style="border:0;padding:0 1em 0 0.5em" | [Display]-[Cartoon]
| style="border:0;padding:0 0.5em 0 1em" | Change the format to cartoon expression.
|-
| style="border:0;padding:0 1em 0 0.5em" | 
| style="border:0;padding:0 0.5em 0 1em" | [[Image:JV_center03.png‎|Na(+)/H(+) antiporter 1 from PDB:1zcd. Only the chain A is displayed.]]
|-
| style="border:0;padding:0 1em 0 0.5em" |
| style="border:0;padding:0 0.5em 0 1em" | * In this state, it is not convenient to move the molecule, because the rotation axis doesn't exist at the center of displayed region. To solve it, the following command should be execute.
|-
| style="border:0;padding:0 1em 0 0.5em;font-family:monospace" | center *:a
| style="border:0;padding:0 0.5em 0 1em" | Move the rotation axis and the position of molecule to the center of display area.
|-
| style="border:0;padding:0 1em 0 0.5em" | 
| style="border:0;padding:0 0.5em 0 1em" | [[Image:JV_center04.png‎|Na(+)/H(+) antiporter 1 from PDB:1zcd. Only the chain A is displayed. Moved to the center.]]
|}

* Similar example in Japanese is available from [http://www.pdbj.org/jv/manual/ex003_ja.html here].

== Selecting Atom ==
{| style="border:0;border-collapse:collapse"
|-
| style="border:0;padding:0 1em 0 0.5em;font-family:monospace" | load ftp 1mbn
| style="border:0;padding:0 0.5em 0 1em" | Load the structure file.
|-
| style="border:0;padding:0 1em 0 0.5em" | 
| style="border:0;padding:0 0.5em 0 1em" | [[Image:1mbn_01.png‎|Myoglobin from PDB:1mbn.]]
|-
| style="border:0;padding:0 1em 0 0.5em;font-family:monospace" | select hem
| style="border:0;padding:0 0.5em 0 1em" | Select the heme group of this molecule.
|-
| style="border:0;padding:0 1em 0 0.5em" | [Display]-[Ball&amp;Stick]
| style="border:0;padding:0 0.5em 0 1em" | Change the format to ball and stick expression.
|-
| style="border:0;padding:0 1em 0 0.5em" | 
| style="border:0;padding:0 0.5em 0 1em" | [[Image:1mbn_02.png‎|Myoglobin from PDB:1mbn.The expression of the heme group was changed to ball and stick.]]
|-
| style="border:0;padding:0 1em 0 0.5em;font-family:monospace" | select iron
| style="border:0;padding:0 0.5em 0 1em" | Select the iron atom. The same procedure can be execute by the command "&lt;code&gt;select elemno=26&lt;/code&gt;".
|-
| style="border:0;padding:0 1em 0 0.5em;font-family:monospace" | cpk
| style="border:0;padding:0 0.5em 0 1em" | The expression of the selected atom turned to spacefill expression.
|-
| style="border:0;padding:0 1em 0 0.5em" | 
| style="border:0;padding:0 0.5em 0 1em" | [[Image:1mbn_03.png‎|The expression of the heme group was changed to the ball and stick, and that of iron atom was changed to the spacefill.]]
|-
| style="border:0;padding:0 1em 0 0.5em;font-family:monospace" | select atomno=1217
| style="border:0;padding:0 0.5em 0 1em" | Select the atom with its atom number is 1217 (oxygen).
|-
| style="border:0;padding:0 1em 0 0.5em" | 
| style="border:0;padding:0 0.5em 0 1em" | [[Image:1mbn_04.png‎|Myoglobin from PDB:1mbn.The expression of the heme group was changed to the ball and stick, and those of iron atom and the neighbor oxygen atom were changed to the spacefill.]]
|}

* The atom number is included in the value of the id attribute of "PDBx:atom_siteCategory/PDBx:atom_site" element in each PDBML file.
* Similar example in Japanese is available from [http://www.pdbj.org/jv/manual/ex017_ja.html here].</text>
    <sha1>562aad16ad35a0e17614d4bb7a3a3753127dfd49</sha1>
  </revision>
  <revision>
    <id>398</id>
    <parentid>397</parentid>
    <timestamp>2010-07-14T05:16:58Z</timestamp>
    <contributor>
      <username>Cudo29</username>
      <id>5</id>
    </contributor>
    <comment>/* Moving the Rotation Center */ Some links to the command explanation page were added.</comment>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="6907" xml:space="preserve">__TOC__
== Changing Display Format ==
{| style="border:0;border-collapse:collapse"
|-
| style="border:0;padding:0 1em 0 0.5em;font-family:monospace" | load ftp 1smd
| style="border:0;padding:0 0.5em 0 1em" | Load the structure file (click [[Command_List#load|here]] to see the detail of "load" command).
|-
| style="border:0;padding:0 1em 0 0.5em;font-family:monospace" | select all
| style="border:0;padding:0 0.5em 0 1em" | Select the whole of the molecule (in fact, this procedure is not necessary, because all the atoms are already selected just after the file is loaded). To see the detail of "select" command, click [[Command_List#select|here]].
|-
| style="border:0;padding:0 1em 0 0.5em" | [Display]-[Backbone]
| style="border:0;padding:0 0.5em 0 1em" | Change the format to backbone expression.
|-
| style="border:0;padding:0 1em 0 0.5em" | 
| style="border:0;padding:0 0.5em 0 1em" | [[Image:1smd backbone01.jpg|Amylase from PDB:1smd in backbone expression]]
|-
| style="border:0;padding:0 1em 0 0.5em;font-family:monospace" | select 91-103
| style="border:0;padding:0 0.5em 0 1em" | Select the residues from 91 to 103 of each chain (actually this entry has only one chain).
|-
| style="border:0;padding:0 1em 0 0.5em;font-family:monospace" | color red
| style="border:0;padding:0 0.5em 0 1em" | Change the color of the selected atoms to red (click [[Command_List#color|here]] to see the detail of "color" command).
|-
| style="border:0;padding:0 1em 0 0.5em;font-family:monospace" | backbone 1.0
| style="border:0;padding:0 0.5em 0 1em" | Change the backbone thickness (radius) of the selected atoms to 1.0 angstrom (click [[Command_List#color|here]] to see the detail of "backbone" command).
|-
| style="border:0;padding:0 1em 0 0.5em" | 
| style="border:0;padding:0 0.5em 0 1em" | [[Image:1smd backbone02.png|Amylase from PDB:1smd in backbone expression with the region between 91 and 103 residues are emphasized.]]
|}

* Similar example in Japanese is available from [http://www.pdbj.org/jv/manual/ex001_ja.html here].

== Moving the Rotation Center ==
{| style="border:0;border-collapse:collapse"
|-
| style="border:0;padding:0 1em 0 0.5em;font-family:monospace" | load ftp 1zcd
| style="border:0;padding:0 0.5em 0 1em" | Load the structure file (click [[Command_List#load|here]] to see the detail of "load" command).
|-
| style="border:0;padding:0 1em 0 0.5em" | 
| style="border:0;padding:0 0.5em 0 1em" | [[Image:JV_center01.png‎|Na(+)/H(+) antiporter 1 from PDB:1zcd.]]
|-
| style="border:0;padding:0 1em 0 0.5em;font-family:monospace" | select all
| style="border:0;padding:0 0.5em 0 1em" | Select the whole of the molecule (in fact, this procedure is not necessary, because all the atoms are already selected just after the file is loaded). To see the detail of "select" command, click [[Command_List#select|here]].
|-
| style="border:0;padding:0 1em 0 0.5em;font-family:monospace" | wireframe off
| style="border:0;padding:0 0.5em 0 1em" | Turn off the wireframe expression of the selected region (click [[Command_List#wireframe|here]] to see the detail of "wireframe" command).
|-
| style="border:0;padding:0 1em 0 0.5em" | 
| style="border:0;padding:0 0.5em 0 1em" | [[Image:JV_center02.png‎|Na(+)/H(+) antiporter 1 from PDB:1zcd. All display of the atoms are turned off.]]
|-
| style="border:0;padding:0 1em 0 0.5em;font-family:monospace" | select *:a
| style="border:0;padding:0 0.5em 0 1em" | Select all the atoms in chain a.
|-
| style="border:0;padding:0 1em 0 0.5em" | [Display]-[Cartoon]
| style="border:0;padding:0 0.5em 0 1em" | Change the format to cartoon expression.
|-
| style="border:0;padding:0 1em 0 0.5em" | 
| style="border:0;padding:0 0.5em 0 1em" | [[Image:JV_center03.png‎|Na(+)/H(+) antiporter 1 from PDB:1zcd. Only the chain A is displayed.]]
|-
| style="border:0;padding:0 1em 0 0.5em" |
| style="border:0;padding:0 0.5em 0 1em" | * In this state, it is not convenient to move the molecule, because the rotation axis doesn't exist at the center of displayed region. To solve it, the following command should be execute.
|-
| style="border:0;padding:0 1em 0 0.5em;font-family:monospace" | center *:a
| style="border:0;padding:0 0.5em 0 1em" | Move the rotation axis and the position of molecule to the center of display area (click [[Command_List#center|here]] to see the detail of "center" command).
|-
| style="border:0;padding:0 1em 0 0.5em" | 
| style="border:0;padding:0 0.5em 0 1em" | [[Image:JV_center04.png‎|Na(+)/H(+) antiporter 1 from PDB:1zcd. Only the chain A is displayed. Moved to the center.]]
|}

* Similar example in Japanese is available from [http://www.pdbj.org/jv/manual/ex003_ja.html here].

== Selecting Atom ==
{| style="border:0;border-collapse:collapse"
|-
| style="border:0;padding:0 1em 0 0.5em;font-family:monospace" | load ftp 1mbn
| style="border:0;padding:0 0.5em 0 1em" | Load the structure file.
|-
| style="border:0;padding:0 1em 0 0.5em" | 
| style="border:0;padding:0 0.5em 0 1em" | [[Image:1mbn_01.png‎|Myoglobin from PDB:1mbn.]]
|-
| style="border:0;padding:0 1em 0 0.5em;font-family:monospace" | select hem
| style="border:0;padding:0 0.5em 0 1em" | Select the heme group of this molecule.
|-
| style="border:0;padding:0 1em 0 0.5em" | [Display]-[Ball&amp;Stick]
| style="border:0;padding:0 0.5em 0 1em" | Change the format to ball and stick expression.
|-
| style="border:0;padding:0 1em 0 0.5em" | 
| style="border:0;padding:0 0.5em 0 1em" | [[Image:1mbn_02.png‎|Myoglobin from PDB:1mbn.The expression of the heme group was changed to ball and stick.]]
|-
| style="border:0;padding:0 1em 0 0.5em;font-family:monospace" | select iron
| style="border:0;padding:0 0.5em 0 1em" | Select the iron atom. The same procedure can be execute by the command "&lt;code&gt;select elemno=26&lt;/code&gt;".
|-
| style="border:0;padding:0 1em 0 0.5em;font-family:monospace" | cpk
| style="border:0;padding:0 0.5em 0 1em" | The expression of the selected atom turned to spacefill expression.
|-
| style="border:0;padding:0 1em 0 0.5em" | 
| style="border:0;padding:0 0.5em 0 1em" | [[Image:1mbn_03.png‎|The expression of the heme group was changed to the ball and stick, and that of iron atom was changed to the spacefill.]]
|-
| style="border:0;padding:0 1em 0 0.5em;font-family:monospace" | select atomno=1217
| style="border:0;padding:0 0.5em 0 1em" | Select the atom with its atom number is 1217 (oxygen).
|-
| style="border:0;padding:0 1em 0 0.5em" | 
| style="border:0;padding:0 0.5em 0 1em" | [[Image:1mbn_04.png‎|Myoglobin from PDB:1mbn.The expression of the heme group was changed to the ball and stick, and those of iron atom and the neighbor oxygen atom were changed to the spacefill.]]
|}

* The atom number is included in the value of the id attribute of "PDBx:atom_siteCategory/PDBx:atom_site" element in each PDBML file.
* Similar example in Japanese is available from [http://www.pdbj.org/jv/manual/ex017_ja.html here].</text>
    <sha1>964d595cc200793b650f99bb7e90db0c56c99cce</sha1>
  </revision>
  <revision>
    <id>399</id>
    <parentid>398</parentid>
    <timestamp>2010-07-14T05:19:05Z</timestamp>
    <contributor>
      <username>Cudo29</username>
      <id>5</id>
    </contributor>
    <comment>/* Selecting Atom */ Some links to the command explanation page were added.</comment>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="7157" xml:space="preserve">__TOC__
== Changing Display Format ==
{| style="border:0;border-collapse:collapse"
|-
| style="border:0;padding:0 1em 0 0.5em;font-family:monospace" | load ftp 1smd
| style="border:0;padding:0 0.5em 0 1em" | Load the structure file (click [[Command_List#load|here]] to see the detail of "load" command).
|-
| style="border:0;padding:0 1em 0 0.5em;font-family:monospace" | select all
| style="border:0;padding:0 0.5em 0 1em" | Select the whole of the molecule (in fact, this procedure is not necessary, because all the atoms are already selected just after the file is loaded). To see the detail of "select" command, click [[Command_List#select|here]].
|-
| style="border:0;padding:0 1em 0 0.5em" | [Display]-[Backbone]
| style="border:0;padding:0 0.5em 0 1em" | Change the format to backbone expression.
|-
| style="border:0;padding:0 1em 0 0.5em" | 
| style="border:0;padding:0 0.5em 0 1em" | [[Image:1smd backbone01.jpg|Amylase from PDB:1smd in backbone expression]]
|-
| style="border:0;padding:0 1em 0 0.5em;font-family:monospace" | select 91-103
| style="border:0;padding:0 0.5em 0 1em" | Select the residues from 91 to 103 of each chain (actually this entry has only one chain).
|-
| style="border:0;padding:0 1em 0 0.5em;font-family:monospace" | color red
| style="border:0;padding:0 0.5em 0 1em" | Change the color of the selected atoms to red (click [[Command_List#color|here]] to see the detail of "color" command).
|-
| style="border:0;padding:0 1em 0 0.5em;font-family:monospace" | backbone 1.0
| style="border:0;padding:0 0.5em 0 1em" | Change the backbone thickness (radius) of the selected atoms to 1.0 angstrom (click [[Command_List#color|here]] to see the detail of "backbone" command).
|-
| style="border:0;padding:0 1em 0 0.5em" | 
| style="border:0;padding:0 0.5em 0 1em" | [[Image:1smd backbone02.png|Amylase from PDB:1smd in backbone expression with the region between 91 and 103 residues are emphasized.]]
|}

* Similar example in Japanese is available from [http://www.pdbj.org/jv/manual/ex001_ja.html here].

== Moving the Rotation Center ==
{| style="border:0;border-collapse:collapse"
|-
| style="border:0;padding:0 1em 0 0.5em;font-family:monospace" | load ftp 1zcd
| style="border:0;padding:0 0.5em 0 1em" | Load the structure file (click [[Command_List#load|here]] to see the detail of "load" command).
|-
| style="border:0;padding:0 1em 0 0.5em" | 
| style="border:0;padding:0 0.5em 0 1em" | [[Image:JV_center01.png‎|Na(+)/H(+) antiporter 1 from PDB:1zcd.]]
|-
| style="border:0;padding:0 1em 0 0.5em;font-family:monospace" | select all
| style="border:0;padding:0 0.5em 0 1em" | Select the whole of the molecule (in fact, this procedure is not necessary, because all the atoms are already selected just after the file is loaded). To see the detail of "select" command, click [[Command_List#select|here]].
|-
| style="border:0;padding:0 1em 0 0.5em;font-family:monospace" | wireframe off
| style="border:0;padding:0 0.5em 0 1em" | Turn off the wireframe expression of the selected region (click [[Command_List#wireframe|here]] to see the detail of "wireframe" command).
|-
| style="border:0;padding:0 1em 0 0.5em" | 
| style="border:0;padding:0 0.5em 0 1em" | [[Image:JV_center02.png‎|Na(+)/H(+) antiporter 1 from PDB:1zcd. All display of the atoms are turned off.]]
|-
| style="border:0;padding:0 1em 0 0.5em;font-family:monospace" | select *:a
| style="border:0;padding:0 0.5em 0 1em" | Select all the atoms in chain a.
|-
| style="border:0;padding:0 1em 0 0.5em" | [Display]-[Cartoon]
| style="border:0;padding:0 0.5em 0 1em" | Change the format to cartoon expression.
|-
| style="border:0;padding:0 1em 0 0.5em" | 
| style="border:0;padding:0 0.5em 0 1em" | [[Image:JV_center03.png‎|Na(+)/H(+) antiporter 1 from PDB:1zcd. Only the chain A is displayed.]]
|-
| style="border:0;padding:0 1em 0 0.5em" |
| style="border:0;padding:0 0.5em 0 1em" | * In this state, it is not convenient to move the molecule, because the rotation axis doesn't exist at the center of displayed region. To solve it, the following command should be execute.
|-
| style="border:0;padding:0 1em 0 0.5em;font-family:monospace" | center *:a
| style="border:0;padding:0 0.5em 0 1em" | Move the rotation axis and the position of molecule to the center of display area (click [[Command_List#center|here]] to see the detail of "center" command).
|-
| style="border:0;padding:0 1em 0 0.5em" | 
| style="border:0;padding:0 0.5em 0 1em" | [[Image:JV_center04.png‎|Na(+)/H(+) antiporter 1 from PDB:1zcd. Only the chain A is displayed. Moved to the center.]]
|}

* Similar example in Japanese is available from [http://www.pdbj.org/jv/manual/ex003_ja.html here].

== Selecting Atom ==
{| style="border:0;border-collapse:collapse"
|-
| style="border:0;padding:0 1em 0 0.5em;font-family:monospace" | load ftp 1mbn
| style="border:0;padding:0 0.5em 0 1em" | Load the structure file (click [[Command_List#load|here]] to see the detail of "load" command).
|-
| style="border:0;padding:0 1em 0 0.5em" | 
| style="border:0;padding:0 0.5em 0 1em" | [[Image:1mbn_01.png‎|Myoglobin from PDB:1mbn.]]
|-
| style="border:0;padding:0 1em 0 0.5em;font-family:monospace" | select hem
| style="border:0;padding:0 0.5em 0 1em" | Select the heme group of this molecule (click [[Command_List#select|here]] to see the detail of "select" command).
|-
| style="border:0;padding:0 1em 0 0.5em" | [Display]-[Ball&amp;Stick]
| style="border:0;padding:0 0.5em 0 1em" | Change the format to ball and stick expression.
|-
| style="border:0;padding:0 1em 0 0.5em" | 
| style="border:0;padding:0 0.5em 0 1em" | [[Image:1mbn_02.png‎|Myoglobin from PDB:1mbn.The expression of the heme group was changed to ball and stick.]]
|-
| style="border:0;padding:0 1em 0 0.5em;font-family:monospace" | select iron
| style="border:0;padding:0 0.5em 0 1em" | Select the iron atom. The same procedure can be execute by the command "&lt;code&gt;select elemno=26&lt;/code&gt;".
|-
| style="border:0;padding:0 1em 0 0.5em;font-family:monospace" | cpk
| style="border:0;padding:0 0.5em 0 1em" | The expression of the selected atom turned to spacefill expression (click [[Command_List#spacefill|here]] to see the detail of "cpk" command equal to "spacefill" command).
|-
| style="border:0;padding:0 1em 0 0.5em" | 
| style="border:0;padding:0 0.5em 0 1em" | [[Image:1mbn_03.png‎|The expression of the heme group was changed to the ball and stick, and that of iron atom was changed to the spacefill.]]
|-
| style="border:0;padding:0 1em 0 0.5em;font-family:monospace" | select atomno=1217
| style="border:0;padding:0 0.5em 0 1em" | Select the atom with its atom number is 1217 (oxygen).
|-
| style="border:0;padding:0 1em 0 0.5em" | 
| style="border:0;padding:0 0.5em 0 1em" | [[Image:1mbn_04.png‎|Myoglobin from PDB:1mbn.The expression of the heme group was changed to the ball and stick, and those of iron atom and the neighbor oxygen atom were changed to the spacefill.]]
|}

* The atom number is included in the value of the id attribute of "PDBx:atom_siteCategory/PDBx:atom_site" element in each PDBML file.
* Similar example in Japanese is available from [http://www.pdbj.org/jv/manual/ex017_ja.html here].</text>
    <sha1>44935d4f07a7e15eee563b985320192d62aaba94</sha1>
  </revision>
</page>
<page arvcontinue="20091113083303|354">
  <title>File:JV center01.png</title>
  <ns>6</ns>
  <id>52</id>
  <revision>
    <id>387</id>
    <timestamp>2010-07-14T03:02:18Z</timestamp>
    <contributor>
      <username>Cudo29</username>
      <id>5</id>
    </contributor>
    <comment>Na(+)/H(+) antiporter 1 from PDB:1zcd, created with jV.</comment>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="55" xml:space="preserve">Na(+)/H(+) antiporter 1 from PDB:1zcd, created with jV.</text>
    <sha1>1cea8d50aa44109b8acc064fb839cb5afee89128</sha1>
  </revision>
</page>
<page arvcontinue="20091113083303|354">
  <title>File:JV center02.png</title>
  <ns>6</ns>
  <id>53</id>
  <revision>
    <id>388</id>
    <timestamp>2010-07-14T03:03:04Z</timestamp>
    <contributor>
      <username>Cudo29</username>
      <id>5</id>
    </contributor>
    <comment>Na(+)/H(+) antiporter 1 from PDB:1zcd, created with jV. All display of the atoms are turned off.</comment>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="96" xml:space="preserve">Na(+)/H(+) antiporter 1 from PDB:1zcd, created with jV. All display of the atoms are turned off.</text>
    <sha1>bfaff676a65d727b106c241a5d1ef32ba2f79fe8</sha1>
  </revision>
</page>
<page arvcontinue="20091113083303|354">
  <title>File:JV center03.png</title>
  <ns>6</ns>
  <id>54</id>
  <revision>
    <id>389</id>
    <timestamp>2010-07-14T03:03:48Z</timestamp>
    <contributor>
      <username>Cudo29</username>
      <id>5</id>
    </contributor>
    <comment>Na(+)/H(+) antiporter 1 from PDB:1zcd, created with jV. Only the chain A is displayed.</comment>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="86" xml:space="preserve">Na(+)/H(+) antiporter 1 from PDB:1zcd, created with jV. Only the chain A is displayed.</text>
    <sha1>7b6b1634e55832cb84e9f6c59a119225882c8e08</sha1>
  </revision>
</page>
<page arvcontinue="20091113083303|354">
  <title>File:JV center04.png</title>
  <ns>6</ns>
  <id>55</id>
  <revision>
    <id>390</id>
    <timestamp>2010-07-14T03:04:10Z</timestamp>
    <contributor>
      <username>Cudo29</username>
      <id>5</id>
    </contributor>
    <comment>Na(+)/H(+) antiporter 1 from PDB:1zcd, created with jV. Only the chain A is displayed. Moved to the center.</comment>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="107" xml:space="preserve">Na(+)/H(+) antiporter 1 from PDB:1zcd, created with jV. Only the chain A is displayed. Moved to the center.</text>
    <sha1>e66888c61b357d0361f12b9a422591b5dc187731</sha1>
  </revision>
</page>
<page arvcontinue="20091113083303|354">
  <title>File:1mbn 01.png</title>
  <ns>6</ns>
  <id>56</id>
  <revision>
    <id>392</id>
    <timestamp>2010-07-14T04:43:41Z</timestamp>
    <contributor>
      <username>Cudo29</username>
      <id>5</id>
    </contributor>
    <comment>Myoglobin from PDB:1mbn, created with jV.</comment>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="41" xml:space="preserve">Myoglobin from PDB:1mbn, created with jV.</text>
    <sha1>c3c4819d0fb4dc69fec0bd1d592aec0f0d6dafda</sha1>
  </revision>
</page>
<page arvcontinue="20091113083303|354">
  <title>File:1mbn 02.png</title>
  <ns>6</ns>
  <id>57</id>
  <revision>
    <id>393</id>
    <timestamp>2010-07-14T04:44:47Z</timestamp>
    <contributor>
      <username>Cudo29</username>
      <id>5</id>
    </contributor>
    <comment>Myoglobin from PDB:1mbn, created with jV. The expression of the heme group was changed to ball and stick.</comment>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="105" xml:space="preserve">Myoglobin from PDB:1mbn, created with jV. The expression of the heme group was changed to ball and stick.</text>
    <sha1>9159b9d9138d4b2ee574b48059bab4cbba3e4daa</sha1>
  </revision>
</page>
<page arvcontinue="20091113083303|354">
  <title>File:1mbn 03.png</title>
  <ns>6</ns>
  <id>58</id>
  <revision>
    <id>394</id>
    <timestamp>2010-07-14T04:45:43Z</timestamp>
    <contributor>
      <username>Cudo29</username>
      <id>5</id>
    </contributor>
    <comment>Myoglobin from PDB:1mbn, created with jV. The expression of the heme group was changed to the ball and stick, and that of iron atom was changed to the spacefill.</comment>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="161" xml:space="preserve">Myoglobin from PDB:1mbn, created with jV. The expression of the heme group was changed to the ball and stick, and that of iron atom was changed to the spacefill.</text>
    <sha1>014516487799b4411027d9d646ce1c26c7a99f80</sha1>
  </revision>
</page>
<page arvcontinue="20091113083303|354">
  <title>File:1mbn 04.png</title>
  <ns>6</ns>
  <id>59</id>
  <revision>
    <id>395</id>
    <timestamp>2010-07-14T04:46:17Z</timestamp>
    <contributor>
      <username>Cudo29</username>
      <id>5</id>
    </contributor>
    <comment>Myoglobin from PDB:1mbn, created with jV. The expression of the heme group was changed to the ball and stick, and those of iron atom and the neighbor oxygen atom were changed to the spacefill.</comment>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="192" xml:space="preserve">Myoglobin from PDB:1mbn, created with jV. The expression of the heme group was changed to the ball and stick, and those of iron atom and the neighbor oxygen atom were changed to the spacefill.</text>
    <sha1>3b12ff3b9d630a7cacd9006f5e09f75460439cd8</sha1>
  </revision>
</page>
<page arvcontinue="20091113083303|354">
  <title>File:Jv menu win.png</title>
  <ns>6</ns>
  <id>60</id>
  <revision>
    <id>400</id>
    <timestamp>2010-07-23T07:45:53Z</timestamp>
    <contributor>
      <username>Cudo29</username>
      <id>5</id>
    </contributor>
    <comment>The menu location of the Windows version jV.</comment>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="44" xml:space="preserve">The menu location of the Windows version jV.</text>
    <sha1>88bda645472f105c74613dbf0e329a967ec85274</sha1>
  </revision>
</page>
<page arvcontinue="20091113083303|354">
  <title>File:Jv menu mac.png</title>
  <ns>6</ns>
  <id>61</id>
  <revision>
    <id>401</id>
    <timestamp>2010-07-23T07:46:08Z</timestamp>
    <contributor>
      <username>Cudo29</username>
      <id>5</id>
    </contributor>
    <comment>The menu location of the Mac version jV.</comment>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="40" xml:space="preserve">The menu location of the Mac version jV.</text>
    <sha1>6421285cacfdc3fafeed3cf5818f6264a5e88aed</sha1>
  </revision>
</page>
<page arvcontinue="20091113083303|354">
  <title>File:Popupmenu en.png</title>
  <ns>6</ns>
  <id>62</id>
  <revision>
    <id>402</id>
    <timestamp>2010-07-23T07:46:32Z</timestamp>
    <contributor>
      <username>Cudo29</username>
      <id>5</id>
    </contributor>
    <comment>The menu location of the applet version jV.</comment>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="43" xml:space="preserve">The menu location of the applet version jV.</text>
    <sha1>160c35ff79de5ed8284963bab0362043bb1ba491</sha1>
  </revision>
</page>
<page arvcontinue="20100805022053|404">
  <title>Atom Expression</title>
  <ns>0</ns>
  <id>21</id>
  <revision>
    <id>404</id>
    <parentid>380</parentid>
    <timestamp>2010-08-05T02:20:53Z</timestamp>
    <contributor>
      <username>IMSsato</username>
      <id>4</id>
    </contributor>
    <comment>/* set based on residue property */</comment>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="10495" xml:space="preserve">{| style="float:right"
 |__TOC__
 |}
In order to specify a group of atoms in a molecule, the following five expressions are available.

The standard boolean connectives 'and', 'or' and 'not', and brackets can be used to construct a complex expression. The boolean connectives may be abbreviated as '&amp;', '|', and '|', respectively. 

== predefined set ==
=== element name ===
Element names, such as carbon or nitrogen, can be used to select atoms. 
=== set based on residue property ===
a) amino acids in protein molecule
&lt;table border="1"&gt;
&lt;tr&gt;
&lt;td&gt;&lt;/td&gt;
&lt;td&gt;ALA&lt;/td&gt;&lt;td&gt;ARG&lt;/td&gt;&lt;td&gt;ASN&lt;/td&gt;&lt;td&gt;ASP&lt;/td&gt;&lt;td&gt;CYS&lt;/td&gt;
&lt;td&gt;GLU&lt;/td&gt;&lt;td&gt;GLN&lt;/td&gt;&lt;td&gt;GLY&lt;/td&gt;&lt;td&gt;HIS&lt;/td&gt;&lt;td&gt;ILE&lt;/td&gt;
&lt;td&gt;LEU&lt;/td&gt;&lt;td&gt;LYS&lt;/td&gt;&lt;td&gt;MET&lt;/td&gt;&lt;td&gt;PHE&lt;/td&gt;&lt;td&gt;PRO&lt;/td&gt;
&lt;td&gt;SER&lt;/td&gt;&lt;td&gt;THR&lt;/td&gt;&lt;td&gt;TRP&lt;/td&gt;&lt;td&gt;TYR&lt;/td&gt;&lt;td&gt;VAL&lt;/td&gt;
&lt;/tr&gt;
&lt;tr&gt;
&lt;td&gt;Acidic&lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;/tr&gt;
&lt;tr&gt;
&lt;td&gt;Acyclic&lt;/td&gt;
&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;
&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;
&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;&lt;/td&gt;&lt;td&gt;&lt;/td&gt;
&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;&lt;/td&gt;&lt;td&gt;&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;
&lt;/tr&gt;
&lt;tr&gt;
&lt;td&gt;Aliphatic&lt;/td&gt;
&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;
&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;
&lt;/tr&gt;
&lt;tr&gt;
&lt;td&gt;Aromatic&lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;/tr&gt;
&lt;tr&gt;
&lt;td&gt;Basic&lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;/tr&gt;
&lt;tr&gt;
&lt;td&gt;Buried&lt;/td&gt;
&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;
&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;
&lt;/tr&gt;
&lt;tr&gt;
&lt;td&gt;Charged&lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;/tr&gt;
&lt;tr&gt;
&lt;td&gt;Cyclic&lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;/tr&gt;
&lt;tr&gt;
&lt;td&gt;Hydrophobic&lt;/td&gt;
&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;
&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;
&lt;/tr&gt;
&lt;tr&gt;
&lt;td&gt;Large&lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;
&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;/tr&gt;
&lt;tr&gt;
&lt;td&gt;Medium&lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;
&lt;/tr&gt;
&lt;tr&gt;
&lt;td&gt;Negative&lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;/tr&gt;
&lt;tr&gt;
&lt;td&gt;Neutral&lt;/td&gt;
&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;
&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;
&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;
&lt;/tr&gt;
&lt;tr&gt;
&lt;td&gt;Polar&lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;
&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;/tr&gt;
&lt;tr&gt;
&lt;td&gt;Positive&lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;/tr&gt;
&lt;tr&gt;
&lt;td&gt;Small&lt;/td&gt;
&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;/tr&gt;
&lt;tr&gt;
&lt;td&gt;Surface&lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;
&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;/tr&gt;
&lt;tr&gt;
&lt;td&gt;Cysteine&lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;/tr&gt;
&lt;tr&gt;
&lt;td&gt;Amino&lt;/td&gt;
&lt;td colspan="20"&gt;above 20 amino acids + ASX, GLX, PCA, HYP, MSE, MLY, CME, SEP, CGU, KCX, MLE, TPO, CSO, PTR, DLE, ABA, CSD, DAL, LLP, SMC, DVA, OCS, TYS, AIB, NLE, CSW, MVA, SAR, CRO, CAS, TPQ, CXM&lt;/td&gt;
&lt;/tr&gt;
&lt;tr&gt;
&lt;td&gt;Protein&lt;/td&gt;
&lt;td colspan="20"&gt;above 'Amino' set + UNK, ACE, FOR&lt;/td&gt;
&lt;/tr&gt;
&lt;/table&gt;

b1) nucleotides (for PDB version 2.3)
&lt;table border="1"&gt;
&lt;tr&gt;
&lt;td&gt;&lt;/td&gt;
&lt;td&gt;  A&lt;/td&gt;&lt;td&gt;  C&lt;/td&gt;&lt;td&gt;  G&lt;/td&gt;&lt;td&gt;  T&lt;/td&gt;&lt;td&gt;  U&lt;/td&gt;
&lt;td&gt; +U&lt;/td&gt;&lt;td&gt;  I&lt;/td&gt;&lt;td&gt;1MA&lt;/td&gt;&lt;td&gt;5MC&lt;/td&gt;&lt;td&gt;OMC&lt;/td&gt;
&lt;td&gt;1MG&lt;/td&gt;&lt;td&gt;2MG&lt;/td&gt;&lt;td&gt;M2G&lt;/td&gt;&lt;td&gt;7MG&lt;/td&gt;&lt;td&gt;OMG&lt;/td&gt;
&lt;td&gt; YG&lt;/td&gt;&lt;td&gt;H2U&lt;/td&gt;&lt;td&gt;5MU&lt;/td&gt;&lt;td&gt;PSU&lt;/td&gt;
&lt;/tr&gt;
&lt;tr&gt;
&lt;td&gt;AT&lt;/td&gt;
&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;/tr&gt;
&lt;tr&gt;
&lt;td&gt;CG&lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;/tr&gt;
&lt;tr&gt;
&lt;td&gt;Purine&lt;/td&gt;
&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;/tr&gt;
&lt;tr&gt;
&lt;td&gt;Pyrimidine&lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;/tr&gt;
&lt;tr&gt;
&lt;td&gt;DNA&lt;/td&gt;
&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;/tr&gt;
&lt;tr&gt;
&lt;td&gt;RNA&lt;/td&gt;
&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;
&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;
&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;
&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;
&lt;/tr&gt;
&lt;tr&gt;
&lt;td&gt;Nucleic&lt;/td&gt;
&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;
&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;
&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;
&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;
&lt;/tr&gt;
&lt;/table&gt;

b2) nucleotides (for PDB version 3)
&lt;table border="1"&gt;
&lt;tr&gt;
&lt;td&gt;&lt;/td&gt;
&lt;td&gt; DA&lt;/td&gt;&lt;td&gt; DC&lt;/td&gt;&lt;td&gt; DG&lt;/td&gt;&lt;td&gt; DT&lt;/td&gt;
&lt;td&gt;  A&lt;/td&gt;&lt;td&gt;  C&lt;/td&gt;&lt;td&gt;  G&lt;/td&gt;&lt;td&gt;  U&lt;/td&gt;
&lt;td&gt;other DNA&lt;/td&gt;&lt;td&gt;other RNA&lt;/td&gt;
&lt;/tr&gt;
&lt;tr&gt;
&lt;td&gt;AT&lt;/td&gt;
&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;/tr&gt;
&lt;tr&gt;
&lt;td&gt;CG&lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;/tr&gt;
&lt;tr&gt;
&lt;td&gt;Purine&lt;/td&gt;
&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;/tr&gt;
&lt;tr&gt;
&lt;td&gt;Pyrimidine&lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;/tr&gt;
&lt;tr&gt;
&lt;td&gt;DNA&lt;/td&gt;
&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;/tr&gt;
&lt;tr&gt;
&lt;td&gt;RNA&lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;
&lt;/tr&gt;
&lt;tr&gt;
&lt;td&gt;Nucleic&lt;/td&gt;
&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;
&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;
&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;
&lt;/tr&gt;
&lt;/table&gt;

c) others
&lt;table border="1"&gt;
&lt;tr&gt;
&lt;td&gt;&lt;/td&gt;
&lt;td&gt;HOH&lt;/td&gt;&lt;td&gt;DOD&lt;/td&gt;&lt;td&gt;SO4&lt;/td&gt;&lt;td&gt;PO4&lt;/td&gt;
&lt;/tr&gt;
&lt;tr&gt;
&lt;td&gt;Water&lt;/td&gt;
&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;/tr&gt;
&lt;tr&gt;
&lt;td&gt;Ions&lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;
&lt;/tr&gt;
&lt;tr&gt;
&lt;td&gt;Solvent&lt;/td&gt;
&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;
&lt;/tr&gt;
&lt;/table&gt;

=== others ===


== comparison operators ==
Parts of a molecule can be selected using equality, inequality and ordering operators on their properties. Possible operators are =, ==, &lt;&gt;, !=, /=, &lt;, &lt;=, &gt; and &gt;=, and possible property names are as follows.
{| border="1"
 |-
 | AtomNo || atom ID in PDB files.
 |-
 | ElemNo || atomic number.
 |-
 | ResNo || residue ID in PDB files.
 |-
 | Radius || radius of a ball image of atoms.
 |-
 | Temperature || temperature factor of atoms.
 |-
 | Model || model ID in PDB files.
 |-
 | File || File ID.
 |}

== residue range ==
A group of atoms in a molecule can be selected by the residue ID. For example, command 'select 3' selects atoms whose residue ID is 3, and 'select 3-10' selects atoms whose residue ID is larger than or equal to 3 and smaller than or equal to 10. 
Optionally, the chain ID can be specified after residue range with a colon.
For example, command 'select 3:A' selects atoms
whose residue ID is 3 in the A chain.

== within expression ==
A within expression selects atoms that exist within a specified distance from another set of atoms. For example, 'select within(3.0, backbone) selects atoms within a 3.0 Angstrom radius of any atom in a protein or nucleic acid backbone. 

== PDBj expression ==
A PDBj expression selects a group of atoms according to molecule's properties defined in the PDBMLplus file. It takes the following form;
 pdbj:keyword
For example, 'select pdbj:binding'. The keywords available for each molecule are obtained by the 'show pdbj' command.

== primitive expression ==
A primitive expression takes such a form as
 residue name[residue ID][:chain ID][.atom name][;alternate location][/model ID][@file ID]
Here, residue name and atom name are three letter and four letter name, respectively, and terms in square brackets can be omitted. For example, command 'select SER.CA' selects all alpha carbon atoms in serine.</text>
    <sha1>10bfa40a68a0583aa935209abab462396ec2d8e8</sha1>
  </revision>
  <revision>
    <id>405</id>
    <parentid>404</parentid>
    <timestamp>2010-08-05T02:23:23Z</timestamp>
    <contributor>
      <username>IMSsato</username>
      <id>4</id>
    </contributor>
    <comment>/* others */</comment>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="11419" xml:space="preserve">{| style="float:right"
 |__TOC__
 |}
In order to specify a group of atoms in a molecule, the following five expressions are available.

The standard boolean connectives 'and', 'or' and 'not', and brackets can be used to construct a complex expression. The boolean connectives may be abbreviated as '&amp;', '|', and '|', respectively. 

== predefined set ==
=== element name ===
Element names, such as carbon or nitrogen, can be used to select atoms. 
=== set based on residue property ===
a) amino acids in protein molecule
&lt;table border="1"&gt;
&lt;tr&gt;
&lt;td&gt;&lt;/td&gt;
&lt;td&gt;ALA&lt;/td&gt;&lt;td&gt;ARG&lt;/td&gt;&lt;td&gt;ASN&lt;/td&gt;&lt;td&gt;ASP&lt;/td&gt;&lt;td&gt;CYS&lt;/td&gt;
&lt;td&gt;GLU&lt;/td&gt;&lt;td&gt;GLN&lt;/td&gt;&lt;td&gt;GLY&lt;/td&gt;&lt;td&gt;HIS&lt;/td&gt;&lt;td&gt;ILE&lt;/td&gt;
&lt;td&gt;LEU&lt;/td&gt;&lt;td&gt;LYS&lt;/td&gt;&lt;td&gt;MET&lt;/td&gt;&lt;td&gt;PHE&lt;/td&gt;&lt;td&gt;PRO&lt;/td&gt;
&lt;td&gt;SER&lt;/td&gt;&lt;td&gt;THR&lt;/td&gt;&lt;td&gt;TRP&lt;/td&gt;&lt;td&gt;TYR&lt;/td&gt;&lt;td&gt;VAL&lt;/td&gt;
&lt;/tr&gt;
&lt;tr&gt;
&lt;td&gt;Acidic&lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;/tr&gt;
&lt;tr&gt;
&lt;td&gt;Acyclic&lt;/td&gt;
&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;
&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;
&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;&lt;/td&gt;&lt;td&gt;&lt;/td&gt;
&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;&lt;/td&gt;&lt;td&gt;&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;
&lt;/tr&gt;
&lt;tr&gt;
&lt;td&gt;Aliphatic&lt;/td&gt;
&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;
&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;
&lt;/tr&gt;
&lt;tr&gt;
&lt;td&gt;Aromatic&lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;/tr&gt;
&lt;tr&gt;
&lt;td&gt;Basic&lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;/tr&gt;
&lt;tr&gt;
&lt;td&gt;Buried&lt;/td&gt;
&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;
&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;
&lt;/tr&gt;
&lt;tr&gt;
&lt;td&gt;Charged&lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;/tr&gt;
&lt;tr&gt;
&lt;td&gt;Cyclic&lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;/tr&gt;
&lt;tr&gt;
&lt;td&gt;Hydrophobic&lt;/td&gt;
&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;
&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;
&lt;/tr&gt;
&lt;tr&gt;
&lt;td&gt;Large&lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;
&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;/tr&gt;
&lt;tr&gt;
&lt;td&gt;Medium&lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;
&lt;/tr&gt;
&lt;tr&gt;
&lt;td&gt;Negative&lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;/tr&gt;
&lt;tr&gt;
&lt;td&gt;Neutral&lt;/td&gt;
&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;
&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;
&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;
&lt;/tr&gt;
&lt;tr&gt;
&lt;td&gt;Polar&lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;
&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;/tr&gt;
&lt;tr&gt;
&lt;td&gt;Positive&lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;/tr&gt;
&lt;tr&gt;
&lt;td&gt;Small&lt;/td&gt;
&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;/tr&gt;
&lt;tr&gt;
&lt;td&gt;Surface&lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;
&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;/tr&gt;
&lt;tr&gt;
&lt;td&gt;Cysteine&lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;/tr&gt;
&lt;tr&gt;
&lt;td&gt;Amino&lt;/td&gt;
&lt;td colspan="20"&gt;above 20 amino acids + ASX, GLX, PCA, HYP, MSE, MLY, CME, SEP, CGU, KCX, MLE, TPO, CSO, PTR, DLE, ABA, CSD, DAL, LLP, SMC, DVA, OCS, TYS, AIB, NLE, CSW, MVA, SAR, CRO, CAS, TPQ, CXM&lt;/td&gt;
&lt;/tr&gt;
&lt;tr&gt;
&lt;td&gt;Protein&lt;/td&gt;
&lt;td colspan="20"&gt;above 'Amino' set + UNK, ACE, FOR&lt;/td&gt;
&lt;/tr&gt;
&lt;/table&gt;

b1) nucleotides (for PDB version 2.3)
&lt;table border="1"&gt;
&lt;tr&gt;
&lt;td&gt;&lt;/td&gt;
&lt;td&gt;  A&lt;/td&gt;&lt;td&gt;  C&lt;/td&gt;&lt;td&gt;  G&lt;/td&gt;&lt;td&gt;  T&lt;/td&gt;&lt;td&gt;  U&lt;/td&gt;
&lt;td&gt; +U&lt;/td&gt;&lt;td&gt;  I&lt;/td&gt;&lt;td&gt;1MA&lt;/td&gt;&lt;td&gt;5MC&lt;/td&gt;&lt;td&gt;OMC&lt;/td&gt;
&lt;td&gt;1MG&lt;/td&gt;&lt;td&gt;2MG&lt;/td&gt;&lt;td&gt;M2G&lt;/td&gt;&lt;td&gt;7MG&lt;/td&gt;&lt;td&gt;OMG&lt;/td&gt;
&lt;td&gt; YG&lt;/td&gt;&lt;td&gt;H2U&lt;/td&gt;&lt;td&gt;5MU&lt;/td&gt;&lt;td&gt;PSU&lt;/td&gt;
&lt;/tr&gt;
&lt;tr&gt;
&lt;td&gt;AT&lt;/td&gt;
&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;/tr&gt;
&lt;tr&gt;
&lt;td&gt;CG&lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;/tr&gt;
&lt;tr&gt;
&lt;td&gt;Purine&lt;/td&gt;
&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;/tr&gt;
&lt;tr&gt;
&lt;td&gt;Pyrimidine&lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;/tr&gt;
&lt;tr&gt;
&lt;td&gt;DNA&lt;/td&gt;
&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;/tr&gt;
&lt;tr&gt;
&lt;td&gt;RNA&lt;/td&gt;
&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;
&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;
&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;
&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;
&lt;/tr&gt;
&lt;tr&gt;
&lt;td&gt;Nucleic&lt;/td&gt;
&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;
&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;
&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;
&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;
&lt;/tr&gt;
&lt;/table&gt;

b2) nucleotides (for PDB version 3)
&lt;table border="1"&gt;
&lt;tr&gt;
&lt;td&gt;&lt;/td&gt;
&lt;td&gt; DA&lt;/td&gt;&lt;td&gt; DC&lt;/td&gt;&lt;td&gt; DG&lt;/td&gt;&lt;td&gt; DT&lt;/td&gt;
&lt;td&gt;  A&lt;/td&gt;&lt;td&gt;  C&lt;/td&gt;&lt;td&gt;  G&lt;/td&gt;&lt;td&gt;  U&lt;/td&gt;
&lt;td&gt;other DNA&lt;/td&gt;&lt;td&gt;other RNA&lt;/td&gt;
&lt;/tr&gt;
&lt;tr&gt;
&lt;td&gt;AT&lt;/td&gt;
&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;/tr&gt;
&lt;tr&gt;
&lt;td&gt;CG&lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;/tr&gt;
&lt;tr&gt;
&lt;td&gt;Purine&lt;/td&gt;
&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;/tr&gt;
&lt;tr&gt;
&lt;td&gt;Pyrimidine&lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;/tr&gt;
&lt;tr&gt;
&lt;td&gt;DNA&lt;/td&gt;
&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;/tr&gt;
&lt;tr&gt;
&lt;td&gt;RNA&lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;
&lt;/tr&gt;
&lt;tr&gt;
&lt;td&gt;Nucleic&lt;/td&gt;
&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;
&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;
&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;
&lt;/tr&gt;
&lt;/table&gt;

c) others
&lt;table border="1"&gt;
&lt;tr&gt;
&lt;td&gt;&lt;/td&gt;
&lt;td&gt;HOH&lt;/td&gt;&lt;td&gt;DOD&lt;/td&gt;&lt;td&gt;SO4&lt;/td&gt;&lt;td&gt;PO4&lt;/td&gt;
&lt;/tr&gt;
&lt;tr&gt;
&lt;td&gt;Water&lt;/td&gt;
&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;/tr&gt;
&lt;tr&gt;
&lt;td&gt;Ions&lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;
&lt;/tr&gt;
&lt;tr&gt;
&lt;td&gt;Solvent&lt;/td&gt;
&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;
&lt;/tr&gt;
&lt;/table&gt;

=== others ===
&lt;table border="1"&gt;
&lt;tr&gt;
&lt;td&gt;Alpha&lt;/td&gt;
&lt;td&gt;
atoms whose name is CA.
&lt;/td&gt;
&lt;/tr&gt;
&lt;tr&gt;
&lt;td&gt;Hetero&lt;/td&gt;
&lt;td&gt;
atoms written as HETATM in PDB files or atoms in Solvent set.
&lt;/td&gt;
&lt;/tr&gt;
&lt;tr&gt;
&lt;td&gt;Ligand&lt;/td&gt;
&lt;td&gt;
atoms in Hetero set and not in Solvent set.
&lt;/td&gt;
&lt;/tr&gt;
&lt;tr&gt;
&lt;td&gt;Backbone&lt;br&gt;Mainchain&lt;/td&gt;
&lt;td&gt;
atoms in Amino set whose name is N, CA, C or O, or atoms in Nuceic set
whose name is P,O1P,O2P,O5*,C5*,C4*,O4*,C3*,O3*,C2*,O2* or C1*.
&lt;/td&gt;
&lt;/tr&gt;
&lt;tr&gt;
&lt;td&gt;Sidechain&lt;/td&gt;
&lt;td&gt;
atoms in Amino set or Nucleic set and not in Backbone set.
&lt;/td&gt;
&lt;/tr&gt;
&lt;tr&gt;
&lt;td&gt;Bonded&lt;/td&gt;
&lt;td&gt;
atoms that is connected to at least one other atom.
&lt;/td&gt;
&lt;/tr&gt;
&lt;tr&gt;
&lt;td&gt;Selected&lt;/td&gt;
&lt;td&gt;
atoms currently selected.
&lt;/td&gt;
&lt;/tr&gt;
&lt;tr&gt;
&lt;td&gt;Helix&lt;/td&gt;
&lt;td&gt;
atoms in the alpha-helix structure.
&lt;/td&gt;
&lt;/tr&gt;
&lt;tr&gt;
&lt;td&gt;Sheet&lt;/td&gt;
&lt;td&gt;
atoms in the beta-sheet structure.
&lt;/td&gt;
&lt;/tr&gt;
&lt;tr&gt;
&lt;td&gt;Turn&lt;/td&gt;
&lt;td&gt;
atoms in the turn structure.
&lt;/td&gt;
&lt;/tr&gt;
&lt;/table&gt;

== comparison operators ==
Parts of a molecule can be selected using equality, inequality and ordering operators on their properties. Possible operators are =, ==, &lt;&gt;, !=, /=, &lt;, &lt;=, &gt; and &gt;=, and possible property names are as follows.
{| border="1"
 |-
 | AtomNo || atom ID in PDB files.
 |-
 | ElemNo || atomic number.
 |-
 | ResNo || residue ID in PDB files.
 |-
 | Radius || radius of a ball image of atoms.
 |-
 | Temperature || temperature factor of atoms.
 |-
 | Model || model ID in PDB files.
 |-
 | File || File ID.
 |}

== residue range ==
A group of atoms in a molecule can be selected by the residue ID. For example, command 'select 3' selects atoms whose residue ID is 3, and 'select 3-10' selects atoms whose residue ID is larger than or equal to 3 and smaller than or equal to 10. 
Optionally, the chain ID can be specified after residue range with a colon.
For example, command 'select 3:A' selects atoms
whose residue ID is 3 in the A chain.

== within expression ==
A within expression selects atoms that exist within a specified distance from another set of atoms. For example, 'select within(3.0, backbone) selects atoms within a 3.0 Angstrom radius of any atom in a protein or nucleic acid backbone. 

== PDBj expression ==
A PDBj expression selects a group of atoms according to molecule's properties defined in the PDBMLplus file. It takes the following form;
 pdbj:keyword
For example, 'select pdbj:binding'. The keywords available for each molecule are obtained by the 'show pdbj' command.

== primitive expression ==
A primitive expression takes such a form as
 residue name[residue ID][:chain ID][.atom name][;alternate location][/model ID][@file ID]
Here, residue name and atom name are three letter and four letter name, respectively, and terms in square brackets can be omitted. For example, command 'select SER.CA' selects all alpha carbon atoms in serine.</text>
    <sha1>656e9d1fc90df0f549a774b0d5c3a88804e25ba2</sha1>
  </revision>
  <revision>
    <id>414</id>
    <parentid>405</parentid>
    <timestamp>2010-09-14T07:58:42Z</timestamp>
    <contributor>
      <username>IMSsato</username>
      <id>4</id>
    </contributor>
    <comment>/* set based on residue property */</comment>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="11845" xml:space="preserve">{| style="float:right"
 |__TOC__
 |}
In order to specify a group of atoms in a molecule, the following five expressions are available.

The standard boolean connectives 'and', 'or' and 'not', and brackets can be used to construct a complex expression. The boolean connectives may be abbreviated as '&amp;', '|', and '|', respectively. 

== predefined set ==
=== element name ===
Element names, such as carbon or nitrogen, can be used to select atoms. 
=== set based on residue property ===
a) amino acids in protein molecule
&lt;table border="1"&gt;
&lt;tr&gt;
&lt;td&gt;&lt;/td&gt;
&lt;td&gt;ALA&lt;/td&gt;&lt;td&gt;ARG&lt;/td&gt;&lt;td&gt;ASN&lt;/td&gt;&lt;td&gt;ASP&lt;/td&gt;&lt;td&gt;CYS&lt;/td&gt;
&lt;td&gt;GLU&lt;/td&gt;&lt;td&gt;GLN&lt;/td&gt;&lt;td&gt;GLY&lt;/td&gt;&lt;td&gt;HIS&lt;/td&gt;&lt;td&gt;ILE&lt;/td&gt;
&lt;td&gt;LEU&lt;/td&gt;&lt;td&gt;LYS&lt;/td&gt;&lt;td&gt;MET&lt;/td&gt;&lt;td&gt;PHE&lt;/td&gt;&lt;td&gt;PRO&lt;/td&gt;
&lt;td&gt;SER&lt;/td&gt;&lt;td&gt;THR&lt;/td&gt;&lt;td&gt;TRP&lt;/td&gt;&lt;td&gt;TYR&lt;/td&gt;&lt;td&gt;VAL&lt;/td&gt;
&lt;/tr&gt;
&lt;tr&gt;
&lt;td&gt;Acidic&lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;/tr&gt;
&lt;tr&gt;
&lt;td&gt;Acyclic&lt;/td&gt;
&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;
&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;
&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;&lt;/td&gt;&lt;td&gt;&lt;/td&gt;
&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;&lt;/td&gt;&lt;td&gt;&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;
&lt;/tr&gt;
&lt;tr&gt;
&lt;td&gt;Aliphatic&lt;/td&gt;
&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;
&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;
&lt;/tr&gt;
&lt;tr&gt;
&lt;td&gt;Aromatic&lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;/tr&gt;
&lt;tr&gt;
&lt;td&gt;Basic&lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;/tr&gt;
&lt;tr&gt;
&lt;td&gt;Buried&lt;/td&gt;
&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;
&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;
&lt;/tr&gt;
&lt;tr&gt;
&lt;td&gt;Charged&lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;/tr&gt;
&lt;tr&gt;
&lt;td&gt;Cyclic&lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;/tr&gt;
&lt;tr&gt;
&lt;td&gt;Hydrophobic&lt;/td&gt;
&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;
&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;
&lt;/tr&gt;
&lt;tr&gt;
&lt;td&gt;Large&lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;
&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;/tr&gt;
&lt;tr&gt;
&lt;td&gt;Medium&lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;
&lt;/tr&gt;
&lt;tr&gt;
&lt;td&gt;Negative&lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;/tr&gt;
&lt;tr&gt;
&lt;td&gt;Neutral&lt;/td&gt;
&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;
&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;
&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;
&lt;/tr&gt;
&lt;tr&gt;
&lt;td&gt;Polar&lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;
&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;/tr&gt;
&lt;tr&gt;
&lt;td&gt;Positive&lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;/tr&gt;
&lt;tr&gt;
&lt;td&gt;Small&lt;/td&gt;
&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;/tr&gt;
&lt;tr&gt;
&lt;td&gt;Surface&lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;
&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;/tr&gt;
&lt;tr&gt;
&lt;td&gt;Cysteine&lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;/tr&gt;
&lt;tr&gt;
&lt;td&gt;Amino&lt;/td&gt;
&lt;td colspan="20"&gt;above 20 amino acids + other amino acids&lt;/td&gt;
&lt;/tr&gt;
&lt;tr&gt;
&lt;td&gt;Protein&lt;/td&gt;
&lt;td colspan="20"&gt;above 'Amino' set + UNK, ACE + FOR (PDB version 2.3 only)&lt;/td&gt;
&lt;/tr&gt;
&lt;/table&gt;
Here, 'other amino acids' stands for components whose type is one of the followings in [http://remediation.wwpdb.org/ccd.html Chemical Component Dictionary].&lt;br/&gt;
D-PEPTIDE LINKING&lt;br/&gt;
D-PEPTIDE NH3 AMINO TERMINUS&lt;br/&gt;
L-PEPTIDE COOH CARBOXY TERMINUS&lt;br/&gt;
L-PEPTIDE LINKING&lt;br/&gt;
L-PEPTIDE NH3 AMINO TERMINUS&lt;br/&gt;
PEPTIDE LINKING&lt;br/&gt;
PEPTIDE-LIKE&lt;br/&gt;

b1) nucleotides (for PDB version 2.3)
&lt;table border="1"&gt;
&lt;tr&gt;
&lt;td&gt;&lt;/td&gt;
&lt;td&gt;  A&lt;/td&gt;&lt;td&gt;  C&lt;/td&gt;&lt;td&gt;  G&lt;/td&gt;&lt;td&gt;  T&lt;/td&gt;&lt;td&gt;  U&lt;/td&gt;
&lt;td&gt; +U&lt;/td&gt;&lt;td&gt;  I&lt;/td&gt;&lt;td&gt;1MA&lt;/td&gt;&lt;td&gt;5MC&lt;/td&gt;&lt;td&gt;OMC&lt;/td&gt;
&lt;td&gt;1MG&lt;/td&gt;&lt;td&gt;2MG&lt;/td&gt;&lt;td&gt;M2G&lt;/td&gt;&lt;td&gt;7MG&lt;/td&gt;&lt;td&gt;OMG&lt;/td&gt;
&lt;td&gt; YG&lt;/td&gt;&lt;td&gt;H2U&lt;/td&gt;&lt;td&gt;5MU&lt;/td&gt;&lt;td&gt;PSU&lt;/td&gt;
&lt;/tr&gt;
&lt;tr&gt;
&lt;td&gt;AT&lt;/td&gt;
&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;/tr&gt;
&lt;tr&gt;
&lt;td&gt;CG&lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;/tr&gt;
&lt;tr&gt;
&lt;td&gt;Purine&lt;/td&gt;
&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;/tr&gt;
&lt;tr&gt;
&lt;td&gt;Pyrimidine&lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;/tr&gt;
&lt;tr&gt;
&lt;td&gt;DNA&lt;/td&gt;
&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;/tr&gt;
&lt;tr&gt;
&lt;td&gt;RNA&lt;/td&gt;
&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;
&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;
&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;
&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;
&lt;/tr&gt;
&lt;tr&gt;
&lt;td&gt;Nucleic&lt;/td&gt;
&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;
&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;
&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;
&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;
&lt;/tr&gt;
&lt;/table&gt;

b2) nucleotides (for PDB version 3)
&lt;table border="1"&gt;
&lt;tr&gt;
&lt;td&gt;&lt;/td&gt;
&lt;td&gt; DA&lt;/td&gt;&lt;td&gt; DC&lt;/td&gt;&lt;td&gt; DG&lt;/td&gt;&lt;td&gt; DT&lt;/td&gt;
&lt;td&gt;  A&lt;/td&gt;&lt;td&gt;  C&lt;/td&gt;&lt;td&gt;  G&lt;/td&gt;&lt;td&gt;  U&lt;/td&gt;
&lt;td&gt;other DNA&lt;/td&gt;&lt;td&gt;other RNA&lt;/td&gt;
&lt;/tr&gt;
&lt;tr&gt;
&lt;td&gt;AT&lt;/td&gt;
&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;/tr&gt;
&lt;tr&gt;
&lt;td&gt;CG&lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;/tr&gt;
&lt;tr&gt;
&lt;td&gt;Purine&lt;/td&gt;
&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;/tr&gt;
&lt;tr&gt;
&lt;td&gt;Pyrimidine&lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;/tr&gt;
&lt;tr&gt;
&lt;td&gt;DNA&lt;/td&gt;
&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;/tr&gt;
&lt;tr&gt;
&lt;td&gt;RNA&lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;
&lt;/tr&gt;
&lt;tr&gt;
&lt;td&gt;Nucleic&lt;/td&gt;
&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;
&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;
&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;
&lt;/tr&gt;
&lt;/table&gt;
Here, 'other DNA' and 'other RNA' stand for components whose type is 
DNA LINKING and RNA LINKING respectively in [http://remediation.wwpdb.org/ccd.html Chemical Component Dictionary].&lt;br/&gt;

c) others
&lt;table border="1"&gt;
&lt;tr&gt;
&lt;td&gt;&lt;/td&gt;
&lt;td&gt;HOH&lt;/td&gt;&lt;td&gt;DOD&lt;/td&gt;&lt;td&gt;SO4&lt;/td&gt;&lt;td&gt;PO4&lt;/td&gt;
&lt;/tr&gt;
&lt;tr&gt;
&lt;td&gt;Water&lt;/td&gt;
&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;/tr&gt;
&lt;tr&gt;
&lt;td&gt;Ions&lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;
&lt;/tr&gt;
&lt;tr&gt;
&lt;td&gt;Solvent&lt;/td&gt;
&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;
&lt;/tr&gt;
&lt;/table&gt;

=== others ===
&lt;table border="1"&gt;
&lt;tr&gt;
&lt;td&gt;Alpha&lt;/td&gt;
&lt;td&gt;
atoms whose name is CA.
&lt;/td&gt;
&lt;/tr&gt;
&lt;tr&gt;
&lt;td&gt;Hetero&lt;/td&gt;
&lt;td&gt;
atoms written as HETATM in PDB files or atoms in Solvent set.
&lt;/td&gt;
&lt;/tr&gt;
&lt;tr&gt;
&lt;td&gt;Ligand&lt;/td&gt;
&lt;td&gt;
atoms in Hetero set and not in Solvent set.
&lt;/td&gt;
&lt;/tr&gt;
&lt;tr&gt;
&lt;td&gt;Backbone&lt;br&gt;Mainchain&lt;/td&gt;
&lt;td&gt;
atoms in Amino set whose name is N, CA, C or O, or atoms in Nuceic set
whose name is P,O1P,O2P,O5*,C5*,C4*,O4*,C3*,O3*,C2*,O2* or C1*.
&lt;/td&gt;
&lt;/tr&gt;
&lt;tr&gt;
&lt;td&gt;Sidechain&lt;/td&gt;
&lt;td&gt;
atoms in Amino set or Nucleic set and not in Backbone set.
&lt;/td&gt;
&lt;/tr&gt;
&lt;tr&gt;
&lt;td&gt;Bonded&lt;/td&gt;
&lt;td&gt;
atoms that is connected to at least one other atom.
&lt;/td&gt;
&lt;/tr&gt;
&lt;tr&gt;
&lt;td&gt;Selected&lt;/td&gt;
&lt;td&gt;
atoms currently selected.
&lt;/td&gt;
&lt;/tr&gt;
&lt;tr&gt;
&lt;td&gt;Helix&lt;/td&gt;
&lt;td&gt;
atoms in the alpha-helix structure.
&lt;/td&gt;
&lt;/tr&gt;
&lt;tr&gt;
&lt;td&gt;Sheet&lt;/td&gt;
&lt;td&gt;
atoms in the beta-sheet structure.
&lt;/td&gt;
&lt;/tr&gt;
&lt;tr&gt;
&lt;td&gt;Turn&lt;/td&gt;
&lt;td&gt;
atoms in the turn structure.
&lt;/td&gt;
&lt;/tr&gt;
&lt;/table&gt;

== comparison operators ==
Parts of a molecule can be selected using equality, inequality and ordering operators on their properties. Possible operators are =, ==, &lt;&gt;, !=, /=, &lt;, &lt;=, &gt; and &gt;=, and possible property names are as follows.
{| border="1"
 |-
 | AtomNo || atom ID in PDB files.
 |-
 | ElemNo || atomic number.
 |-
 | ResNo || residue ID in PDB files.
 |-
 | Radius || radius of a ball image of atoms.
 |-
 | Temperature || temperature factor of atoms.
 |-
 | Model || model ID in PDB files.
 |-
 | File || File ID.
 |}

== residue range ==
A group of atoms in a molecule can be selected by the residue ID. For example, command 'select 3' selects atoms whose residue ID is 3, and 'select 3-10' selects atoms whose residue ID is larger than or equal to 3 and smaller than or equal to 10. 
Optionally, the chain ID can be specified after residue range with a colon.
For example, command 'select 3:A' selects atoms
whose residue ID is 3 in the A chain.

== within expression ==
A within expression selects atoms that exist within a specified distance from another set of atoms. For example, 'select within(3.0, backbone) selects atoms within a 3.0 Angstrom radius of any atom in a protein or nucleic acid backbone. 

== PDBj expression ==
A PDBj expression selects a group of atoms according to molecule's properties defined in the PDBMLplus file. It takes the following form;
 pdbj:keyword
For example, 'select pdbj:binding'. The keywords available for each molecule are obtained by the 'show pdbj' command.

== primitive expression ==
A primitive expression takes such a form as
 residue name[residue ID][:chain ID][.atom name][;alternate location][/model ID][@file ID]
Here, residue name and atom name are three letter and four letter name, respectively, and terms in square brackets can be omitted. For example, command 'select SER.CA' selects all alpha carbon atoms in serine.</text>
    <sha1>9302b09a1ec5e2c71216e054422e0adb81c610e5</sha1>
  </revision>
  <revision>
    <id>428</id>
    <parentid>414</parentid>
    <timestamp>2010-12-03T05:44:20Z</timestamp>
    <contributor>
      <username>IMSsato</username>
      <id>4</id>
    </contributor>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="11845" xml:space="preserve">{| style="float:right"
 |__TOC__
 |}
In order to specify a group of atoms in a molecule, the following five expressions are available.

The standard boolean connectives 'and', 'or' and 'not', and brackets can be used to construct a complex expression. The boolean connectives may be abbreviated as '&amp;', '|', and '!', respectively. 

== predefined set ==
=== element name ===
Element names, such as carbon or nitrogen, can be used to select atoms. 
=== set based on residue property ===
a) amino acids in protein molecule
&lt;table border="1"&gt;
&lt;tr&gt;
&lt;td&gt;&lt;/td&gt;
&lt;td&gt;ALA&lt;/td&gt;&lt;td&gt;ARG&lt;/td&gt;&lt;td&gt;ASN&lt;/td&gt;&lt;td&gt;ASP&lt;/td&gt;&lt;td&gt;CYS&lt;/td&gt;
&lt;td&gt;GLU&lt;/td&gt;&lt;td&gt;GLN&lt;/td&gt;&lt;td&gt;GLY&lt;/td&gt;&lt;td&gt;HIS&lt;/td&gt;&lt;td&gt;ILE&lt;/td&gt;
&lt;td&gt;LEU&lt;/td&gt;&lt;td&gt;LYS&lt;/td&gt;&lt;td&gt;MET&lt;/td&gt;&lt;td&gt;PHE&lt;/td&gt;&lt;td&gt;PRO&lt;/td&gt;
&lt;td&gt;SER&lt;/td&gt;&lt;td&gt;THR&lt;/td&gt;&lt;td&gt;TRP&lt;/td&gt;&lt;td&gt;TYR&lt;/td&gt;&lt;td&gt;VAL&lt;/td&gt;
&lt;/tr&gt;
&lt;tr&gt;
&lt;td&gt;Acidic&lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;/tr&gt;
&lt;tr&gt;
&lt;td&gt;Acyclic&lt;/td&gt;
&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;
&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;
&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;&lt;/td&gt;&lt;td&gt;&lt;/td&gt;
&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;&lt;/td&gt;&lt;td&gt;&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;
&lt;/tr&gt;
&lt;tr&gt;
&lt;td&gt;Aliphatic&lt;/td&gt;
&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;
&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;
&lt;/tr&gt;
&lt;tr&gt;
&lt;td&gt;Aromatic&lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;/tr&gt;
&lt;tr&gt;
&lt;td&gt;Basic&lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;/tr&gt;
&lt;tr&gt;
&lt;td&gt;Buried&lt;/td&gt;
&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;
&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;
&lt;/tr&gt;
&lt;tr&gt;
&lt;td&gt;Charged&lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;/tr&gt;
&lt;tr&gt;
&lt;td&gt;Cyclic&lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;/tr&gt;
&lt;tr&gt;
&lt;td&gt;Hydrophobic&lt;/td&gt;
&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;
&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;
&lt;/tr&gt;
&lt;tr&gt;
&lt;td&gt;Large&lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;
&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;/tr&gt;
&lt;tr&gt;
&lt;td&gt;Medium&lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;
&lt;/tr&gt;
&lt;tr&gt;
&lt;td&gt;Negative&lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;/tr&gt;
&lt;tr&gt;
&lt;td&gt;Neutral&lt;/td&gt;
&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;
&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;
&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;
&lt;/tr&gt;
&lt;tr&gt;
&lt;td&gt;Polar&lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;
&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;/tr&gt;
&lt;tr&gt;
&lt;td&gt;Positive&lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;/tr&gt;
&lt;tr&gt;
&lt;td&gt;Small&lt;/td&gt;
&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;/tr&gt;
&lt;tr&gt;
&lt;td&gt;Surface&lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;
&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;/tr&gt;
&lt;tr&gt;
&lt;td&gt;Cysteine&lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;/tr&gt;
&lt;tr&gt;
&lt;td&gt;Amino&lt;/td&gt;
&lt;td colspan="20"&gt;above 20 amino acids + other amino acids&lt;/td&gt;
&lt;/tr&gt;
&lt;tr&gt;
&lt;td&gt;Protein&lt;/td&gt;
&lt;td colspan="20"&gt;above 'Amino' set + UNK, ACE + FOR (PDB version 2.3 only)&lt;/td&gt;
&lt;/tr&gt;
&lt;/table&gt;
Here, 'other amino acids' stands for components whose type is one of the followings in [http://remediation.wwpdb.org/ccd.html Chemical Component Dictionary].&lt;br/&gt;
D-PEPTIDE LINKING&lt;br/&gt;
D-PEPTIDE NH3 AMINO TERMINUS&lt;br/&gt;
L-PEPTIDE COOH CARBOXY TERMINUS&lt;br/&gt;
L-PEPTIDE LINKING&lt;br/&gt;
L-PEPTIDE NH3 AMINO TERMINUS&lt;br/&gt;
PEPTIDE LINKING&lt;br/&gt;
PEPTIDE-LIKE&lt;br/&gt;

b1) nucleotides (for PDB version 2.3)
&lt;table border="1"&gt;
&lt;tr&gt;
&lt;td&gt;&lt;/td&gt;
&lt;td&gt;  A&lt;/td&gt;&lt;td&gt;  C&lt;/td&gt;&lt;td&gt;  G&lt;/td&gt;&lt;td&gt;  T&lt;/td&gt;&lt;td&gt;  U&lt;/td&gt;
&lt;td&gt; +U&lt;/td&gt;&lt;td&gt;  I&lt;/td&gt;&lt;td&gt;1MA&lt;/td&gt;&lt;td&gt;5MC&lt;/td&gt;&lt;td&gt;OMC&lt;/td&gt;
&lt;td&gt;1MG&lt;/td&gt;&lt;td&gt;2MG&lt;/td&gt;&lt;td&gt;M2G&lt;/td&gt;&lt;td&gt;7MG&lt;/td&gt;&lt;td&gt;OMG&lt;/td&gt;
&lt;td&gt; YG&lt;/td&gt;&lt;td&gt;H2U&lt;/td&gt;&lt;td&gt;5MU&lt;/td&gt;&lt;td&gt;PSU&lt;/td&gt;
&lt;/tr&gt;
&lt;tr&gt;
&lt;td&gt;AT&lt;/td&gt;
&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;/tr&gt;
&lt;tr&gt;
&lt;td&gt;CG&lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;/tr&gt;
&lt;tr&gt;
&lt;td&gt;Purine&lt;/td&gt;
&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;/tr&gt;
&lt;tr&gt;
&lt;td&gt;Pyrimidine&lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;/tr&gt;
&lt;tr&gt;
&lt;td&gt;DNA&lt;/td&gt;
&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;/tr&gt;
&lt;tr&gt;
&lt;td&gt;RNA&lt;/td&gt;
&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;
&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;
&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;
&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;
&lt;/tr&gt;
&lt;tr&gt;
&lt;td&gt;Nucleic&lt;/td&gt;
&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;
&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;
&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;
&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;
&lt;/tr&gt;
&lt;/table&gt;

b2) nucleotides (for PDB version 3)
&lt;table border="1"&gt;
&lt;tr&gt;
&lt;td&gt;&lt;/td&gt;
&lt;td&gt; DA&lt;/td&gt;&lt;td&gt; DC&lt;/td&gt;&lt;td&gt; DG&lt;/td&gt;&lt;td&gt; DT&lt;/td&gt;
&lt;td&gt;  A&lt;/td&gt;&lt;td&gt;  C&lt;/td&gt;&lt;td&gt;  G&lt;/td&gt;&lt;td&gt;  U&lt;/td&gt;
&lt;td&gt;other DNA&lt;/td&gt;&lt;td&gt;other RNA&lt;/td&gt;
&lt;/tr&gt;
&lt;tr&gt;
&lt;td&gt;AT&lt;/td&gt;
&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;/tr&gt;
&lt;tr&gt;
&lt;td&gt;CG&lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;/tr&gt;
&lt;tr&gt;
&lt;td&gt;Purine&lt;/td&gt;
&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;/tr&gt;
&lt;tr&gt;
&lt;td&gt;Pyrimidine&lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;/tr&gt;
&lt;tr&gt;
&lt;td&gt;DNA&lt;/td&gt;
&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;/tr&gt;
&lt;tr&gt;
&lt;td&gt;RNA&lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;
&lt;/tr&gt;
&lt;tr&gt;
&lt;td&gt;Nucleic&lt;/td&gt;
&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;
&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;
&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;
&lt;/tr&gt;
&lt;/table&gt;
Here, 'other DNA' and 'other RNA' stand for components whose type is 
DNA LINKING and RNA LINKING respectively in [http://remediation.wwpdb.org/ccd.html Chemical Component Dictionary].&lt;br/&gt;

c) others
&lt;table border="1"&gt;
&lt;tr&gt;
&lt;td&gt;&lt;/td&gt;
&lt;td&gt;HOH&lt;/td&gt;&lt;td&gt;DOD&lt;/td&gt;&lt;td&gt;SO4&lt;/td&gt;&lt;td&gt;PO4&lt;/td&gt;
&lt;/tr&gt;
&lt;tr&gt;
&lt;td&gt;Water&lt;/td&gt;
&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;/tr&gt;
&lt;tr&gt;
&lt;td&gt;Ions&lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;
&lt;/tr&gt;
&lt;tr&gt;
&lt;td&gt;Solvent&lt;/td&gt;
&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;
&lt;/tr&gt;
&lt;/table&gt;

=== others ===
&lt;table border="1"&gt;
&lt;tr&gt;
&lt;td&gt;Alpha&lt;/td&gt;
&lt;td&gt;
atoms whose name is CA.
&lt;/td&gt;
&lt;/tr&gt;
&lt;tr&gt;
&lt;td&gt;Hetero&lt;/td&gt;
&lt;td&gt;
atoms written as HETATM in PDB files or atoms in Solvent set.
&lt;/td&gt;
&lt;/tr&gt;
&lt;tr&gt;
&lt;td&gt;Ligand&lt;/td&gt;
&lt;td&gt;
atoms in Hetero set and not in Solvent set.
&lt;/td&gt;
&lt;/tr&gt;
&lt;tr&gt;
&lt;td&gt;Backbone&lt;br&gt;Mainchain&lt;/td&gt;
&lt;td&gt;
atoms in Amino set whose name is N, CA, C or O, or atoms in Nuceic set
whose name is P,O1P,O2P,O5*,C5*,C4*,O4*,C3*,O3*,C2*,O2* or C1*.
&lt;/td&gt;
&lt;/tr&gt;
&lt;tr&gt;
&lt;td&gt;Sidechain&lt;/td&gt;
&lt;td&gt;
atoms in Amino set or Nucleic set and not in Backbone set.
&lt;/td&gt;
&lt;/tr&gt;
&lt;tr&gt;
&lt;td&gt;Bonded&lt;/td&gt;
&lt;td&gt;
atoms that is connected to at least one other atom.
&lt;/td&gt;
&lt;/tr&gt;
&lt;tr&gt;
&lt;td&gt;Selected&lt;/td&gt;
&lt;td&gt;
atoms currently selected.
&lt;/td&gt;
&lt;/tr&gt;
&lt;tr&gt;
&lt;td&gt;Helix&lt;/td&gt;
&lt;td&gt;
atoms in the alpha-helix structure.
&lt;/td&gt;
&lt;/tr&gt;
&lt;tr&gt;
&lt;td&gt;Sheet&lt;/td&gt;
&lt;td&gt;
atoms in the beta-sheet structure.
&lt;/td&gt;
&lt;/tr&gt;
&lt;tr&gt;
&lt;td&gt;Turn&lt;/td&gt;
&lt;td&gt;
atoms in the turn structure.
&lt;/td&gt;
&lt;/tr&gt;
&lt;/table&gt;

== comparison operators ==
Parts of a molecule can be selected using equality, inequality and ordering operators on their properties. Possible operators are =, ==, &lt;&gt;, !=, /=, &lt;, &lt;=, &gt; and &gt;=, and possible property names are as follows.
{| border="1"
 |-
 | AtomNo || atom ID in PDB files.
 |-
 | ElemNo || atomic number.
 |-
 | ResNo || residue ID in PDB files.
 |-
 | Radius || radius of a ball image of atoms.
 |-
 | Temperature || temperature factor of atoms.
 |-
 | Model || model ID in PDB files.
 |-
 | File || File ID.
 |}

== residue range ==
A group of atoms in a molecule can be selected by the residue ID. For example, command 'select 3' selects atoms whose residue ID is 3, and 'select 3-10' selects atoms whose residue ID is larger than or equal to 3 and smaller than or equal to 10. 
Optionally, the chain ID can be specified after residue range with a colon.
For example, command 'select 3:A' selects atoms
whose residue ID is 3 in the A chain.

== within expression ==
A within expression selects atoms that exist within a specified distance from another set of atoms. For example, 'select within(3.0, backbone) selects atoms within a 3.0 Angstrom radius of any atom in a protein or nucleic acid backbone. 

== PDBj expression ==
A PDBj expression selects a group of atoms according to molecule's properties defined in the PDBMLplus file. It takes the following form;
 pdbj:keyword
For example, 'select pdbj:binding'. The keywords available for each molecule are obtained by the 'show pdbj' command.

== primitive expression ==
A primitive expression takes such a form as
 residue name[residue ID][:chain ID][.atom name][;alternate location][/model ID][@file ID]
Here, residue name and atom name are three letter and four letter name, respectively, and terms in square brackets can be omitted. For example, command 'select SER.CA' selects all alpha carbon atoms in serine.</text>
    <sha1>2b88c434bfbf48272dd8386e1dadb38285c8960e</sha1>
  </revision>
</page>
<page arvcontinue="20100805022053|404">
  <title>Trouble shooting</title>
  <ns>0</ns>
  <id>48</id>
  <revision>
    <id>406</id>
    <parentid>355</parentid>
    <timestamp>2010-08-17T08:21:25Z</timestamp>
    <contributor>
      <username>IMSsato</username>
      <id>4</id>
    </contributor>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="3617" xml:space="preserve">{| style="left"
 |__TOC__
 |}

== Certificate error on applet ==

When you use JRE6 Update15 (1.6.0_15) or JRE6 Update16 (1.6.0_16) on Windows or Linux,
jV applet and applet-launcher fail to start up with the following error.

 Error:java.io.IOException:Cannot find certificates for JNLP AppletLauncher class

Please use JRE6 Update17 (1.6.0_17) or later.

== JOGL library conflict ==

If you cannot start jV via Java Web Start or view jV applets due to a failure of locating the JOGL library, try the followings.

===clear cached files===

On JRE of version 1.6.0_15 and 1.6.0_16, previously cached JOGL files cause a problem
even if newer files are placed on the server.
JRE of version 1.6.0_17 or later is recommended.
On Mac OS X Snow Leopard, however, the latest JRE is of version 1.6.0_15 at the moment.
The following steps show how to clear cached files.

1) Double-click the [Macintosh HD]-[Applications]-[Utilities]-[Java Preferences] icon, then the Java Preferences window appears.

[[File:Java_prefs1.png|center|500px]]

2) Choose 'Network' tab.

[[File:Java_prefs2.png|center|500px]]

3) Press 'Delete Files...' button and click 'OK' on the subsequent confirmation dialog.

===remove local JOGL library===

Locally-installed JOGL libraries of different version cause conflicts with Java Web Start technology.
JOGL library files are different between operating systems.

'''Mac OS X'''

Open the [Macintosh HD]-[Library]-[Java]-[Extensions] folder.
If some of the following files

* jogl.jar
* gluegen-rt.jar
* libjogl.jnilib
* libjogl_awt.jnilib
* libjogl_cg.jnilib
* libgluegen-rt.jnilib

exist in the folder, remove them.
Here, this operation requires root privilege.

'''Windows'''

Files that should be removed are as follows.

* &lt;JRE&gt;\lib\ext\jogl.jar
* &lt;JRE&gt;\lib\ext\gluegen-rt.jar
* &lt;JRE&gt;\bin\jogl.dll
* &lt;JRE&gt;\bin\jogl_cg.dll
* &lt;JRE&gt;\bin\jogl_awt.dll
* &lt;JRE&gt;\bin\gluegen-rt.dll

Here, &lt;JRE&gt; denotes the folder that JRE has been installed; typically &lt;JRE&gt;=C:\Program Files\Java\jre6.

'''Linux'''

Files that should be removed are as follows.

* &lt;JRE&gt;/lib/ext/jogl.jar
* &lt;JRE&gt;/lib/ext/gluegen-rt.jar
* &lt;JRE&gt;/lib/&lt;arch&gt;/libjogl.so
* &lt;JRE&gt;/lib/&lt;arch&gt;/libjogl_cg.so
* &lt;JRE&gt;/lib/&lt;arch&gt;/libjogl_awt.so
* &lt;JRE&gt;/lib/&lt;arch&gt;/libjogl_drihack.so
* &lt;JRE&gt;/lib/&lt;arch&gt;/libgluegen-rt.so

Here, &lt;JRE&gt; denotes the directory that JRE has been installed; typically &lt;JRE&gt;=/usr/java/jdk1.6.0_17/jre,
and &lt;arch&gt; the processor architecture such as &lt;arch&gt;=i386.

== jV applet with Internet Explorer ==

When visiting a web page that contains a jV applet with Internet Explorer, there sometimes occurs trouble in working with native JOGL libraries especially on Windows Vista. Please use Firefox web browser in that case.

== Class not found error on applet ==

When you use JRE6 Update21 (1.6.0_21) with the next-generation Java Plug-in enabled on Windows or Linux, 
the following error occurs for the combination of jV applet and applet-launcher.

 Error: Class not found: org.pdbj.viewer.gui.ViewerApplet

You can avoid this problem by disabling the next-generation Java Plug-in.
[http://www.java.com/en/download/help/new_plugin.xml Here] is how to do that for Windows users.
On Linux platform, users can manually replace the symbolic link to new plug-in &lt;tt&gt;libnpjp2.so&lt;/tt&gt;
with the symbolic link to classic plug-in &lt;tt&gt;libjavaplugin_oji.so&lt;/tt&gt;
(see [http://www.oracle.com/technetwork/java/javase/manual-plugin-install-linux-136395.html this page] for help).
If you are using firefox 3.6 or later, however, you need downgrade JRE to 1.6.0_20
because firefox of those versions run applets only with the new Java Plug-in.</text>
    <sha1>cd79512565b6a4f0d14b0fa8bb3df92a8724e73d</sha1>
  </revision>
  <revision>
    <id>407</id>
    <parentid>406</parentid>
    <timestamp>2010-08-17T08:35:36Z</timestamp>
    <contributor>
      <username>IMSsato</username>
      <id>4</id>
    </contributor>
    <comment>/* Class not found error on applet */</comment>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="3620" xml:space="preserve">{| style="left"
 |__TOC__
 |}

== Certificate error on applet ==

When you use JRE6 Update15 (1.6.0_15) or JRE6 Update16 (1.6.0_16) on Windows or Linux,
jV applet and applet-launcher fail to start up with the following error.

 Error:java.io.IOException:Cannot find certificates for JNLP AppletLauncher class

Please use JRE6 Update17 (1.6.0_17) or later.

== JOGL library conflict ==

If you cannot start jV via Java Web Start or view jV applets due to a failure of locating the JOGL library, try the followings.

===clear cached files===

On JRE of version 1.6.0_15 and 1.6.0_16, previously cached JOGL files cause a problem
even if newer files are placed on the server.
JRE of version 1.6.0_17 or later is recommended.
On Mac OS X Snow Leopard, however, the latest JRE is of version 1.6.0_15 at the moment.
The following steps show how to clear cached files.

1) Double-click the [Macintosh HD]-[Applications]-[Utilities]-[Java Preferences] icon, then the Java Preferences window appears.

[[File:Java_prefs1.png|center|500px]]

2) Choose 'Network' tab.

[[File:Java_prefs2.png|center|500px]]

3) Press 'Delete Files...' button and click 'OK' on the subsequent confirmation dialog.

===remove local JOGL library===

Locally-installed JOGL libraries of different version cause conflicts with Java Web Start technology.
JOGL library files are different between operating systems.

'''Mac OS X'''

Open the [Macintosh HD]-[Library]-[Java]-[Extensions] folder.
If some of the following files

* jogl.jar
* gluegen-rt.jar
* libjogl.jnilib
* libjogl_awt.jnilib
* libjogl_cg.jnilib
* libgluegen-rt.jnilib

exist in the folder, remove them.
Here, this operation requires root privilege.

'''Windows'''

Files that should be removed are as follows.

* &lt;JRE&gt;\lib\ext\jogl.jar
* &lt;JRE&gt;\lib\ext\gluegen-rt.jar
* &lt;JRE&gt;\bin\jogl.dll
* &lt;JRE&gt;\bin\jogl_cg.dll
* &lt;JRE&gt;\bin\jogl_awt.dll
* &lt;JRE&gt;\bin\gluegen-rt.dll

Here, &lt;JRE&gt; denotes the folder that JRE has been installed; typically &lt;JRE&gt;=C:\Program Files\Java\jre6.

'''Linux'''

Files that should be removed are as follows.

* &lt;JRE&gt;/lib/ext/jogl.jar
* &lt;JRE&gt;/lib/ext/gluegen-rt.jar
* &lt;JRE&gt;/lib/&lt;arch&gt;/libjogl.so
* &lt;JRE&gt;/lib/&lt;arch&gt;/libjogl_cg.so
* &lt;JRE&gt;/lib/&lt;arch&gt;/libjogl_awt.so
* &lt;JRE&gt;/lib/&lt;arch&gt;/libjogl_drihack.so
* &lt;JRE&gt;/lib/&lt;arch&gt;/libgluegen-rt.so

Here, &lt;JRE&gt; denotes the directory that JRE has been installed; typically &lt;JRE&gt;=/usr/java/jdk1.6.0_17/jre,
and &lt;arch&gt; the processor architecture such as &lt;arch&gt;=i386.

== jV applet with Internet Explorer ==

When visiting a web page that contains a jV applet with Internet Explorer, there sometimes occurs trouble in working with native JOGL libraries especially on Windows Vista. Please use Firefox web browser in that case.

== Class not found error on applet ==

When you use JRE6 Update21 (1.6.0_21) with the next-generation Java Plug-in enabled on Windows or Linux, 
the following error occurs for the combination of jV applet and applet-launcher.

 Error: Class not found: org.pdbj.viewer.gui.ViewerApplet

You can avoid this problem by disabling the next-generation Java Plug-in.
[http://www.java.com/en/download/help/new_plugin.xml Here] is how to do that for Windows users.
On Linux platform, users can manually replace the symbolic link to new plug-in &lt;tt&gt;libnpjp2.so&lt;/tt&gt;
with the symbolic link to classic plug-in &lt;tt&gt;libjavaplugin_oji.so&lt;/tt&gt;
(see [http://www.oracle.com/technetwork/java/javase/manual-plugin-install-linux-136395.html this page] for help).
If you are using firefox 3.6 or later, however, you need to downgrade JRE to 1.6.0_20
because firefox of those versions run applets only with the new Java Plug-in.</text>
    <sha1>fb797a5e8e9d19fa92a306f72392e3c6530e9a4c</sha1>
  </revision>
  <revision>
    <id>408</id>
    <parentid>407</parentid>
    <timestamp>2010-08-19T01:58:54Z</timestamp>
    <contributor>
      <username>Cudo29</username>
      <id>5</id>
    </contributor>
    <comment>/* Class not found error on applet */ The link to the download site of the previous JRE was added.</comment>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="3813" xml:space="preserve">{| style="left"
 |__TOC__
 |}

== Certificate error on applet ==

When you use JRE6 Update15 (1.6.0_15) or JRE6 Update16 (1.6.0_16) on Windows or Linux,
jV applet and applet-launcher fail to start up with the following error.

 Error:java.io.IOException:Cannot find certificates for JNLP AppletLauncher class

Please use JRE6 Update17 (1.6.0_17) or later.

== JOGL library conflict ==

If you cannot start jV via Java Web Start or view jV applets due to a failure of locating the JOGL library, try the followings.

===clear cached files===

On JRE of version 1.6.0_15 and 1.6.0_16, previously cached JOGL files cause a problem
even if newer files are placed on the server.
JRE of version 1.6.0_17 or later is recommended.
On Mac OS X Snow Leopard, however, the latest JRE is of version 1.6.0_15 at the moment.
The following steps show how to clear cached files.

1) Double-click the [Macintosh HD]-[Applications]-[Utilities]-[Java Preferences] icon, then the Java Preferences window appears.

[[File:Java_prefs1.png|center|500px]]

2) Choose 'Network' tab.

[[File:Java_prefs2.png|center|500px]]

3) Press 'Delete Files...' button and click 'OK' on the subsequent confirmation dialog.

===remove local JOGL library===

Locally-installed JOGL libraries of different version cause conflicts with Java Web Start technology.
JOGL library files are different between operating systems.

'''Mac OS X'''

Open the [Macintosh HD]-[Library]-[Java]-[Extensions] folder.
If some of the following files

* jogl.jar
* gluegen-rt.jar
* libjogl.jnilib
* libjogl_awt.jnilib
* libjogl_cg.jnilib
* libgluegen-rt.jnilib

exist in the folder, remove them.
Here, this operation requires root privilege.

'''Windows'''

Files that should be removed are as follows.

* &lt;JRE&gt;\lib\ext\jogl.jar
* &lt;JRE&gt;\lib\ext\gluegen-rt.jar
* &lt;JRE&gt;\bin\jogl.dll
* &lt;JRE&gt;\bin\jogl_cg.dll
* &lt;JRE&gt;\bin\jogl_awt.dll
* &lt;JRE&gt;\bin\gluegen-rt.dll

Here, &lt;JRE&gt; denotes the folder that JRE has been installed; typically &lt;JRE&gt;=C:\Program Files\Java\jre6.

'''Linux'''

Files that should be removed are as follows.

* &lt;JRE&gt;/lib/ext/jogl.jar
* &lt;JRE&gt;/lib/ext/gluegen-rt.jar
* &lt;JRE&gt;/lib/&lt;arch&gt;/libjogl.so
* &lt;JRE&gt;/lib/&lt;arch&gt;/libjogl_cg.so
* &lt;JRE&gt;/lib/&lt;arch&gt;/libjogl_awt.so
* &lt;JRE&gt;/lib/&lt;arch&gt;/libjogl_drihack.so
* &lt;JRE&gt;/lib/&lt;arch&gt;/libgluegen-rt.so

Here, &lt;JRE&gt; denotes the directory that JRE has been installed; typically &lt;JRE&gt;=/usr/java/jdk1.6.0_17/jre,
and &lt;arch&gt; the processor architecture such as &lt;arch&gt;=i386.

== jV applet with Internet Explorer ==

When visiting a web page that contains a jV applet with Internet Explorer, there sometimes occurs trouble in working with native JOGL libraries especially on Windows Vista. Please use Firefox web browser in that case.

== Class not found error on applet ==

When you use JRE6 Update21 (1.6.0_21) with the next-generation Java Plug-in enabled on Windows or Linux, 
the following error occurs for the combination of jV applet and applet-launcher.

 Error: Class not found: org.pdbj.viewer.gui.ViewerApplet

You can avoid this problem by disabling the next-generation Java Plug-in.
[http://www.java.com/en/download/help/new_plugin.xml Here] is how to do that for Windows users.
On Linux platform, users can manually replace the symbolic link to new plug-in &lt;tt&gt;libnpjp2.so&lt;/tt&gt;
with the symbolic link to classic plug-in &lt;tt&gt;libjavaplugin_oji.so&lt;/tt&gt;
(see [http://www.oracle.com/technetwork/java/javase/manual-plugin-install-linux-136395.html this page] for help).
If you are using firefox 3.6 or later, however, you need to downgrade JRE to 1.6.0_20
because firefox of those versions run applets only with the new Java Plug-in.
To get JRE 1.6.0_20, see [https://cds.sun.com/is-bin/INTERSHOP.enfinity/WFS/CDS-CDS_Developer-Site/en_US/-/USD/ViewProductDetail-Start?ProductRef=jre-6u20-oth-JPR@CDS-CDS_Developer this page].</text>
    <sha1>cd0d94aff5370432410a2f3c61d7599453d6e2b9</sha1>
  </revision>
</page>
<page arvcontinue="20100805022053|404">
  <title>Main Page</title>
  <ns>0</ns>
  <id>1</id>
  <revision>
    <id>409</id>
    <parentid>403</parentid>
    <timestamp>2010-09-14T07:23:39Z</timestamp>
    <contributor>
      <username>IMSsato</username>
      <id>4</id>
    </contributor>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="6409" xml:space="preserve">&lt;big&gt;'''Welcome to jV wiki.'''&lt;/big&gt;

jV version 3 (formerly known as PDBjViewer) is a program to display molecular graphics of protein and nucleic acids. 
jV supports the following features:
* jV can read and display PDBML files, the canonical XML format for the Protein Data Bank.
* Of course, jV can read and display the traditional PDB format files, too.
* RasMol-like usability.
* jV can process more than one molecules.
* jV can display polygons specified by XML. ([http://ef-site.hgc.jp/eF-site/schema/polygon12.xsd XML Schema for polygons] is available.)
* Multiple polygons can be processed simultaneously, and be superimposed onto molecular images.
* Animation can be realized.
* jV runs on the Java Runtime Environment ([http://java.sun.com/javase/index.jsp JRE]) so that it can work as a stand-alone application as well as an applet.
* The graphics of jV is based on OpenGL ([http://kenai.com/projects/jogl JOGL]), thereby producing fairly beautiful pictures.


The program 'jV' has been developed by [http://www.hgc.jp/~kinosita/TOP.html Kengo Kinoshita] ([http://www.is.tohoku.ac.jp/index-e.html Graduate School of Information Sciences], [http://www.tohoku.ac.jp/english/ Tohoku University]) and [http://www.protein.osaka-u.ac.jp/rcsfp/pi/ Haruki Nakamura] ([http://www.protein.osaka-u.ac.jp/index_e.php Institute for Protein Research], [http://www.osaka-u.ac.jp/eng/index.html Osaka Univeristy]), with the support from [http://www-bird.jst.go.jp/index_e.html JST-BIRD].


&lt;gallery&gt;
File:Spacefill.jpg
File:Cartoon.jpg
File:Surface.jpg
File:edmap.jpg
&lt;/gallery&gt;


== Start up ==
You can start up jV (3.8.1) with Java Web Start technology immediately from here.
* [http://ef-site.hgc.jp/eF-site/servlet/stable/jV.jnlp stable JOGL version] (recommended)
* [http://ef-site.hgc.jp/eF-site/servlet/current/jV.jnlp recent JOGL version]

== Basic Usage ==
You can execute basic operations such as rotation and translation with mouse action. Major actions are described in the following table:
{| style="margin:auto;border:1px solid gray"
! rowspan="2" style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap;font-weight:bold" |Action
! colspan="2" style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap;font-weight:bold" |Mouse Operation
|-
! style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap;font-weight:bold" |Windows, Linux
! style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap;font-weight:bold" |Mac OS X
|-
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |rotate around X (horizontal) axis&lt;br /&gt;rotate around Y (vertical) axis
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |left drag
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |drag
|-
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |translate along X axis (holizontally)&lt;br /&gt;translate along Y axis (vertically)
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |right drag
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |Command + drag
|-
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |translate along Z axis (zoom in/out)
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |Shift + left drag
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |Shift + drag
|}

Operations such as changing display models and colors and saving the image, can be executed with a menu. The location of the menu is at the top of the application window in Windows and at the top of screen in Mac as the stand-alone application. As an applet usage, a popup menu appears by clicking the right mouse button on the display screen, or clicking with a "Command" button in case of Mac.

{| style="margin:auto;border:0"
|-
| [[File:Jv_menu_win.png|The location of menu in jV stand-alone version in Windows.|250px]]
| [[File:Jv_menu_mac.png|The location of menu in jV stand-alone version in Mac.|250px]]
| [[File:popupmenu_en.png|The location of menu in applet version.|250px]]
|-
| style="text-align:center" |Stand-alone (Windows)
| style="text-align:center" |Stand-alone (Mac)
| style="text-align:center" |Applet
|}

Basic menu operations are following (see also [[GUI]] for details):

{| style="margin:auto;border:1px solid gray;border-collapse:collapse"
! style="padding:0 0.5em;border:1px solid gray" | Operations
! style="padding:0 0.5em;border:1px solid gray" | Menu location
|-
| style="padding:0 0.5em;border:1px solid gray" | Save a static image
| style="padding:0 0.5em;border:1px solid gray" | [File]-[Save]-[PNG/JPEG]
|-
| style="padding:0 0.5em;border:1px solid gray" | Change the expression format
| style="padding:0 0.5em;border:1px solid gray" | [File]-[Display]-[Wireframe/Backbone/Sticks/Spacefill/Ball&amp;amp;Stick/Ribbons/Cartoon]
|-
| style="padding:0 0.5em;border:1px solid gray" | Change the color
| style="padding:0 0.5em;border:1px solid gray" | [File]-[Colors]-[Monochrome/CPK/Shapely/Group/Chain/Temperature/Structure/Charge/Amino]
|}

To execute more complicated operation such as diplaying some piece of the molecule or changing some part of molecule in another style, use command line operation.

See also [[#Other resources]] for details:


== Download ==
You can also download the program and start it up locally.
In this case, installing JOGL is required in advance (see [[Installation_of_jV3 | Installation]] page).
The following links take you to the download pages. (latest version is 3.8.1@2010/9/14)
* [http://ef-site.hgc.jp/eF-site/servlet/DownloadViewerBinary binary (3.8.1)] 
* [http://ef-site.hgc.jp/eF-site/servlet/Registration source code (3.8.1)] (registration will be required)

== Other resources ==
* [http://ef-site.hgc.jp/eF-site/jV/jV_manual.html Manual] (html in English)
* [[How_to_use]] (in this site in English)
* [http://www.pdbj.org/jv/manual/index_ja.html Manual] (html in Japanese)
* [http://www.pdbj.org/jv/manual/jV_manual.pdf Manual] (pdf in English, for ver. 3.3)
* [http://ef-site.hgc.jp/eF-site/jV/jV3_User'sGuide.pdf User's guide] (for ver. 3.3 in English)</text>
    <sha1>71762c8d2132652dd26c09364550d4c7664f8201</sha1>
  </revision>
  <revision>
    <id>416</id>
    <parentid>409</parentid>
    <timestamp>2010-10-04T06:06:19Z</timestamp>
    <contributor>
      <username>IMSsato</username>
      <id>4</id>
    </contributor>
    <comment>/* Start up */</comment>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="6409" xml:space="preserve">&lt;big&gt;'''Welcome to jV wiki.'''&lt;/big&gt;

jV version 3 (formerly known as PDBjViewer) is a program to display molecular graphics of protein and nucleic acids. 
jV supports the following features:
* jV can read and display PDBML files, the canonical XML format for the Protein Data Bank.
* Of course, jV can read and display the traditional PDB format files, too.
* RasMol-like usability.
* jV can process more than one molecules.
* jV can display polygons specified by XML. ([http://ef-site.hgc.jp/eF-site/schema/polygon12.xsd XML Schema for polygons] is available.)
* Multiple polygons can be processed simultaneously, and be superimposed onto molecular images.
* Animation can be realized.
* jV runs on the Java Runtime Environment ([http://java.sun.com/javase/index.jsp JRE]) so that it can work as a stand-alone application as well as an applet.
* The graphics of jV is based on OpenGL ([http://kenai.com/projects/jogl JOGL]), thereby producing fairly beautiful pictures.


The program 'jV' has been developed by [http://www.hgc.jp/~kinosita/TOP.html Kengo Kinoshita] ([http://www.is.tohoku.ac.jp/index-e.html Graduate School of Information Sciences], [http://www.tohoku.ac.jp/english/ Tohoku University]) and [http://www.protein.osaka-u.ac.jp/rcsfp/pi/ Haruki Nakamura] ([http://www.protein.osaka-u.ac.jp/index_e.php Institute for Protein Research], [http://www.osaka-u.ac.jp/eng/index.html Osaka Univeristy]), with the support from [http://www-bird.jst.go.jp/index_e.html JST-BIRD].


&lt;gallery&gt;
File:Spacefill.jpg
File:Cartoon.jpg
File:Surface.jpg
File:edmap.jpg
&lt;/gallery&gt;


== Start up ==
You can start up jV (3.8.2) with Java Web Start technology immediately from here.
* [http://ef-site.hgc.jp/eF-site/servlet/stable/jV.jnlp stable JOGL version] (recommended)
* [http://ef-site.hgc.jp/eF-site/servlet/current/jV.jnlp recent JOGL version]

== Basic Usage ==
You can execute basic operations such as rotation and translation with mouse action. Major actions are described in the following table:
{| style="margin:auto;border:1px solid gray"
! rowspan="2" style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap;font-weight:bold" |Action
! colspan="2" style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap;font-weight:bold" |Mouse Operation
|-
! style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap;font-weight:bold" |Windows, Linux
! style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap;font-weight:bold" |Mac OS X
|-
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |rotate around X (horizontal) axis&lt;br /&gt;rotate around Y (vertical) axis
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |left drag
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |drag
|-
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |translate along X axis (holizontally)&lt;br /&gt;translate along Y axis (vertically)
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |right drag
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |Command + drag
|-
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |translate along Z axis (zoom in/out)
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |Shift + left drag
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |Shift + drag
|}

Operations such as changing display models and colors and saving the image, can be executed with a menu. The location of the menu is at the top of the application window in Windows and at the top of screen in Mac as the stand-alone application. As an applet usage, a popup menu appears by clicking the right mouse button on the display screen, or clicking with a "Command" button in case of Mac.

{| style="margin:auto;border:0"
|-
| [[File:Jv_menu_win.png|The location of menu in jV stand-alone version in Windows.|250px]]
| [[File:Jv_menu_mac.png|The location of menu in jV stand-alone version in Mac.|250px]]
| [[File:popupmenu_en.png|The location of menu in applet version.|250px]]
|-
| style="text-align:center" |Stand-alone (Windows)
| style="text-align:center" |Stand-alone (Mac)
| style="text-align:center" |Applet
|}

Basic menu operations are following (see also [[GUI]] for details):

{| style="margin:auto;border:1px solid gray;border-collapse:collapse"
! style="padding:0 0.5em;border:1px solid gray" | Operations
! style="padding:0 0.5em;border:1px solid gray" | Menu location
|-
| style="padding:0 0.5em;border:1px solid gray" | Save a static image
| style="padding:0 0.5em;border:1px solid gray" | [File]-[Save]-[PNG/JPEG]
|-
| style="padding:0 0.5em;border:1px solid gray" | Change the expression format
| style="padding:0 0.5em;border:1px solid gray" | [File]-[Display]-[Wireframe/Backbone/Sticks/Spacefill/Ball&amp;amp;Stick/Ribbons/Cartoon]
|-
| style="padding:0 0.5em;border:1px solid gray" | Change the color
| style="padding:0 0.5em;border:1px solid gray" | [File]-[Colors]-[Monochrome/CPK/Shapely/Group/Chain/Temperature/Structure/Charge/Amino]
|}

To execute more complicated operation such as diplaying some piece of the molecule or changing some part of molecule in another style, use command line operation.

See also [[#Other resources]] for details:


== Download ==
You can also download the program and start it up locally.
In this case, installing JOGL is required in advance (see [[Installation_of_jV3 | Installation]] page).
The following links take you to the download pages. (latest version is 3.8.1@2010/9/14)
* [http://ef-site.hgc.jp/eF-site/servlet/DownloadViewerBinary binary (3.8.1)] 
* [http://ef-site.hgc.jp/eF-site/servlet/Registration source code (3.8.1)] (registration will be required)

== Other resources ==
* [http://ef-site.hgc.jp/eF-site/jV/jV_manual.html Manual] (html in English)
* [[How_to_use]] (in this site in English)
* [http://www.pdbj.org/jv/manual/index_ja.html Manual] (html in Japanese)
* [http://www.pdbj.org/jv/manual/jV_manual.pdf Manual] (pdf in English, for ver. 3.3)
* [http://ef-site.hgc.jp/eF-site/jV/jV3_User'sGuide.pdf User's guide] (for ver. 3.3 in English)</text>
    <sha1>3ba1bbbdc4ca9e3d9a4e33a2edde38870c6a61ec</sha1>
  </revision>
  <revision>
    <id>417</id>
    <parentid>416</parentid>
    <timestamp>2010-10-04T06:06:57Z</timestamp>
    <contributor>
      <username>IMSsato</username>
      <id>4</id>
    </contributor>
    <comment>/* Download */</comment>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="6409" xml:space="preserve">&lt;big&gt;'''Welcome to jV wiki.'''&lt;/big&gt;

jV version 3 (formerly known as PDBjViewer) is a program to display molecular graphics of protein and nucleic acids. 
jV supports the following features:
* jV can read and display PDBML files, the canonical XML format for the Protein Data Bank.
* Of course, jV can read and display the traditional PDB format files, too.
* RasMol-like usability.
* jV can process more than one molecules.
* jV can display polygons specified by XML. ([http://ef-site.hgc.jp/eF-site/schema/polygon12.xsd XML Schema for polygons] is available.)
* Multiple polygons can be processed simultaneously, and be superimposed onto molecular images.
* Animation can be realized.
* jV runs on the Java Runtime Environment ([http://java.sun.com/javase/index.jsp JRE]) so that it can work as a stand-alone application as well as an applet.
* The graphics of jV is based on OpenGL ([http://kenai.com/projects/jogl JOGL]), thereby producing fairly beautiful pictures.


The program 'jV' has been developed by [http://www.hgc.jp/~kinosita/TOP.html Kengo Kinoshita] ([http://www.is.tohoku.ac.jp/index-e.html Graduate School of Information Sciences], [http://www.tohoku.ac.jp/english/ Tohoku University]) and [http://www.protein.osaka-u.ac.jp/rcsfp/pi/ Haruki Nakamura] ([http://www.protein.osaka-u.ac.jp/index_e.php Institute for Protein Research], [http://www.osaka-u.ac.jp/eng/index.html Osaka Univeristy]), with the support from [http://www-bird.jst.go.jp/index_e.html JST-BIRD].


&lt;gallery&gt;
File:Spacefill.jpg
File:Cartoon.jpg
File:Surface.jpg
File:edmap.jpg
&lt;/gallery&gt;


== Start up ==
You can start up jV (3.8.2) with Java Web Start technology immediately from here.
* [http://ef-site.hgc.jp/eF-site/servlet/stable/jV.jnlp stable JOGL version] (recommended)
* [http://ef-site.hgc.jp/eF-site/servlet/current/jV.jnlp recent JOGL version]

== Basic Usage ==
You can execute basic operations such as rotation and translation with mouse action. Major actions are described in the following table:
{| style="margin:auto;border:1px solid gray"
! rowspan="2" style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap;font-weight:bold" |Action
! colspan="2" style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap;font-weight:bold" |Mouse Operation
|-
! style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap;font-weight:bold" |Windows, Linux
! style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap;font-weight:bold" |Mac OS X
|-
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |rotate around X (horizontal) axis&lt;br /&gt;rotate around Y (vertical) axis
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |left drag
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |drag
|-
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |translate along X axis (holizontally)&lt;br /&gt;translate along Y axis (vertically)
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |right drag
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |Command + drag
|-
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |translate along Z axis (zoom in/out)
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |Shift + left drag
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |Shift + drag
|}

Operations such as changing display models and colors and saving the image, can be executed with a menu. The location of the menu is at the top of the application window in Windows and at the top of screen in Mac as the stand-alone application. As an applet usage, a popup menu appears by clicking the right mouse button on the display screen, or clicking with a "Command" button in case of Mac.

{| style="margin:auto;border:0"
|-
| [[File:Jv_menu_win.png|The location of menu in jV stand-alone version in Windows.|250px]]
| [[File:Jv_menu_mac.png|The location of menu in jV stand-alone version in Mac.|250px]]
| [[File:popupmenu_en.png|The location of menu in applet version.|250px]]
|-
| style="text-align:center" |Stand-alone (Windows)
| style="text-align:center" |Stand-alone (Mac)
| style="text-align:center" |Applet
|}

Basic menu operations are following (see also [[GUI]] for details):

{| style="margin:auto;border:1px solid gray;border-collapse:collapse"
! style="padding:0 0.5em;border:1px solid gray" | Operations
! style="padding:0 0.5em;border:1px solid gray" | Menu location
|-
| style="padding:0 0.5em;border:1px solid gray" | Save a static image
| style="padding:0 0.5em;border:1px solid gray" | [File]-[Save]-[PNG/JPEG]
|-
| style="padding:0 0.5em;border:1px solid gray" | Change the expression format
| style="padding:0 0.5em;border:1px solid gray" | [File]-[Display]-[Wireframe/Backbone/Sticks/Spacefill/Ball&amp;amp;Stick/Ribbons/Cartoon]
|-
| style="padding:0 0.5em;border:1px solid gray" | Change the color
| style="padding:0 0.5em;border:1px solid gray" | [File]-[Colors]-[Monochrome/CPK/Shapely/Group/Chain/Temperature/Structure/Charge/Amino]
|}

To execute more complicated operation such as diplaying some piece of the molecule or changing some part of molecule in another style, use command line operation.

See also [[#Other resources]] for details:


== Download ==
You can also download the program and start it up locally.
In this case, installing JOGL is required in advance (see [[Installation_of_jV3 | Installation]] page).
The following links take you to the download pages. (latest version is 3.8.2@2010/10/4)
* [http://ef-site.hgc.jp/eF-site/servlet/DownloadViewerBinary binary (3.8.2)] 
* [http://ef-site.hgc.jp/eF-site/servlet/Registration source code (3.8.2)] (registration will be required)

== Other resources ==
* [http://ef-site.hgc.jp/eF-site/jV/jV_manual.html Manual] (html in English)
* [[How_to_use]] (in this site in English)
* [http://www.pdbj.org/jv/manual/index_ja.html Manual] (html in Japanese)
* [http://www.pdbj.org/jv/manual/jV_manual.pdf Manual] (pdf in English, for ver. 3.3)
* [http://ef-site.hgc.jp/eF-site/jV/jV3_User'sGuide.pdf User's guide] (for ver. 3.3 in English)</text>
    <sha1>89ee9f9c362efb777679ac2418e2010a2f4b3b52</sha1>
  </revision>
  <revision>
    <id>452</id>
    <parentid>417</parentid>
    <timestamp>2011-01-06T07:38:30Z</timestamp>
    <contributor>
      <username>IMSsato</username>
      <id>4</id>
    </contributor>
    <comment>/* Start up */</comment>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="6409" xml:space="preserve">&lt;big&gt;'''Welcome to jV wiki.'''&lt;/big&gt;

jV version 3 (formerly known as PDBjViewer) is a program to display molecular graphics of protein and nucleic acids. 
jV supports the following features:
* jV can read and display PDBML files, the canonical XML format for the Protein Data Bank.
* Of course, jV can read and display the traditional PDB format files, too.
* RasMol-like usability.
* jV can process more than one molecules.
* jV can display polygons specified by XML. ([http://ef-site.hgc.jp/eF-site/schema/polygon12.xsd XML Schema for polygons] is available.)
* Multiple polygons can be processed simultaneously, and be superimposed onto molecular images.
* Animation can be realized.
* jV runs on the Java Runtime Environment ([http://java.sun.com/javase/index.jsp JRE]) so that it can work as a stand-alone application as well as an applet.
* The graphics of jV is based on OpenGL ([http://kenai.com/projects/jogl JOGL]), thereby producing fairly beautiful pictures.


The program 'jV' has been developed by [http://www.hgc.jp/~kinosita/TOP.html Kengo Kinoshita] ([http://www.is.tohoku.ac.jp/index-e.html Graduate School of Information Sciences], [http://www.tohoku.ac.jp/english/ Tohoku University]) and [http://www.protein.osaka-u.ac.jp/rcsfp/pi/ Haruki Nakamura] ([http://www.protein.osaka-u.ac.jp/index_e.php Institute for Protein Research], [http://www.osaka-u.ac.jp/eng/index.html Osaka Univeristy]), with the support from [http://www-bird.jst.go.jp/index_e.html JST-BIRD].


&lt;gallery&gt;
File:Spacefill.jpg
File:Cartoon.jpg
File:Surface.jpg
File:edmap.jpg
&lt;/gallery&gt;


== Start up ==
You can start up jV (3.8.3) with Java Web Start technology immediately from here.
* [http://ef-site.hgc.jp/eF-site/servlet/stable/jV.jnlp stable JOGL version] (recommended)
* [http://ef-site.hgc.jp/eF-site/servlet/current/jV.jnlp recent JOGL version]

== Basic Usage ==
You can execute basic operations such as rotation and translation with mouse action. Major actions are described in the following table:
{| style="margin:auto;border:1px solid gray"
! rowspan="2" style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap;font-weight:bold" |Action
! colspan="2" style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap;font-weight:bold" |Mouse Operation
|-
! style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap;font-weight:bold" |Windows, Linux
! style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap;font-weight:bold" |Mac OS X
|-
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |rotate around X (horizontal) axis&lt;br /&gt;rotate around Y (vertical) axis
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |left drag
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |drag
|-
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |translate along X axis (holizontally)&lt;br /&gt;translate along Y axis (vertically)
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |right drag
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |Command + drag
|-
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |translate along Z axis (zoom in/out)
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |Shift + left drag
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |Shift + drag
|}

Operations such as changing display models and colors and saving the image, can be executed with a menu. The location of the menu is at the top of the application window in Windows and at the top of screen in Mac as the stand-alone application. As an applet usage, a popup menu appears by clicking the right mouse button on the display screen, or clicking with a "Command" button in case of Mac.

{| style="margin:auto;border:0"
|-
| [[File:Jv_menu_win.png|The location of menu in jV stand-alone version in Windows.|250px]]
| [[File:Jv_menu_mac.png|The location of menu in jV stand-alone version in Mac.|250px]]
| [[File:popupmenu_en.png|The location of menu in applet version.|250px]]
|-
| style="text-align:center" |Stand-alone (Windows)
| style="text-align:center" |Stand-alone (Mac)
| style="text-align:center" |Applet
|}

Basic menu operations are following (see also [[GUI]] for details):

{| style="margin:auto;border:1px solid gray;border-collapse:collapse"
! style="padding:0 0.5em;border:1px solid gray" | Operations
! style="padding:0 0.5em;border:1px solid gray" | Menu location
|-
| style="padding:0 0.5em;border:1px solid gray" | Save a static image
| style="padding:0 0.5em;border:1px solid gray" | [File]-[Save]-[PNG/JPEG]
|-
| style="padding:0 0.5em;border:1px solid gray" | Change the expression format
| style="padding:0 0.5em;border:1px solid gray" | [File]-[Display]-[Wireframe/Backbone/Sticks/Spacefill/Ball&amp;amp;Stick/Ribbons/Cartoon]
|-
| style="padding:0 0.5em;border:1px solid gray" | Change the color
| style="padding:0 0.5em;border:1px solid gray" | [File]-[Colors]-[Monochrome/CPK/Shapely/Group/Chain/Temperature/Structure/Charge/Amino]
|}

To execute more complicated operation such as diplaying some piece of the molecule or changing some part of molecule in another style, use command line operation.

See also [[#Other resources]] for details:


== Download ==
You can also download the program and start it up locally.
In this case, installing JOGL is required in advance (see [[Installation_of_jV3 | Installation]] page).
The following links take you to the download pages. (latest version is 3.8.2@2010/10/4)
* [http://ef-site.hgc.jp/eF-site/servlet/DownloadViewerBinary binary (3.8.2)] 
* [http://ef-site.hgc.jp/eF-site/servlet/Registration source code (3.8.2)] (registration will be required)

== Other resources ==
* [http://ef-site.hgc.jp/eF-site/jV/jV_manual.html Manual] (html in English)
* [[How_to_use]] (in this site in English)
* [http://www.pdbj.org/jv/manual/index_ja.html Manual] (html in Japanese)
* [http://www.pdbj.org/jv/manual/jV_manual.pdf Manual] (pdf in English, for ver. 3.3)
* [http://ef-site.hgc.jp/eF-site/jV/jV3_User'sGuide.pdf User's guide] (for ver. 3.3 in English)</text>
    <sha1>6e3ea14d92296dba46a6072c706131102b0b7c31</sha1>
  </revision>
  <revision>
    <id>453</id>
    <parentid>452</parentid>
    <timestamp>2011-01-06T07:38:51Z</timestamp>
    <contributor>
      <username>IMSsato</username>
      <id>4</id>
    </contributor>
    <comment>/* Download */</comment>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="6408" xml:space="preserve">&lt;big&gt;'''Welcome to jV wiki.'''&lt;/big&gt;

jV version 3 (formerly known as PDBjViewer) is a program to display molecular graphics of protein and nucleic acids. 
jV supports the following features:
* jV can read and display PDBML files, the canonical XML format for the Protein Data Bank.
* Of course, jV can read and display the traditional PDB format files, too.
* RasMol-like usability.
* jV can process more than one molecules.
* jV can display polygons specified by XML. ([http://ef-site.hgc.jp/eF-site/schema/polygon12.xsd XML Schema for polygons] is available.)
* Multiple polygons can be processed simultaneously, and be superimposed onto molecular images.
* Animation can be realized.
* jV runs on the Java Runtime Environment ([http://java.sun.com/javase/index.jsp JRE]) so that it can work as a stand-alone application as well as an applet.
* The graphics of jV is based on OpenGL ([http://kenai.com/projects/jogl JOGL]), thereby producing fairly beautiful pictures.


The program 'jV' has been developed by [http://www.hgc.jp/~kinosita/TOP.html Kengo Kinoshita] ([http://www.is.tohoku.ac.jp/index-e.html Graduate School of Information Sciences], [http://www.tohoku.ac.jp/english/ Tohoku University]) and [http://www.protein.osaka-u.ac.jp/rcsfp/pi/ Haruki Nakamura] ([http://www.protein.osaka-u.ac.jp/index_e.php Institute for Protein Research], [http://www.osaka-u.ac.jp/eng/index.html Osaka Univeristy]), with the support from [http://www-bird.jst.go.jp/index_e.html JST-BIRD].


&lt;gallery&gt;
File:Spacefill.jpg
File:Cartoon.jpg
File:Surface.jpg
File:edmap.jpg
&lt;/gallery&gt;


== Start up ==
You can start up jV (3.8.3) with Java Web Start technology immediately from here.
* [http://ef-site.hgc.jp/eF-site/servlet/stable/jV.jnlp stable JOGL version] (recommended)
* [http://ef-site.hgc.jp/eF-site/servlet/current/jV.jnlp recent JOGL version]

== Basic Usage ==
You can execute basic operations such as rotation and translation with mouse action. Major actions are described in the following table:
{| style="margin:auto;border:1px solid gray"
! rowspan="2" style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap;font-weight:bold" |Action
! colspan="2" style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap;font-weight:bold" |Mouse Operation
|-
! style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap;font-weight:bold" |Windows, Linux
! style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap;font-weight:bold" |Mac OS X
|-
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |rotate around X (horizontal) axis&lt;br /&gt;rotate around Y (vertical) axis
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |left drag
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |drag
|-
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |translate along X axis (holizontally)&lt;br /&gt;translate along Y axis (vertically)
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |right drag
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |Command + drag
|-
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |translate along Z axis (zoom in/out)
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |Shift + left drag
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |Shift + drag
|}

Operations such as changing display models and colors and saving the image, can be executed with a menu. The location of the menu is at the top of the application window in Windows and at the top of screen in Mac as the stand-alone application. As an applet usage, a popup menu appears by clicking the right mouse button on the display screen, or clicking with a "Command" button in case of Mac.

{| style="margin:auto;border:0"
|-
| [[File:Jv_menu_win.png|The location of menu in jV stand-alone version in Windows.|250px]]
| [[File:Jv_menu_mac.png|The location of menu in jV stand-alone version in Mac.|250px]]
| [[File:popupmenu_en.png|The location of menu in applet version.|250px]]
|-
| style="text-align:center" |Stand-alone (Windows)
| style="text-align:center" |Stand-alone (Mac)
| style="text-align:center" |Applet
|}

Basic menu operations are following (see also [[GUI]] for details):

{| style="margin:auto;border:1px solid gray;border-collapse:collapse"
! style="padding:0 0.5em;border:1px solid gray" | Operations
! style="padding:0 0.5em;border:1px solid gray" | Menu location
|-
| style="padding:0 0.5em;border:1px solid gray" | Save a static image
| style="padding:0 0.5em;border:1px solid gray" | [File]-[Save]-[PNG/JPEG]
|-
| style="padding:0 0.5em;border:1px solid gray" | Change the expression format
| style="padding:0 0.5em;border:1px solid gray" | [File]-[Display]-[Wireframe/Backbone/Sticks/Spacefill/Ball&amp;amp;Stick/Ribbons/Cartoon]
|-
| style="padding:0 0.5em;border:1px solid gray" | Change the color
| style="padding:0 0.5em;border:1px solid gray" | [File]-[Colors]-[Monochrome/CPK/Shapely/Group/Chain/Temperature/Structure/Charge/Amino]
|}

To execute more complicated operation such as diplaying some piece of the molecule or changing some part of molecule in another style, use command line operation.

See also [[#Other resources]] for details:


== Download ==
You can also download the program and start it up locally.
In this case, installing JOGL is required in advance (see [[Installation_of_jV3 | Installation]] page).
The following links take you to the download pages. (latest version is 3.8.3@2011/1/6)
* [http://ef-site.hgc.jp/eF-site/servlet/DownloadViewerBinary binary (3.8.3)] 
* [http://ef-site.hgc.jp/eF-site/servlet/Registration source code (3.8.3)] (registration will be required)

== Other resources ==
* [http://ef-site.hgc.jp/eF-site/jV/jV_manual.html Manual] (html in English)
* [[How_to_use]] (in this site in English)
* [http://www.pdbj.org/jv/manual/index_ja.html Manual] (html in Japanese)
* [http://www.pdbj.org/jv/manual/jV_manual.pdf Manual] (pdf in English, for ver. 3.3)
* [http://ef-site.hgc.jp/eF-site/jV/jV3_User'sGuide.pdf User's guide] (for ver. 3.3 in English)</text>
    <sha1>7f3167c1249afa12978931afa5f157b733c83422</sha1>
  </revision>
</page>
<page arvcontinue="20100805022053|404">
  <title>Release note</title>
  <ns>0</ns>
  <id>17</id>
  <revision>
    <id>410</id>
    <parentid>376</parentid>
    <timestamp>2010-09-14T07:41:34Z</timestamp>
    <contributor>
      <username>IMSsato</username>
      <id>4</id>
    </contributor>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="3789" xml:space="preserve">Changes and improvements have been made as follows.

* version 3.1
** The following commands have been added; 'animrange', 'set adjustview', 'show godata', and 'show xps3'.
** The xPSSS expression has been added in order to select a group of atoms.
** Several public methods have been added to the applet so as to append molecule or polygon files after the applet started.
** The applet can send information about mouse-picked atoms to JavaScript.
* version 3.1.1
** Some problems in GUI menu [Options]-[Hetero Atoms] and [Hydrogens] have been fixed.
** Some problems in 'trace' command have been fixed.
* version 3.1.2
** eF-site ID has been changed to a new format.
* version 3.1.3
** Some problems in xps3 atom selection have been fixed.
* version 3.1.4
** Some problems in finalization process of openGL rendering have been fixed.
* version 3.1.5
** The output of 'show xps3' command has been modified.
** Some problems in 'save png/jpeg' command have been fixed.
* version 3.1.6
** Some problems in loading an empty polygon file have been fixed.
* version 3.1.7
** Some problems in initialization process of the applet have been fixed.
* version 3.2
** 'show site' command has been added.
* version 3.3 beta 1
** Availabe JOGL version is restricted to JSR-231 beta 5 only.
* version 3.3
** Both the previous JOGL (version 1.1.1) and JSR-231 are available.
** The following commands have been added; 'set viewpoint', 'show viewpoint', 'set imagesize', and 'show imagesize'.
* version 3.3.1
** Some problems in reading a pdbMLplus file have been fixed.
* version 3.4
** PDB format version 3 can be processed.
* version 3.5
** Discrimination of DNA and RNA linking nucleotides is based on [http://remediation.wwpdb.org/ccd.html Chemical Component Dictionary] for PDB format version 3.
** The default representation of the cartoon model has been changed. Commands 'set cartoon_loop_tube', 'set cartoon_round' and 'set ribbonback' have been added.
** The default parameters of lighting have been changed. Commands 'set ambient', 'set diffuse1', 'set diffuse1_direction', 'set diffuse2' and 'set diffuse1_direction' have been added.
** Commands 'set pdbml_noatom_url', 'set pdbml_extatom_url', 'set pdbml_plus_url', 'set efsite_url', 'set ext_site_url', 'show pdbml_url', 'show efsite_url' and 'show ext_site_url' have been added.
** The command-line option '-stdin' has been added to receive commands from stdin stream.
* version 3.6
** Users can specify the JavaScript function name used in Applet-to-JavaScript Communication.
** Applet parameter 'file_load_message' has been added.
* version 3.6.1
** Predefined set of residues has been modified.
** Old JOGL API is not supported.
* version 3.6.2
** Latest version of PDBML can be processed.
** Some problems in mouse control on Mac have been fixed.
* version 3.6.3
** Molecule file parsing has been modified to detect chain breaks properly by reading the 'label_asym_id' column in PDBML and the TER line in PDB flat file, respectively.
* version 3.6.4
** Some problems in GUI menu on Mac have been fixed.
* version 3.6.5
** The jV applet can invoke a JavaScript function when it started.
* version 3.7
** Commands 'pdbj_describe' and 'pdbj_execute' have been added.
** Keyword 'xps3' have been replaced by 'pdbj'.
* version 3.7.1
** Default PDBML URLs have been changed.
* version 3.7.2
** Some problems in creating png/jpeg image files have been fixed.
* version 3.8
** Command 'displayatom' has been added.
** The signed jV applet can save PNG/JPEG image files.
* version 3.8.1
** In commands 'cartoon', 'robbons' and 'trace', a backbone will be drawn instead when a chain does not have enough atoms to draw those models.
** Recognition of amino acids is based on [http://remediation.wwpdb.org/ccd.html Chemical Component Dictionary].</text>
    <sha1>4350e62de82d7fc8b4012aecd7fb97650bbb77b6</sha1>
  </revision>
  <revision>
    <id>415</id>
    <parentid>410</parentid>
    <timestamp>2010-09-15T01:09:26Z</timestamp>
    <contributor>
      <username>IMSsato</username>
      <id>4</id>
    </contributor>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="3789" xml:space="preserve">Changes and improvements have been made as follows.

* version 3.1
** The following commands have been added; 'animrange', 'set adjustview', 'show godata', and 'show xps3'.
** The xPSSS expression has been added in order to select a group of atoms.
** Several public methods have been added to the applet so as to append molecule or polygon files after the applet started.
** The applet can send information about mouse-picked atoms to JavaScript.
* version 3.1.1
** Some problems in GUI menu [Options]-[Hetero Atoms] and [Hydrogens] have been fixed.
** Some problems in 'trace' command have been fixed.
* version 3.1.2
** eF-site ID has been changed to a new format.
* version 3.1.3
** Some problems in xps3 atom selection have been fixed.
* version 3.1.4
** Some problems in finalization process of openGL rendering have been fixed.
* version 3.1.5
** The output of 'show xps3' command has been modified.
** Some problems in 'save png/jpeg' command have been fixed.
* version 3.1.6
** Some problems in loading an empty polygon file have been fixed.
* version 3.1.7
** Some problems in initialization process of the applet have been fixed.
* version 3.2
** 'show site' command has been added.
* version 3.3 beta 1
** Availabe JOGL version is restricted to JSR-231 beta 5 only.
* version 3.3
** Both the previous JOGL (version 1.1.1) and JSR-231 are available.
** The following commands have been added; 'set viewpoint', 'show viewpoint', 'set imagesize', and 'show imagesize'.
* version 3.3.1
** Some problems in reading a pdbMLplus file have been fixed.
* version 3.4
** PDB format version 3 can be processed.
* version 3.5
** Discrimination of DNA and RNA linking nucleotides is based on [http://remediation.wwpdb.org/ccd.html Chemical Component Dictionary] for PDB format version 3.
** The default representation of the cartoon model has been changed. Commands 'set cartoon_loop_tube', 'set cartoon_round' and 'set ribbonback' have been added.
** The default parameters of lighting have been changed. Commands 'set ambient', 'set diffuse1', 'set diffuse1_direction', 'set diffuse2' and 'set diffuse1_direction' have been added.
** Commands 'set pdbml_noatom_url', 'set pdbml_extatom_url', 'set pdbml_plus_url', 'set efsite_url', 'set ext_site_url', 'show pdbml_url', 'show efsite_url' and 'show ext_site_url' have been added.
** The command-line option '-stdin' has been added to receive commands from stdin stream.
* version 3.6
** Users can specify the JavaScript function name used in Applet-to-JavaScript Communication.
** Applet parameter 'file_load_message' has been added.
* version 3.6.1
** Predefined set of residues has been modified.
** Old JOGL API is not supported.
* version 3.6.2
** Latest version of PDBML can be processed.
** Some problems in mouse control on Mac have been fixed.
* version 3.6.3
** Molecule file parsing has been modified to detect chain breaks properly by reading the 'label_asym_id' column in PDBML and the TER line in PDB flat file, respectively.
* version 3.6.4
** Some problems in GUI menu on Mac have been fixed.
* version 3.6.5
** The jV applet can invoke a JavaScript function when it started.
* version 3.7
** Commands 'pdbj_describe' and 'pdbj_execute' have been added.
** Keyword 'xps3' have been replaced by 'pdbj'.
* version 3.7.1
** Default PDBML URLs have been changed.
* version 3.7.2
** Some problems in creating png/jpeg image files have been fixed.
* version 3.8
** Command 'displayatom' has been added.
** The signed jV applet can save PNG/JPEG image files.
* version 3.8.1
** In commands 'cartoon', 'ribbons' and 'trace', a backbone will be drawn instead when a chain does not have enough atoms to draw those models.
** Recognition of amino acids is based on [http://remediation.wwpdb.org/ccd.html Chemical Component Dictionary].</text>
    <sha1>ad00eb8e1f5419dd84df00cc433a426622785677</sha1>
  </revision>
  <revision>
    <id>418</id>
    <parentid>415</parentid>
    <timestamp>2010-10-04T06:07:55Z</timestamp>
    <contributor>
      <username>IMSsato</username>
      <id>4</id>
    </contributor>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="3847" xml:space="preserve">Changes and improvements have been made as follows.

* version 3.1
** The following commands have been added; 'animrange', 'set adjustview', 'show godata', and 'show xps3'.
** The xPSSS expression has been added in order to select a group of atoms.
** Several public methods have been added to the applet so as to append molecule or polygon files after the applet started.
** The applet can send information about mouse-picked atoms to JavaScript.
* version 3.1.1
** Some problems in GUI menu [Options]-[Hetero Atoms] and [Hydrogens] have been fixed.
** Some problems in 'trace' command have been fixed.
* version 3.1.2
** eF-site ID has been changed to a new format.
* version 3.1.3
** Some problems in xps3 atom selection have been fixed.
* version 3.1.4
** Some problems in finalization process of openGL rendering have been fixed.
* version 3.1.5
** The output of 'show xps3' command has been modified.
** Some problems in 'save png/jpeg' command have been fixed.
* version 3.1.6
** Some problems in loading an empty polygon file have been fixed.
* version 3.1.7
** Some problems in initialization process of the applet have been fixed.
* version 3.2
** 'show site' command has been added.
* version 3.3 beta 1
** Availabe JOGL version is restricted to JSR-231 beta 5 only.
* version 3.3
** Both the previous JOGL (version 1.1.1) and JSR-231 are available.
** The following commands have been added; 'set viewpoint', 'show viewpoint', 'set imagesize', and 'show imagesize'.
* version 3.3.1
** Some problems in reading a pdbMLplus file have been fixed.
* version 3.4
** PDB format version 3 can be processed.
* version 3.5
** Discrimination of DNA and RNA linking nucleotides is based on [http://remediation.wwpdb.org/ccd.html Chemical Component Dictionary] for PDB format version 3.
** The default representation of the cartoon model has been changed. Commands 'set cartoon_loop_tube', 'set cartoon_round' and 'set ribbonback' have been added.
** The default parameters of lighting have been changed. Commands 'set ambient', 'set diffuse1', 'set diffuse1_direction', 'set diffuse2' and 'set diffuse1_direction' have been added.
** Commands 'set pdbml_noatom_url', 'set pdbml_extatom_url', 'set pdbml_plus_url', 'set efsite_url', 'set ext_site_url', 'show pdbml_url', 'show efsite_url' and 'show ext_site_url' have been added.
** The command-line option '-stdin' has been added to receive commands from stdin stream.
* version 3.6
** Users can specify the JavaScript function name used in Applet-to-JavaScript Communication.
** Applet parameter 'file_load_message' has been added.
* version 3.6.1
** Predefined set of residues has been modified.
** Old JOGL API is not supported.
* version 3.6.2
** Latest version of PDBML can be processed.
** Some problems in mouse control on Mac have been fixed.
* version 3.6.3
** Molecule file parsing has been modified to detect chain breaks properly by reading the 'label_asym_id' column in PDBML and the TER line in PDB flat file, respectively.
* version 3.6.4
** Some problems in GUI menu on Mac have been fixed.
* version 3.6.5
** The jV applet can invoke a JavaScript function when it started.
* version 3.7
** Commands 'pdbj_describe' and 'pdbj_execute' have been added.
** Keyword 'xps3' have been replaced by 'pdbj'.
* version 3.7.1
** Default PDBML URLs have been changed.
* version 3.7.2
** Some problems in creating png/jpeg image files have been fixed.
* version 3.8
** Command 'displayatom' has been added.
** The signed jV applet can save PNG/JPEG image files.
* version 3.8.1
** In commands 'cartoon', 'ribbons' and 'trace', a backbone will be drawn instead when a chain does not have enough atoms to draw those models.
** Recognition of amino acids is based on [http://remediation.wwpdb.org/ccd.html Chemical Component Dictionary].
* version 3.8
** Command 'ball_and_stick' has been added.</text>
    <sha1>6f549b36baa7f12caa8fbbbb3f036b8476ea0572</sha1>
  </revision>
</page>
<page arvcontinue="20100805022053|404">
  <title>Command List</title>
  <ns>0</ns>
  <id>20</id>
  <revision>
    <id>411</id>
    <parentid>379</parentid>
    <timestamp>2010-09-14T07:48:52Z</timestamp>
    <contributor>
      <username>IMSsato</username>
      <id>4</id>
    </contributor>
    <comment>/* cartoon */</comment>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="21394" xml:space="preserve"> {| style="float:right"
  |__TOC__
  |}
Command usage of jV follows that of [http://www.rasmol.org/ Rasmol] with some modifications. In the following part, command arguments that can take an arbitrary value are denoted as &lt;value&gt; for example, arguments restricted to several possible values are listed with / as a delimiter, and arguments that can be omitted are put in brackets {}. Commands, [[#exit|exit]], [[#load|load]], [[#quit|quit]], [[#save|save]], [[#script|script]], and [[#write|write]], are not available in applet circumstance.

== anim ==
 anim forward {&lt;value&gt;}
Starts animation forward. If the &lt;value&gt; is given, just move frames forward by the specified amount.

 anim backward {&lt;value&gt;}
Starts animation backward. If the &lt;value&gt; is given, just move frames backward by the specified amount.

 anim stop
Stops animation.

== animframe ==
 animframe &lt;frame&gt; {&lt;file_ID&gt;}
Sets the frame of all animation files for the specified value. When &lt;file_ID&gt; is given, only the specified file is processed.

== animmode ==
 animmode once
Sets the behavior of animation for 'once'. When the frame reaches the last one, animation is stopped.

 animmode loop
Sets the behavior of animation for 'loop'. When the frame reaches the last one, animation is reset to the first frame and continues playing.

 animmode swing
Sets the behavior of animation for 'swing'. When the frame reaches the last one, the direction of animation is reversed.

== animrange ==
 animrange &lt;init_frame&gt;-&lt;term_frame&gt; {&lt;file_IDs&gt;}
Sets the range of all animation files. When is given, only the specified file is processed.

== animselect ==
 animselect {-a/-r} &lt;file_IDs&gt;
Selects the specified files and makes the others not selected. More than one file IDs can be specified by putting commas as the delimiter. When the option -a or -r is specified, only the selection status of the specified files are modified, selected or not selected, respectively, and the others remain unchanged.

== animspeed ==
 animspeed &lt;speed&gt;
Sets the animation speed. The argument should be an integer value from 1 to 20.

== animstep ==
 animstep &lt;step&gt; {&lt;file_ID&gt;}
Sets the step of all animation files for the specified value. When &lt;file_ID&gt; is given, only the specified file is processed.

== backbone ==
 backbone {on/true}
Turns on the selected backbone bonds.

 backbone off/false
Turns off the selected backbone bonds.

 backbone &lt;radius&gt;
Turns on the selected backbone bonds with the specified raidus (angstrom or Rasmol unit). The maximum parameter value is 2.0.

== background ==
 background &lt;color&gt;
Changes the background color. The color may be given as RGB values [r,g,b], or predefined color names.

== cartoon ==
 cartoon {on/true}
Turns on the thick ribbons for the selected residues. When a chain does not have enough atoms to draw the ribbon model, a backbone will be shown instead.

 cartoon off/false
Turns off the thick ribbons for the selected residues.

 cartoon &lt;half_width&gt;
Turns on the thick ribbons for the selected residues with the specified half width (angstrom or Rasmol unit). The maximum parameter value is 4.0.

== center ==
 center {-r/-s} {&lt;atom_expression&gt;}
Sets the center of rotation and the center of the screen to the center of a group of atoms specified by the atom expression. When the option -r or -s is specified, only the center of rotation or the center of the screen is modified, respectively.

 center {-r} [x, y, z]
Moves the center of rotation and the center of the screen from the current position by the specified amount. When the option -r is specified, only the center of rotation is modified.

 center {-r} {x, y, z}
Sets the center of rotation and the center of the screen to the specified coordinates. When the option -r is specified, only the center of rotation is modified.

 center -s [x, y]
Moves the center of the screen from the current position by the specified amount.

 center -s {x, y}
Sets the center of the screen to the specified coordinates.

== color ==
 color {atoms} &lt;color&gt;
Sets the color of the selected atoms. The color may be given as RGB values [r,g,b], predefined color names, or predefined color schemes; amino, chain, charge, cpk, group, shapely, structure, and temperature.

 color bonds/backbone/ribbons/hbonds/ssbonds &lt;color&gt;
Sets the color of the specified object. The color may be given as RGB values [r,g,b] or predefined color names. For hydrogen bonds, color scheme 'type' can be specified.

 color bonds/backbone/ribbons/hbonds/ssbonds none
Resets the color of the specified object.

== colorvertex ==
 colorvertex &lt;color&gt;
Sets the color of the selected vertices. The color may be given as RGB values [r,g,b] or predefined color names.

 colorvertex none
Resets the color of the selected vertices.

== cpk ==
 cpk
A synonym of the [[#spacefill|spacefill]] command.

== define ==
 define &lt;name&gt; &lt;atom_expression&gt;
Associates an arbitrary set of atoms with a unique name.

== display ==
 display all
Displays the image of all files.

 display none
Turns off the image of all files.

 display {-a/-r} &lt;file_IDs&gt;
Displays the image of the specified files and turns off the others. More than one file IDs can be specified by putting commas as the delimiter. When the option -a or -r is specified, turns the image of the specified files on or off, respectively, and the others remain unchanged.

== displayatom ==
 displayatom {on/true}
Displays the selected atoms.

 displayatom off/false
Turns off the selected atoms.

== displayvertex ==
 displayvertex {on/true}
Displays the selected vertices.

 displayvertex off/false
Turns off the selected vertices.

== echo ==
 echo &lt;string&gt;
Echoes the specified message back to the message area.

== exit ==
 exit
Terminates the application.

== fit ==
 fit &lt;file1_ID&gt; &lt;file2_ID&gt;
Sets the transform matrix of file1 identical to that of file2. 

== fselect ==
 fselect all
Selects all files.

 fselect none
Selects no files.

 fselect {-a/-r} &lt;file_IDs&gt;
Selects the specified files and makes the others not selected. More than one file IDs can be specified by putting commas as the delimiter. When the option -a or -r is specified, only the selection status of the specified files are modified, selected or not selected, respectively, and the others remain unchanged.

== hbonds ==
 hbonds {on/true}
Turns on the selected hydrogen bonds.

 hbonds off/false
Turns off the selected hydrogen bonds.

 hbonds &lt;radius&gt;
Turns on the selected hydrogen bonds with the specified raidus (angstrom or Rasmol unit). The maximum parameter value is 2.0. 

== load ==
 load {pdbml} &lt;filename&gt; {fit &lt;file_ID&gt;}
Opens a PDBML file. URL can be used to open a remote file. On loading, the transform matrix can be set identical to that of the specified file.

 load pdb &lt;filename&gt; {fit &lt;file_ID&gt;}
Opens a PDB file. URL can be used to open a remote file. On loading, the transform matrix can be set identical to that of the specified file.

 load polygon &lt;filename&gt; {fit &lt;file_ID&gt;}
Opens a polygon file. URL can be used to open a remote file. On loading, the transform matrix can be set identical to that of the specified file.

 load animation &lt;filename&gt; {fit &lt;file_ID&gt;}
Opens an animation file. URL can be used to open a remote file. On loading, the transform matrix can be set identical to that of the specified file.

 load ftp &lt;PDB_code&gt; {fit &lt;file_ID&gt;}
Retrieves a PDBML file from the PDBj FTP site and opens it. On loading, the transform matrix can be set identical to that of the specified file. 

== pause ==
 pause
Stops the execution of a script file until any key is pressed to restart. 

== pdbj_describe ==
 pdbj_describe &lt;file_id&gt; {&lt;name&gt;} 
Shows the document for the jV_command in PDBMLplus specified by file ID and name. When the name is not specified, all available names are listed.

== pdbj_execute ==
 pdbj_execute &lt;file_id&gt; &lt;name&gt; 
Executes the jV_command in PDBMLplus specified by file ID and name.

== quit ==
 quit
A synonym of the [[#exit|exit]] command.

== refresh ==
 refresh
Redraws all images. 

== reset ==
=== default ===
 reset
Restores the original viewing transformation of all images, the center of rotation, and the view point. 

=== cartoon ===
 reset cartoon
Restores the thickness of the cartoon representation. 

=== line_width ===
 reset line_width
Restores the width of lines in polygon images. 

=== pickradius ===
 reset pickradius
Restores the mouse-pickable region of each atom. 

=== point_size ===
 reset point_size
Restores the size of points in polygon images. 

=== polyline_width ===
 reset polyline_width
Restores the width of polylines in polygon images. 

=== transparency ===
 reset transparency
Restores the transparency of polygon images.

 reset point_transparency
Restores the transparency of points in polygon images.

 reset line_transparency
Restores the transparency of lines in polygon images.

 reset triangle_transparency
Restores the transparency of triangles in polygon images.

 reset quad_transparency
Restores the transparency of quads in polygon images.

 reset polyline_transparency
Restores the transparency of polylines in polygon images. 

== ribbons ==
 ribbons {on/true}
Turns on the ribbon surfaces for the selected residues.

 ribbons off/false
Turns off the ribbon surfaces for the selected residues.

 ribbons &lt;half_width&gt;
Turns on the ribbon surfaces for the selected residues with the specified half width (angstrom or Rasmol unit). The maximum parameter value is 4.0. 

== rotate ==
 rotate x/y/z &lt;angle&gt;
Rotates images about the specified axis by the specified angle in degrees. 

== save ==
 save {pdb} &lt;filename&gt;
Saves the currently selected set of atoms in a PDB format file.

 save script &lt;filename&gt;
Creates a script file that reproduces the currently displayed image.

 save png &lt;filename&gt;
Creates a PNG image file of the currently displayed image.

 save jpeg &lt;filename&gt; {&lt;quality&gt;}
Creates a JPEG image file of the currently displayed image. The compression quality can be specified, 0 &lt; quality &lt;= 1, where 'quality = 1' means no compression. 

== script ==
 script &lt;filename&gt;
Opens and executes the specified script file. URL can be used to open a remote file. 

== select ==
 select
Selects all atoms. Whether hetero atoms and hydrogens are selected or not depends on the internal parameters, hetero and hydrogen, respectively.

 select all
Selects all atoms including hetero atoms and hydrogens.

 select none
Selects no atoms.

 select &lt;atom_expression&gt;
Selects a group of atoms specified by the atom expression. 

== selectvertex ==
 selectvertex {all}
Selects all vertices.

 selectvertex none
Selects no vertices.

 selectvertex &lt;vertex_expression&gt;
Selects a group of vertices specified by the vertex expression. 

== set ==
=== ambient ===
 set ambient {&lt;value&gt;}
Sets the amount of ambient light. The value must be between 0 and 100. When the parameter is not specified, it is restored to the default value 33.

=== adjustview ===
 set adjustview on
The view point is automatically adjusted when a new file is loaded.

 set adjustview off
The view point is kept unchanged when a new file is loaded. 

=== background ===
 set background &lt;color&gt;
Changes the background color. The color may be given as RGB values [r,g,b], or predefined color names. 

=== bondmode ===
 set bondmode and
Specifies how to select an individual bonds. A bond is selected when both atoms connected by the bond are selected.

 set bondmode or
Specifies how to select an individual bonds. A bond is selected when either of the connected atoms is selected. 

=== cartoon ===
 set cartoon {&lt;value&gt;}
Specifies the thickness of the cartoon representation (angstrom or Rasmol unit). The maximum parameter value is 2.0. When the parameter is not specified, it is restored to the default value. 

=== cartoon_loop_tube ===
 set cartoon_loop_tube on
The loop region is drawn as tube in the cartoon representation.

 set cartoon_loop_tube off
The loop region is drawn as square pillar in the cartoon representation.

=== cartoon_round ===
 set cartoon_round on
Square pillar with round edge is drawn in the cartoon representation (except beta strands). 

 set cartoon_round off
Square pillar is drawn in the cartoon representation.

=== center ===
 set center &lt;atom_expression&gt;
Sets the default center of the selected files to the center of the specified atoms.

 set center [x, y, z]
Sets the default center of the selected files to the specified coordinates. 

=== diffuse1 ===
 set diffuse1 {&lt;value&gt;}
Sets the amount of the first diffuse light. The value must be between 0 and 100. When the parameter is not specified, it is restored to the default value 50.

=== diffuse1_direction ===
 set diffuse1_direction {[x, y, z]}
Sets the direction of the first diffuse light. When the parameter is not specified, it is restored to the default value [-1, -1, -1].

=== diffuse2 ===
 set diffuse2 {&lt;value&gt;}
Sets the amount of the second diffuse light. The value must be between 0 and 100. When the parameter is not specified, it is restored to the default value 50.

=== diffuse2_direction ===
 set diffuse2_direction {[x, y, z]}
Sets the direction of the second diffuse light. When the parameter is not specified, it is restored to the default value [-1, -1, -1].

=== drawlevel ===
 set drawlevel &lt;value&gt;
Specifies precision of the rendering of spheres and cylinders. The value may be given as an integer (minimum 5) that stands for the number of straight line segments to represent an arc of 180 degrees. 

=== efsite_url ===
 set efsite_url &lt;URL&gt;
Sets the URL for eF-site.

=== ext_site_url ===
 set ext_site_url &lt;prefix&gt; &lt;URL&gt;
Sets the URL for an external database site.

=== hbonds ===
 set hbonds backbone
Hydrogen bonds are displayed between backbones.

 set hbonds sidechain
Hydrogen bonds are displayed between sidechains. 

=== hetero ===
 set hetero on
Sets the default behavior of the select command such that hetero atoms are selected.

 set hetero off
Sets the default behavior of the select command such that hetero atoms are not selected. 

=== hydrogen ===
 set hydrogen on
Sets the default behavior of the select command such that hydrogens are selected.

 set hydrogen off
Sets the default behavior of the select command such that hydrogens are not selected. 

=== imagesize ===
 set imagesize &lt;width&gt; &lt;height&gt;
Sets the size of the 3D-rendering panel in pixels. The size will be set within the screen size with the width being an even integer. 

=== line_width ===
 set line_width &lt;value&gt;
Sets the width of lines in polygon images. The &lt;value&gt; should be larger than 0. 

=== loadcenter ===
 set loadcenter on
When a file is opened, sets the default center of that file to the center of all files that have already opened.

 set loadcenter off
When a file is opened, sets the default center of that file according to its own coordiantes. 

=== pdbml_noatom_url ===
 set pdbml_noatom_url &lt;URL&gt;
Sets the URL for PDBML noatom files.

=== pdbml_extatom_url ===
 set pdbml_extatom_url &lt;URL&gt;
Sets the URL for PDBML extatom files.

=== pdbml_plus_url ===
 set pdbml_plus_url &lt;URL&gt;
Sets the URL for PDBMLplus files.

=== picking ===
 set picking off
Turns off the mouse picking.

 set picking ident
Sets the mouse picking behavior to show atom identification.

 set picking coord
Sets the mouse picking behavior to show atom coordinates with identification.

 set picking distance
Sets the mouse picking behavior to show the distance between atoms successively picked.

 set picking center
Sets the mouse picking behavior to specify the center of rotation and center of the screen.

 set picking select
Sets the mouse picking behavior to select the file that contains the atom picked. 

=== pickradius ===
 set pickradius &lt;value&gt;
Sets the mouse-pickable region of each atom to be the sphere centered to each atom with the specified radius (angstrom or Rasmol unit). 

=== point_size ===
 set point_size &lt;value&gt;
Sets the size of points in polygon images. The &lt;value&gt; should be larger than 0. 

=== polyline_width ===
 set polyline_width &lt;value&gt;
Sets the width of polylines in polygon images. The &lt;value&gt; should be larger than 0. 

=== projection ===
 set projection perspective
Sets the projection mode for a perspective projection.

 set projection parallel {&lt;size&gt;}
Sets the projection mode for a parallel projection. The size of image (fit to the height of the screen) can be specified (angstrom or Rasmol unit). 

=== ribbonback ===
 set ribbonback &lt;color&gt;
Sets the color of the back of ribbon models. The color may be given as RGB values [r,g,b] or predefined color names.

 set ribbonback none
Resets the color of the back of ribbon models.

=== specular ===
 set specular on/true
Enables the display of specular highlights on solid objects.

 set specular off/false
Disables the display of specular highlights on solid objects.

 set specular &lt;value&gt;
Enables the display of specular highlights on solid objects. The value between 0 and 100 specifies the specular color in gray scale with 0 and 100 being black and white, respectively. The default value is 50.0. 

=== specpower ===
 set specpower &lt;value&gt;
Sets the shininess of solid objects. The value between 0 and 100 specifies a material reflection coefficient with 0 being diffuse surfaces and 100 being shiny surfaces. 

=== ssbonds ===
 set ssbonds backbone
Disulfide bonds are displayed between backbones.

 set ssbonds sidechain
Disulfide bonds are displayed between sidechains. 

=== stereo ===
 set stereo
A synonym of the [[#stereo_2|stereo]] command.

=== transparency ===
 set transparency &lt;value&gt;
Sets the transparency of polygon images.

 set point_transparency &lt;value&gt;
Sets the transparency of points in polygon images.

 set line_transparency &lt;value&gt;
Sets the transparency of lines in polygon images.

 set triangle_transparency &lt;value&gt;
Sets the transparency of triangles in polygon images.

 set quad_transparency &lt;value&gt;
Sets the transparency of quads in polygon images.

 set polyline_transparency &lt;value&gt;
Sets the transparency of polylines in polygon images. 

=== viewpoint ===
 set viewpoint {x, y, z}
Sets the viewpoint to the specified coordinates. 

== show ==
 show godata
Displays gene ontology data of molecules.

 show imagesize
Displays the size of the 3D-rendering panel.

 show information
Displays a detail discription of molecules.

 show site {&lt;prefix&gt;:&lt;db&gt;:&lt;category&gt;}
Displays site information in an external database.

 show transform
Displays the transform matrix of molecules.

 show viewpoint
Displays the current viewpoint.

 show pdbj
Displays keywords available in PDBj expression.

== slab ==
 slab {on/true}
Enables the z-clipping plane of molecules and polygons.

 slab off/false
Disables the z-clipping plane of molecules and polygons.

 slab &lt;ratio&gt;
Sets the position of the z-clipping plane of molecules and polygons. The parameter may be given as a number from 0 to 100. The values 0 and 100 represent that image as a whole is completely invisible and visible, respectively.

 slab -v &lt;value&gt;
Sets the position of the z-clipping plane of molecules and polygons by specifying the z coordinate value. 

== spacefill ==
 spacefill {on/true}
Turns on the ball image of the selected atoms.

 spacefill off/false
Turns off the ball image of the selected atoms.

 spacefill &lt;radius&gt;
Turns on the ball image of the selected atoms with the specified radius (angstrom or Rasmol unit). The maximum parameter value is 3.0.

 spacefill temperature
Turns on the ball image of the selected atoms using the temperature factor as radius. 

== ssbonds ==
 ssbonds {on/true}
Turns on the selected disulfide bonds.

 ssbonds off/false
Turns off the selected disulfide bonds.

 ssbonds &lt;radius&gt;
Turns on the selected disulfide bonds with the specified raidus (angstrom or Rasmol unit). The maximum parameter value is 2.0. 

== stereo ==
 stereo {on/true}
Enables stereo display. This command without arguments cycles three state; 'stereo off', 'stereo on' in cross-eyed mode and 'stereo on' in parallel-eyed mode.

 stereo off/false
Disables stereo display.

 stereo &lt;angle&gt;
Enables stereo display with the specified separation angle. Positive and negative values represent cross-eyed and parallel-eyed viewing, respectively.


== structure ==
 structure
Estimates the secondary structure using Kabsch and Sander's DSSP algorithm. 

== trace ==
 trace {on/true}
Turns on a tube representation for the selected residues.

 trace off/false
Turns off a tube representation for the selected residues.

 trace &lt;radius&gt;
Turns on a tube representation for the selected residues with the specified radius (angstrom or Rasmol unit). The maximum parameter value is 2.0.


== translate ==
 translate x/y/z &lt;value&gt;
Moves images along the specified axis by the specified amount (angstrom). 

== wireframe ==
 wireframe {on/true}
Turns on the selected bonds.

 wireframe off/false
Turns off the selected bonds.

 wireframe &lt;radius&gt;
Turns on the selected bonds with the specified raidus (angstrom or Rasmol unit). The maximum parameter value is 2.0. 

== write ==
 write
A synonym of the [[#save|save]] command.

== zap ==
 zap {&lt;file_IDs&gt;}
Closes the specified files. More than one file IDs can be specified by putting commas as the delimiter. When the paraneter is absent, all files are closed. 

== zoom ==
 zoom {&lt;value&gt;}
Sets the magnification of the image as a whole. The value stands for the magnification as a percentage of the current scale. The minimum parameter value is 10.0.</text>
    <sha1>b2948d855a474d7e44c121b073679adcb888f72a</sha1>
  </revision>
  <revision>
    <id>412</id>
    <parentid>411</parentid>
    <timestamp>2010-09-14T07:49:33Z</timestamp>
    <contributor>
      <username>IMSsato</username>
      <id>4</id>
    </contributor>
    <comment>/* ribbons */</comment>
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    <format>text/x-wiki</format>
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  |__TOC__
  |}
Command usage of jV follows that of [http://www.rasmol.org/ Rasmol] with some modifications. In the following part, command arguments that can take an arbitrary value are denoted as &lt;value&gt; for example, arguments restricted to several possible values are listed with / as a delimiter, and arguments that can be omitted are put in brackets {}. Commands, [[#exit|exit]], [[#load|load]], [[#quit|quit]], [[#save|save]], [[#script|script]], and [[#write|write]], are not available in applet circumstance.

== anim ==
 anim forward {&lt;value&gt;}
Starts animation forward. If the &lt;value&gt; is given, just move frames forward by the specified amount.

 anim backward {&lt;value&gt;}
Starts animation backward. If the &lt;value&gt; is given, just move frames backward by the specified amount.

 anim stop
Stops animation.

== animframe ==
 animframe &lt;frame&gt; {&lt;file_ID&gt;}
Sets the frame of all animation files for the specified value. When &lt;file_ID&gt; is given, only the specified file is processed.

== animmode ==
 animmode once
Sets the behavior of animation for 'once'. When the frame reaches the last one, animation is stopped.

 animmode loop
Sets the behavior of animation for 'loop'. When the frame reaches the last one, animation is reset to the first frame and continues playing.

 animmode swing
Sets the behavior of animation for 'swing'. When the frame reaches the last one, the direction of animation is reversed.

== animrange ==
 animrange &lt;init_frame&gt;-&lt;term_frame&gt; {&lt;file_IDs&gt;}
Sets the range of all animation files. When is given, only the specified file is processed.

== animselect ==
 animselect {-a/-r} &lt;file_IDs&gt;
Selects the specified files and makes the others not selected. More than one file IDs can be specified by putting commas as the delimiter. When the option -a or -r is specified, only the selection status of the specified files are modified, selected or not selected, respectively, and the others remain unchanged.

== animspeed ==
 animspeed &lt;speed&gt;
Sets the animation speed. The argument should be an integer value from 1 to 20.

== animstep ==
 animstep &lt;step&gt; {&lt;file_ID&gt;}
Sets the step of all animation files for the specified value. When &lt;file_ID&gt; is given, only the specified file is processed.

== backbone ==
 backbone {on/true}
Turns on the selected backbone bonds.

 backbone off/false
Turns off the selected backbone bonds.

 backbone &lt;radius&gt;
Turns on the selected backbone bonds with the specified raidus (angstrom or Rasmol unit). The maximum parameter value is 2.0.

== background ==
 background &lt;color&gt;
Changes the background color. The color may be given as RGB values [r,g,b], or predefined color names.

== cartoon ==
 cartoon {on/true}
Turns on the thick ribbons for the selected residues. When a chain does not have enough atoms to draw the ribbon model, a backbone will be shown instead.

 cartoon off/false
Turns off the thick ribbons for the selected residues.

 cartoon &lt;half_width&gt;
Turns on the thick ribbons for the selected residues with the specified half width (angstrom or Rasmol unit). The maximum parameter value is 4.0.

== center ==
 center {-r/-s} {&lt;atom_expression&gt;}
Sets the center of rotation and the center of the screen to the center of a group of atoms specified by the atom expression. When the option -r or -s is specified, only the center of rotation or the center of the screen is modified, respectively.

 center {-r} [x, y, z]
Moves the center of rotation and the center of the screen from the current position by the specified amount. When the option -r is specified, only the center of rotation is modified.

 center {-r} {x, y, z}
Sets the center of rotation and the center of the screen to the specified coordinates. When the option -r is specified, only the center of rotation is modified.

 center -s [x, y]
Moves the center of the screen from the current position by the specified amount.

 center -s {x, y}
Sets the center of the screen to the specified coordinates.

== color ==
 color {atoms} &lt;color&gt;
Sets the color of the selected atoms. The color may be given as RGB values [r,g,b], predefined color names, or predefined color schemes; amino, chain, charge, cpk, group, shapely, structure, and temperature.

 color bonds/backbone/ribbons/hbonds/ssbonds &lt;color&gt;
Sets the color of the specified object. The color may be given as RGB values [r,g,b] or predefined color names. For hydrogen bonds, color scheme 'type' can be specified.

 color bonds/backbone/ribbons/hbonds/ssbonds none
Resets the color of the specified object.

== colorvertex ==
 colorvertex &lt;color&gt;
Sets the color of the selected vertices. The color may be given as RGB values [r,g,b] or predefined color names.

 colorvertex none
Resets the color of the selected vertices.

== cpk ==
 cpk
A synonym of the [[#spacefill|spacefill]] command.

== define ==
 define &lt;name&gt; &lt;atom_expression&gt;
Associates an arbitrary set of atoms with a unique name.

== display ==
 display all
Displays the image of all files.

 display none
Turns off the image of all files.

 display {-a/-r} &lt;file_IDs&gt;
Displays the image of the specified files and turns off the others. More than one file IDs can be specified by putting commas as the delimiter. When the option -a or -r is specified, turns the image of the specified files on or off, respectively, and the others remain unchanged.

== displayatom ==
 displayatom {on/true}
Displays the selected atoms.

 displayatom off/false
Turns off the selected atoms.

== displayvertex ==
 displayvertex {on/true}
Displays the selected vertices.

 displayvertex off/false
Turns off the selected vertices.

== echo ==
 echo &lt;string&gt;
Echoes the specified message back to the message area.

== exit ==
 exit
Terminates the application.

== fit ==
 fit &lt;file1_ID&gt; &lt;file2_ID&gt;
Sets the transform matrix of file1 identical to that of file2. 

== fselect ==
 fselect all
Selects all files.

 fselect none
Selects no files.

 fselect {-a/-r} &lt;file_IDs&gt;
Selects the specified files and makes the others not selected. More than one file IDs can be specified by putting commas as the delimiter. When the option -a or -r is specified, only the selection status of the specified files are modified, selected or not selected, respectively, and the others remain unchanged.

== hbonds ==
 hbonds {on/true}
Turns on the selected hydrogen bonds.

 hbonds off/false
Turns off the selected hydrogen bonds.

 hbonds &lt;radius&gt;
Turns on the selected hydrogen bonds with the specified raidus (angstrom or Rasmol unit). The maximum parameter value is 2.0. 

== load ==
 load {pdbml} &lt;filename&gt; {fit &lt;file_ID&gt;}
Opens a PDBML file. URL can be used to open a remote file. On loading, the transform matrix can be set identical to that of the specified file.

 load pdb &lt;filename&gt; {fit &lt;file_ID&gt;}
Opens a PDB file. URL can be used to open a remote file. On loading, the transform matrix can be set identical to that of the specified file.

 load polygon &lt;filename&gt; {fit &lt;file_ID&gt;}
Opens a polygon file. URL can be used to open a remote file. On loading, the transform matrix can be set identical to that of the specified file.

 load animation &lt;filename&gt; {fit &lt;file_ID&gt;}
Opens an animation file. URL can be used to open a remote file. On loading, the transform matrix can be set identical to that of the specified file.

 load ftp &lt;PDB_code&gt; {fit &lt;file_ID&gt;}
Retrieves a PDBML file from the PDBj FTP site and opens it. On loading, the transform matrix can be set identical to that of the specified file. 

== pause ==
 pause
Stops the execution of a script file until any key is pressed to restart. 

== pdbj_describe ==
 pdbj_describe &lt;file_id&gt; {&lt;name&gt;} 
Shows the document for the jV_command in PDBMLplus specified by file ID and name. When the name is not specified, all available names are listed.

== pdbj_execute ==
 pdbj_execute &lt;file_id&gt; &lt;name&gt; 
Executes the jV_command in PDBMLplus specified by file ID and name.

== quit ==
 quit
A synonym of the [[#exit|exit]] command.

== refresh ==
 refresh
Redraws all images. 

== reset ==
=== default ===
 reset
Restores the original viewing transformation of all images, the center of rotation, and the view point. 

=== cartoon ===
 reset cartoon
Restores the thickness of the cartoon representation. 

=== line_width ===
 reset line_width
Restores the width of lines in polygon images. 

=== pickradius ===
 reset pickradius
Restores the mouse-pickable region of each atom. 

=== point_size ===
 reset point_size
Restores the size of points in polygon images. 

=== polyline_width ===
 reset polyline_width
Restores the width of polylines in polygon images. 

=== transparency ===
 reset transparency
Restores the transparency of polygon images.

 reset point_transparency
Restores the transparency of points in polygon images.

 reset line_transparency
Restores the transparency of lines in polygon images.

 reset triangle_transparency
Restores the transparency of triangles in polygon images.

 reset quad_transparency
Restores the transparency of quads in polygon images.

 reset polyline_transparency
Restores the transparency of polylines in polygon images. 

== ribbons ==
 ribbons {on/true}
Turns on the ribbon surfaces for the selected residues. When a chain does not have enough atoms to draw the ribbon model, a backbone will be shown instead.

 ribbons off/false
Turns off the ribbon surfaces for the selected residues.

 ribbons &lt;half_width&gt;
Turns on the ribbon surfaces for the selected residues with the specified half width (angstrom or Rasmol unit). The maximum parameter value is 4.0.

== rotate ==
 rotate x/y/z &lt;angle&gt;
Rotates images about the specified axis by the specified angle in degrees. 

== save ==
 save {pdb} &lt;filename&gt;
Saves the currently selected set of atoms in a PDB format file.

 save script &lt;filename&gt;
Creates a script file that reproduces the currently displayed image.

 save png &lt;filename&gt;
Creates a PNG image file of the currently displayed image.

 save jpeg &lt;filename&gt; {&lt;quality&gt;}
Creates a JPEG image file of the currently displayed image. The compression quality can be specified, 0 &lt; quality &lt;= 1, where 'quality = 1' means no compression. 

== script ==
 script &lt;filename&gt;
Opens and executes the specified script file. URL can be used to open a remote file. 

== select ==
 select
Selects all atoms. Whether hetero atoms and hydrogens are selected or not depends on the internal parameters, hetero and hydrogen, respectively.

 select all
Selects all atoms including hetero atoms and hydrogens.

 select none
Selects no atoms.

 select &lt;atom_expression&gt;
Selects a group of atoms specified by the atom expression. 

== selectvertex ==
 selectvertex {all}
Selects all vertices.

 selectvertex none
Selects no vertices.

 selectvertex &lt;vertex_expression&gt;
Selects a group of vertices specified by the vertex expression. 

== set ==
=== ambient ===
 set ambient {&lt;value&gt;}
Sets the amount of ambient light. The value must be between 0 and 100. When the parameter is not specified, it is restored to the default value 33.

=== adjustview ===
 set adjustview on
The view point is automatically adjusted when a new file is loaded.

 set adjustview off
The view point is kept unchanged when a new file is loaded. 

=== background ===
 set background &lt;color&gt;
Changes the background color. The color may be given as RGB values [r,g,b], or predefined color names. 

=== bondmode ===
 set bondmode and
Specifies how to select an individual bonds. A bond is selected when both atoms connected by the bond are selected.

 set bondmode or
Specifies how to select an individual bonds. A bond is selected when either of the connected atoms is selected. 

=== cartoon ===
 set cartoon {&lt;value&gt;}
Specifies the thickness of the cartoon representation (angstrom or Rasmol unit). The maximum parameter value is 2.0. When the parameter is not specified, it is restored to the default value. 

=== cartoon_loop_tube ===
 set cartoon_loop_tube on
The loop region is drawn as tube in the cartoon representation.

 set cartoon_loop_tube off
The loop region is drawn as square pillar in the cartoon representation.

=== cartoon_round ===
 set cartoon_round on
Square pillar with round edge is drawn in the cartoon representation (except beta strands). 

 set cartoon_round off
Square pillar is drawn in the cartoon representation.

=== center ===
 set center &lt;atom_expression&gt;
Sets the default center of the selected files to the center of the specified atoms.

 set center [x, y, z]
Sets the default center of the selected files to the specified coordinates. 

=== diffuse1 ===
 set diffuse1 {&lt;value&gt;}
Sets the amount of the first diffuse light. The value must be between 0 and 100. When the parameter is not specified, it is restored to the default value 50.

=== diffuse1_direction ===
 set diffuse1_direction {[x, y, z]}
Sets the direction of the first diffuse light. When the parameter is not specified, it is restored to the default value [-1, -1, -1].

=== diffuse2 ===
 set diffuse2 {&lt;value&gt;}
Sets the amount of the second diffuse light. The value must be between 0 and 100. When the parameter is not specified, it is restored to the default value 50.

=== diffuse2_direction ===
 set diffuse2_direction {[x, y, z]}
Sets the direction of the second diffuse light. When the parameter is not specified, it is restored to the default value [-1, -1, -1].

=== drawlevel ===
 set drawlevel &lt;value&gt;
Specifies precision of the rendering of spheres and cylinders. The value may be given as an integer (minimum 5) that stands for the number of straight line segments to represent an arc of 180 degrees. 

=== efsite_url ===
 set efsite_url &lt;URL&gt;
Sets the URL for eF-site.

=== ext_site_url ===
 set ext_site_url &lt;prefix&gt; &lt;URL&gt;
Sets the URL for an external database site.

=== hbonds ===
 set hbonds backbone
Hydrogen bonds are displayed between backbones.

 set hbonds sidechain
Hydrogen bonds are displayed between sidechains. 

=== hetero ===
 set hetero on
Sets the default behavior of the select command such that hetero atoms are selected.

 set hetero off
Sets the default behavior of the select command such that hetero atoms are not selected. 

=== hydrogen ===
 set hydrogen on
Sets the default behavior of the select command such that hydrogens are selected.

 set hydrogen off
Sets the default behavior of the select command such that hydrogens are not selected. 

=== imagesize ===
 set imagesize &lt;width&gt; &lt;height&gt;
Sets the size of the 3D-rendering panel in pixels. The size will be set within the screen size with the width being an even integer. 

=== line_width ===
 set line_width &lt;value&gt;
Sets the width of lines in polygon images. The &lt;value&gt; should be larger than 0. 

=== loadcenter ===
 set loadcenter on
When a file is opened, sets the default center of that file to the center of all files that have already opened.

 set loadcenter off
When a file is opened, sets the default center of that file according to its own coordiantes. 

=== pdbml_noatom_url ===
 set pdbml_noatom_url &lt;URL&gt;
Sets the URL for PDBML noatom files.

=== pdbml_extatom_url ===
 set pdbml_extatom_url &lt;URL&gt;
Sets the URL for PDBML extatom files.

=== pdbml_plus_url ===
 set pdbml_plus_url &lt;URL&gt;
Sets the URL for PDBMLplus files.

=== picking ===
 set picking off
Turns off the mouse picking.

 set picking ident
Sets the mouse picking behavior to show atom identification.

 set picking coord
Sets the mouse picking behavior to show atom coordinates with identification.

 set picking distance
Sets the mouse picking behavior to show the distance between atoms successively picked.

 set picking center
Sets the mouse picking behavior to specify the center of rotation and center of the screen.

 set picking select
Sets the mouse picking behavior to select the file that contains the atom picked. 

=== pickradius ===
 set pickradius &lt;value&gt;
Sets the mouse-pickable region of each atom to be the sphere centered to each atom with the specified radius (angstrom or Rasmol unit). 

=== point_size ===
 set point_size &lt;value&gt;
Sets the size of points in polygon images. The &lt;value&gt; should be larger than 0. 

=== polyline_width ===
 set polyline_width &lt;value&gt;
Sets the width of polylines in polygon images. The &lt;value&gt; should be larger than 0. 

=== projection ===
 set projection perspective
Sets the projection mode for a perspective projection.

 set projection parallel {&lt;size&gt;}
Sets the projection mode for a parallel projection. The size of image (fit to the height of the screen) can be specified (angstrom or Rasmol unit). 

=== ribbonback ===
 set ribbonback &lt;color&gt;
Sets the color of the back of ribbon models. The color may be given as RGB values [r,g,b] or predefined color names.

 set ribbonback none
Resets the color of the back of ribbon models.

=== specular ===
 set specular on/true
Enables the display of specular highlights on solid objects.

 set specular off/false
Disables the display of specular highlights on solid objects.

 set specular &lt;value&gt;
Enables the display of specular highlights on solid objects. The value between 0 and 100 specifies the specular color in gray scale with 0 and 100 being black and white, respectively. The default value is 50.0. 

=== specpower ===
 set specpower &lt;value&gt;
Sets the shininess of solid objects. The value between 0 and 100 specifies a material reflection coefficient with 0 being diffuse surfaces and 100 being shiny surfaces. 

=== ssbonds ===
 set ssbonds backbone
Disulfide bonds are displayed between backbones.

 set ssbonds sidechain
Disulfide bonds are displayed between sidechains. 

=== stereo ===
 set stereo
A synonym of the [[#stereo_2|stereo]] command.

=== transparency ===
 set transparency &lt;value&gt;
Sets the transparency of polygon images.

 set point_transparency &lt;value&gt;
Sets the transparency of points in polygon images.

 set line_transparency &lt;value&gt;
Sets the transparency of lines in polygon images.

 set triangle_transparency &lt;value&gt;
Sets the transparency of triangles in polygon images.

 set quad_transparency &lt;value&gt;
Sets the transparency of quads in polygon images.

 set polyline_transparency &lt;value&gt;
Sets the transparency of polylines in polygon images. 

=== viewpoint ===
 set viewpoint {x, y, z}
Sets the viewpoint to the specified coordinates. 

== show ==
 show godata
Displays gene ontology data of molecules.

 show imagesize
Displays the size of the 3D-rendering panel.

 show information
Displays a detail discription of molecules.

 show site {&lt;prefix&gt;:&lt;db&gt;:&lt;category&gt;}
Displays site information in an external database.

 show transform
Displays the transform matrix of molecules.

 show viewpoint
Displays the current viewpoint.

 show pdbj
Displays keywords available in PDBj expression.

== slab ==
 slab {on/true}
Enables the z-clipping plane of molecules and polygons.

 slab off/false
Disables the z-clipping plane of molecules and polygons.

 slab &lt;ratio&gt;
Sets the position of the z-clipping plane of molecules and polygons. The parameter may be given as a number from 0 to 100. The values 0 and 100 represent that image as a whole is completely invisible and visible, respectively.

 slab -v &lt;value&gt;
Sets the position of the z-clipping plane of molecules and polygons by specifying the z coordinate value. 

== spacefill ==
 spacefill {on/true}
Turns on the ball image of the selected atoms.

 spacefill off/false
Turns off the ball image of the selected atoms.

 spacefill &lt;radius&gt;
Turns on the ball image of the selected atoms with the specified radius (angstrom or Rasmol unit). The maximum parameter value is 3.0.

 spacefill temperature
Turns on the ball image of the selected atoms using the temperature factor as radius. 

== ssbonds ==
 ssbonds {on/true}
Turns on the selected disulfide bonds.

 ssbonds off/false
Turns off the selected disulfide bonds.

 ssbonds &lt;radius&gt;
Turns on the selected disulfide bonds with the specified raidus (angstrom or Rasmol unit). The maximum parameter value is 2.0. 

== stereo ==
 stereo {on/true}
Enables stereo display. This command without arguments cycles three state; 'stereo off', 'stereo on' in cross-eyed mode and 'stereo on' in parallel-eyed mode.

 stereo off/false
Disables stereo display.

 stereo &lt;angle&gt;
Enables stereo display with the specified separation angle. Positive and negative values represent cross-eyed and parallel-eyed viewing, respectively.


== structure ==
 structure
Estimates the secondary structure using Kabsch and Sander's DSSP algorithm. 

== trace ==
 trace {on/true}
Turns on a tube representation for the selected residues.

 trace off/false
Turns off a tube representation for the selected residues.

 trace &lt;radius&gt;
Turns on a tube representation for the selected residues with the specified radius (angstrom or Rasmol unit). The maximum parameter value is 2.0.


== translate ==
 translate x/y/z &lt;value&gt;
Moves images along the specified axis by the specified amount (angstrom). 

== wireframe ==
 wireframe {on/true}
Turns on the selected bonds.

 wireframe off/false
Turns off the selected bonds.

 wireframe &lt;radius&gt;
Turns on the selected bonds with the specified raidus (angstrom or Rasmol unit). The maximum parameter value is 2.0. 

== write ==
 write
A synonym of the [[#save|save]] command.

== zap ==
 zap {&lt;file_IDs&gt;}
Closes the specified files. More than one file IDs can be specified by putting commas as the delimiter. When the paraneter is absent, all files are closed. 

== zoom ==
 zoom {&lt;value&gt;}
Sets the magnification of the image as a whole. The value stands for the magnification as a percentage of the current scale. The minimum parameter value is 10.0.</text>
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  |}
Command usage of jV follows that of [http://www.rasmol.org/ Rasmol] with some modifications. In the following part, command arguments that can take an arbitrary value are denoted as &lt;value&gt; for example, arguments restricted to several possible values are listed with / as a delimiter, and arguments that can be omitted are put in brackets {}. Commands, [[#exit|exit]], [[#load|load]], [[#quit|quit]], [[#save|save]], [[#script|script]], and [[#write|write]], are not available in applet circumstance.

== anim ==
 anim forward {&lt;value&gt;}
Starts animation forward. If the &lt;value&gt; is given, just move frames forward by the specified amount.

 anim backward {&lt;value&gt;}
Starts animation backward. If the &lt;value&gt; is given, just move frames backward by the specified amount.

 anim stop
Stops animation.

== animframe ==
 animframe &lt;frame&gt; {&lt;file_ID&gt;}
Sets the frame of all animation files for the specified value. When &lt;file_ID&gt; is given, only the specified file is processed.

== animmode ==
 animmode once
Sets the behavior of animation for 'once'. When the frame reaches the last one, animation is stopped.

 animmode loop
Sets the behavior of animation for 'loop'. When the frame reaches the last one, animation is reset to the first frame and continues playing.

 animmode swing
Sets the behavior of animation for 'swing'. When the frame reaches the last one, the direction of animation is reversed.

== animrange ==
 animrange &lt;init_frame&gt;-&lt;term_frame&gt; {&lt;file_IDs&gt;}
Sets the range of all animation files. When is given, only the specified file is processed.

== animselect ==
 animselect {-a/-r} &lt;file_IDs&gt;
Selects the specified files and makes the others not selected. More than one file IDs can be specified by putting commas as the delimiter. When the option -a or -r is specified, only the selection status of the specified files are modified, selected or not selected, respectively, and the others remain unchanged.

== animspeed ==
 animspeed &lt;speed&gt;
Sets the animation speed. The argument should be an integer value from 1 to 20.

== animstep ==
 animstep &lt;step&gt; {&lt;file_ID&gt;}
Sets the step of all animation files for the specified value. When &lt;file_ID&gt; is given, only the specified file is processed.

== backbone ==
 backbone {on/true}
Turns on the selected backbone bonds.

 backbone off/false
Turns off the selected backbone bonds.

 backbone &lt;radius&gt;
Turns on the selected backbone bonds with the specified raidus (angstrom or Rasmol unit). The maximum parameter value is 2.0.

== background ==
 background &lt;color&gt;
Changes the background color. The color may be given as RGB values [r,g,b], or predefined color names.

== cartoon ==
 cartoon {on/true}
Turns on the thick ribbons for the selected residues. When a chain does not have enough atoms to draw the ribbon model, a backbone will be shown instead.

 cartoon off/false
Turns off the thick ribbons for the selected residues.

 cartoon &lt;half_width&gt;
Turns on the thick ribbons for the selected residues with the specified half width (angstrom or Rasmol unit). The maximum parameter value is 4.0.

== center ==
 center {-r/-s} {&lt;atom_expression&gt;}
Sets the center of rotation and the center of the screen to the center of a group of atoms specified by the atom expression. When the option -r or -s is specified, only the center of rotation or the center of the screen is modified, respectively.

 center {-r} [x, y, z]
Moves the center of rotation and the center of the screen from the current position by the specified amount. When the option -r is specified, only the center of rotation is modified.

 center {-r} {x, y, z}
Sets the center of rotation and the center of the screen to the specified coordinates. When the option -r is specified, only the center of rotation is modified.

 center -s [x, y]
Moves the center of the screen from the current position by the specified amount.

 center -s {x, y}
Sets the center of the screen to the specified coordinates.

== color ==
 color {atoms} &lt;color&gt;
Sets the color of the selected atoms. The color may be given as RGB values [r,g,b], predefined color names, or predefined color schemes; amino, chain, charge, cpk, group, shapely, structure, and temperature.

 color bonds/backbone/ribbons/hbonds/ssbonds &lt;color&gt;
Sets the color of the specified object. The color may be given as RGB values [r,g,b] or predefined color names. For hydrogen bonds, color scheme 'type' can be specified.

 color bonds/backbone/ribbons/hbonds/ssbonds none
Resets the color of the specified object.

== colorvertex ==
 colorvertex &lt;color&gt;
Sets the color of the selected vertices. The color may be given as RGB values [r,g,b] or predefined color names.

 colorvertex none
Resets the color of the selected vertices.

== cpk ==
 cpk
A synonym of the [[#spacefill|spacefill]] command.

== define ==
 define &lt;name&gt; &lt;atom_expression&gt;
Associates an arbitrary set of atoms with a unique name.

== display ==
 display all
Displays the image of all files.

 display none
Turns off the image of all files.

 display {-a/-r} &lt;file_IDs&gt;
Displays the image of the specified files and turns off the others. More than one file IDs can be specified by putting commas as the delimiter. When the option -a or -r is specified, turns the image of the specified files on or off, respectively, and the others remain unchanged.

== displayatom ==
 displayatom {on/true}
Displays the selected atoms.

 displayatom off/false
Turns off the selected atoms.

== displayvertex ==
 displayvertex {on/true}
Displays the selected vertices.

 displayvertex off/false
Turns off the selected vertices.

== echo ==
 echo &lt;string&gt;
Echoes the specified message back to the message area.

== exit ==
 exit
Terminates the application.

== fit ==
 fit &lt;file1_ID&gt; &lt;file2_ID&gt;
Sets the transform matrix of file1 identical to that of file2. 

== fselect ==
 fselect all
Selects all files.

 fselect none
Selects no files.

 fselect {-a/-r} &lt;file_IDs&gt;
Selects the specified files and makes the others not selected. More than one file IDs can be specified by putting commas as the delimiter. When the option -a or -r is specified, only the selection status of the specified files are modified, selected or not selected, respectively, and the others remain unchanged.

== hbonds ==
 hbonds {on/true}
Turns on the selected hydrogen bonds.

 hbonds off/false
Turns off the selected hydrogen bonds.

 hbonds &lt;radius&gt;
Turns on the selected hydrogen bonds with the specified raidus (angstrom or Rasmol unit). The maximum parameter value is 2.0. 

== load ==
 load {pdbml} &lt;filename&gt; {fit &lt;file_ID&gt;}
Opens a PDBML file. URL can be used to open a remote file. On loading, the transform matrix can be set identical to that of the specified file.

 load pdb &lt;filename&gt; {fit &lt;file_ID&gt;}
Opens a PDB file. URL can be used to open a remote file. On loading, the transform matrix can be set identical to that of the specified file.

 load polygon &lt;filename&gt; {fit &lt;file_ID&gt;}
Opens a polygon file. URL can be used to open a remote file. On loading, the transform matrix can be set identical to that of the specified file.

 load animation &lt;filename&gt; {fit &lt;file_ID&gt;}
Opens an animation file. URL can be used to open a remote file. On loading, the transform matrix can be set identical to that of the specified file.

 load ftp &lt;PDB_code&gt; {fit &lt;file_ID&gt;}
Retrieves a PDBML file from the PDBj FTP site and opens it. On loading, the transform matrix can be set identical to that of the specified file. 

== pause ==
 pause
Stops the execution of a script file until any key is pressed to restart. 

== pdbj_describe ==
 pdbj_describe &lt;file_id&gt; {&lt;name&gt;} 
Shows the document for the jV_command in PDBMLplus specified by file ID and name. When the name is not specified, all available names are listed.

== pdbj_execute ==
 pdbj_execute &lt;file_id&gt; &lt;name&gt; 
Executes the jV_command in PDBMLplus specified by file ID and name.

== quit ==
 quit
A synonym of the [[#exit|exit]] command.

== refresh ==
 refresh
Redraws all images. 

== reset ==
=== default ===
 reset
Restores the original viewing transformation of all images, the center of rotation, and the view point. 

=== cartoon ===
 reset cartoon
Restores the thickness of the cartoon representation. 

=== line_width ===
 reset line_width
Restores the width of lines in polygon images. 

=== pickradius ===
 reset pickradius
Restores the mouse-pickable region of each atom. 

=== point_size ===
 reset point_size
Restores the size of points in polygon images. 

=== polyline_width ===
 reset polyline_width
Restores the width of polylines in polygon images. 

=== transparency ===
 reset transparency
Restores the transparency of polygon images.

 reset point_transparency
Restores the transparency of points in polygon images.

 reset line_transparency
Restores the transparency of lines in polygon images.

 reset triangle_transparency
Restores the transparency of triangles in polygon images.

 reset quad_transparency
Restores the transparency of quads in polygon images.

 reset polyline_transparency
Restores the transparency of polylines in polygon images. 

== ribbons ==
 ribbons {on/true}
Turns on the ribbon surfaces for the selected residues. When a chain does not have enough atoms to draw the ribbon model, a backbone will be shown instead.

 ribbons off/false
Turns off the ribbon surfaces for the selected residues.

 ribbons &lt;half_width&gt;
Turns on the ribbon surfaces for the selected residues with the specified half width (angstrom or Rasmol unit). The maximum parameter value is 4.0.

== rotate ==
 rotate x/y/z &lt;angle&gt;
Rotates images about the specified axis by the specified angle in degrees. 

== save ==
 save {pdb} &lt;filename&gt;
Saves the currently selected set of atoms in a PDB format file.

 save script &lt;filename&gt;
Creates a script file that reproduces the currently displayed image.

 save png &lt;filename&gt;
Creates a PNG image file of the currently displayed image.

 save jpeg &lt;filename&gt; {&lt;quality&gt;}
Creates a JPEG image file of the currently displayed image. The compression quality can be specified, 0 &lt; quality &lt;= 1, where 'quality = 1' means no compression. 

== script ==
 script &lt;filename&gt;
Opens and executes the specified script file. URL can be used to open a remote file. 

== select ==
 select
Selects all atoms. Whether hetero atoms and hydrogens are selected or not depends on the internal parameters, hetero and hydrogen, respectively.

 select all
Selects all atoms including hetero atoms and hydrogens.

 select none
Selects no atoms.

 select &lt;atom_expression&gt;
Selects a group of atoms specified by the atom expression. 

== selectvertex ==
 selectvertex {all}
Selects all vertices.

 selectvertex none
Selects no vertices.

 selectvertex &lt;vertex_expression&gt;
Selects a group of vertices specified by the vertex expression. 

== set ==
=== ambient ===
 set ambient {&lt;value&gt;}
Sets the amount of ambient light. The value must be between 0 and 100. When the parameter is not specified, it is restored to the default value 33.

=== adjustview ===
 set adjustview on
The view point is automatically adjusted when a new file is loaded.

 set adjustview off
The view point is kept unchanged when a new file is loaded. 

=== background ===
 set background &lt;color&gt;
Changes the background color. The color may be given as RGB values [r,g,b], or predefined color names. 

=== bondmode ===
 set bondmode and
Specifies how to select an individual bonds. A bond is selected when both atoms connected by the bond are selected.

 set bondmode or
Specifies how to select an individual bonds. A bond is selected when either of the connected atoms is selected. 

=== cartoon ===
 set cartoon {&lt;value&gt;}
Specifies the thickness of the cartoon representation (angstrom or Rasmol unit). The maximum parameter value is 2.0. When the parameter is not specified, it is restored to the default value. 

=== cartoon_loop_tube ===
 set cartoon_loop_tube on
The loop region is drawn as tube in the cartoon representation.

 set cartoon_loop_tube off
The loop region is drawn as square pillar in the cartoon representation.

=== cartoon_round ===
 set cartoon_round on
Square pillar with round edge is drawn in the cartoon representation (except beta strands). 

 set cartoon_round off
Square pillar is drawn in the cartoon representation.

=== center ===
 set center &lt;atom_expression&gt;
Sets the default center of the selected files to the center of the specified atoms.

 set center [x, y, z]
Sets the default center of the selected files to the specified coordinates. 

=== diffuse1 ===
 set diffuse1 {&lt;value&gt;}
Sets the amount of the first diffuse light. The value must be between 0 and 100. When the parameter is not specified, it is restored to the default value 50.

=== diffuse1_direction ===
 set diffuse1_direction {[x, y, z]}
Sets the direction of the first diffuse light. When the parameter is not specified, it is restored to the default value [-1, -1, -1].

=== diffuse2 ===
 set diffuse2 {&lt;value&gt;}
Sets the amount of the second diffuse light. The value must be between 0 and 100. When the parameter is not specified, it is restored to the default value 50.

=== diffuse2_direction ===
 set diffuse2_direction {[x, y, z]}
Sets the direction of the second diffuse light. When the parameter is not specified, it is restored to the default value [-1, -1, -1].

=== drawlevel ===
 set drawlevel &lt;value&gt;
Specifies precision of the rendering of spheres and cylinders. The value may be given as an integer (minimum 5) that stands for the number of straight line segments to represent an arc of 180 degrees. 

=== efsite_url ===
 set efsite_url &lt;URL&gt;
Sets the URL for eF-site.

=== ext_site_url ===
 set ext_site_url &lt;prefix&gt; &lt;URL&gt;
Sets the URL for an external database site.

=== hbonds ===
 set hbonds backbone
Hydrogen bonds are displayed between backbones.

 set hbonds sidechain
Hydrogen bonds are displayed between sidechains. 

=== hetero ===
 set hetero on
Sets the default behavior of the select command such that hetero atoms are selected.

 set hetero off
Sets the default behavior of the select command such that hetero atoms are not selected. 

=== hydrogen ===
 set hydrogen on
Sets the default behavior of the select command such that hydrogens are selected.

 set hydrogen off
Sets the default behavior of the select command such that hydrogens are not selected. 

=== imagesize ===
 set imagesize &lt;width&gt; &lt;height&gt;
Sets the size of the 3D-rendering panel in pixels. The size will be set within the screen size with the width being an even integer. 

=== line_width ===
 set line_width &lt;value&gt;
Sets the width of lines in polygon images. The &lt;value&gt; should be larger than 0. 

=== loadcenter ===
 set loadcenter on
When a file is opened, sets the default center of that file to the center of all files that have already opened.

 set loadcenter off
When a file is opened, sets the default center of that file according to its own coordiantes. 

=== pdbml_noatom_url ===
 set pdbml_noatom_url &lt;URL&gt;
Sets the URL for PDBML noatom files.

=== pdbml_extatom_url ===
 set pdbml_extatom_url &lt;URL&gt;
Sets the URL for PDBML extatom files.

=== pdbml_plus_url ===
 set pdbml_plus_url &lt;URL&gt;
Sets the URL for PDBMLplus files.

=== picking ===
 set picking off
Turns off the mouse picking.

 set picking ident
Sets the mouse picking behavior to show atom identification.

 set picking coord
Sets the mouse picking behavior to show atom coordinates with identification.

 set picking distance
Sets the mouse picking behavior to show the distance between atoms successively picked.

 set picking center
Sets the mouse picking behavior to specify the center of rotation and center of the screen.

 set picking select
Sets the mouse picking behavior to select the file that contains the atom picked. 

=== pickradius ===
 set pickradius &lt;value&gt;
Sets the mouse-pickable region of each atom to be the sphere centered to each atom with the specified radius (angstrom or Rasmol unit). 

=== point_size ===
 set point_size &lt;value&gt;
Sets the size of points in polygon images. The &lt;value&gt; should be larger than 0. 

=== polyline_width ===
 set polyline_width &lt;value&gt;
Sets the width of polylines in polygon images. The &lt;value&gt; should be larger than 0. 

=== projection ===
 set projection perspective
Sets the projection mode for a perspective projection.

 set projection parallel {&lt;size&gt;}
Sets the projection mode for a parallel projection. The size of image (fit to the height of the screen) can be specified (angstrom or Rasmol unit). 

=== ribbonback ===
 set ribbonback &lt;color&gt;
Sets the color of the back of ribbon models. The color may be given as RGB values [r,g,b] or predefined color names.

 set ribbonback none
Resets the color of the back of ribbon models.

=== specular ===
 set specular on/true
Enables the display of specular highlights on solid objects.

 set specular off/false
Disables the display of specular highlights on solid objects.

 set specular &lt;value&gt;
Enables the display of specular highlights on solid objects. The value between 0 and 100 specifies the specular color in gray scale with 0 and 100 being black and white, respectively. The default value is 50.0. 

=== specpower ===
 set specpower &lt;value&gt;
Sets the shininess of solid objects. The value between 0 and 100 specifies a material reflection coefficient with 0 being diffuse surfaces and 100 being shiny surfaces. 

=== ssbonds ===
 set ssbonds backbone
Disulfide bonds are displayed between backbones.

 set ssbonds sidechain
Disulfide bonds are displayed between sidechains. 

=== stereo ===
 set stereo
A synonym of the [[#stereo_2|stereo]] command.

=== transparency ===
 set transparency &lt;value&gt;
Sets the transparency of polygon images.

 set point_transparency &lt;value&gt;
Sets the transparency of points in polygon images.

 set line_transparency &lt;value&gt;
Sets the transparency of lines in polygon images.

 set triangle_transparency &lt;value&gt;
Sets the transparency of triangles in polygon images.

 set quad_transparency &lt;value&gt;
Sets the transparency of quads in polygon images.

 set polyline_transparency &lt;value&gt;
Sets the transparency of polylines in polygon images. 

=== viewpoint ===
 set viewpoint {x, y, z}
Sets the viewpoint to the specified coordinates. 

== show ==
 show godata
Displays gene ontology data of molecules.

 show imagesize
Displays the size of the 3D-rendering panel.

 show information
Displays a detail discription of molecules.

 show site {&lt;prefix&gt;:&lt;db&gt;:&lt;category&gt;}
Displays site information in an external database.

 show transform
Displays the transform matrix of molecules.

 show viewpoint
Displays the current viewpoint.

 show pdbj
Displays keywords available in PDBj expression.

== slab ==
 slab {on/true}
Enables the z-clipping plane of molecules and polygons.

 slab off/false
Disables the z-clipping plane of molecules and polygons.

 slab &lt;ratio&gt;
Sets the position of the z-clipping plane of molecules and polygons. The parameter may be given as a number from 0 to 100. The values 0 and 100 represent that image as a whole is completely invisible and visible, respectively.

 slab -v &lt;value&gt;
Sets the position of the z-clipping plane of molecules and polygons by specifying the z coordinate value. 

== spacefill ==
 spacefill {on/true}
Turns on the ball image of the selected atoms.

 spacefill off/false
Turns off the ball image of the selected atoms.

 spacefill &lt;radius&gt;
Turns on the ball image of the selected atoms with the specified radius (angstrom or Rasmol unit). The maximum parameter value is 3.0.

 spacefill temperature
Turns on the ball image of the selected atoms using the temperature factor as radius. 

== ssbonds ==
 ssbonds {on/true}
Turns on the selected disulfide bonds.

 ssbonds off/false
Turns off the selected disulfide bonds.

 ssbonds &lt;radius&gt;
Turns on the selected disulfide bonds with the specified raidus (angstrom or Rasmol unit). The maximum parameter value is 2.0. 

== stereo ==
 stereo {on/true}
Enables stereo display. This command without arguments cycles three state; 'stereo off', 'stereo on' in cross-eyed mode and 'stereo on' in parallel-eyed mode.

 stereo off/false
Disables stereo display.

 stereo &lt;angle&gt;
Enables stereo display with the specified separation angle. Positive and negative values represent cross-eyed and parallel-eyed viewing, respectively.


== structure ==
 structure
Estimates the secondary structure using Kabsch and Sander's DSSP algorithm. 

== trace ==
 trace {on/true}
Turns on a tube representation for the selected residues. When a chain does not have enough atoms to draw the tube model, a backbone will be shown instead.

 trace off/false
Turns off a tube representation for the selected residues.

 trace &lt;radius&gt;
Turns on a tube representation for the selected residues with the specified radius (angstrom or Rasmol unit). The maximum parameter value is 2.0.

== translate ==
 translate x/y/z &lt;value&gt;
Moves images along the specified axis by the specified amount (angstrom). 

== wireframe ==
 wireframe {on/true}
Turns on the selected bonds.

 wireframe off/false
Turns off the selected bonds.

 wireframe &lt;radius&gt;
Turns on the selected bonds with the specified raidus (angstrom or Rasmol unit). The maximum parameter value is 2.0. 

== write ==
 write
A synonym of the [[#save|save]] command.

== zap ==
 zap {&lt;file_IDs&gt;}
Closes the specified files. More than one file IDs can be specified by putting commas as the delimiter. When the paraneter is absent, all files are closed. 

== zoom ==
 zoom {&lt;value&gt;}
Sets the magnification of the image as a whole. The value stands for the magnification as a percentage of the current scale. The minimum parameter value is 10.0.</text>
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Command usage of jV follows that of [http://www.rasmol.org/ Rasmol] with some modifications. In the following part, command arguments that can take an arbitrary value are denoted as &lt;value&gt; for example, arguments restricted to several possible values are listed with / as a delimiter, and arguments that can be omitted are put in brackets {}. Commands, [[#exit|exit]], [[#load|load]], [[#quit|quit]], [[#save|save]], [[#script|script]], and [[#write|write]], are not available in applet circumstance.

== anim ==
 anim forward {&lt;value&gt;}
Starts animation forward. If the &lt;value&gt; is given, just move frames forward by the specified amount.

 anim backward {&lt;value&gt;}
Starts animation backward. If the &lt;value&gt; is given, just move frames backward by the specified amount.

 anim stop
Stops animation.

== animframe ==
 animframe &lt;frame&gt; {&lt;file_ID&gt;}
Sets the frame of all animation files for the specified value. When &lt;file_ID&gt; is given, only the specified file is processed.

== animmode ==
 animmode once
Sets the behavior of animation for 'once'. When the frame reaches the last one, animation is stopped.

 animmode loop
Sets the behavior of animation for 'loop'. When the frame reaches the last one, animation is reset to the first frame and continues playing.

 animmode swing
Sets the behavior of animation for 'swing'. When the frame reaches the last one, the direction of animation is reversed.

== animrange ==
 animrange &lt;init_frame&gt;-&lt;term_frame&gt; {&lt;file_IDs&gt;}
Sets the range of all animation files. When is given, only the specified file is processed.

== animselect ==
 animselect {-a/-r} &lt;file_IDs&gt;
Selects the specified files and makes the others not selected. More than one file IDs can be specified by putting commas as the delimiter. When the option -a or -r is specified, only the selection status of the specified files are modified, selected or not selected, respectively, and the others remain unchanged.

== animspeed ==
 animspeed &lt;speed&gt;
Sets the animation speed. The argument should be an integer value from 1 to 20.

== animstep ==
 animstep &lt;step&gt; {&lt;file_ID&gt;}
Sets the step of all animation files for the specified value. When &lt;file_ID&gt; is given, only the specified file is processed.

== backbone ==
 backbone {on/true}
Turns on the selected backbone bonds.

 backbone off/false
Turns off the selected backbone bonds.

 backbone &lt;radius&gt;
Turns on the selected backbone bonds with the specified raidus (angstrom or Rasmol unit). The maximum parameter value is 2.0.

== background ==
 background &lt;color&gt;
Changes the background color. The color may be given as RGB values [r,g,b], or predefined color names.

== ball_and_stick ==
 ball_and_stick {on/true}
Turns on the ball and stick image of the selected atoms with ball radius 0.5 and stick radius 0.2 in angstrom.

 ball_and_stick off/false
Turns off the ball and stick image of the selected atoms.

 ball_and_stick &lt;ball_radius&gt; &lt;stick_radius&gt;
Turns on the ball and stick image of the selected atoms with the specified ball radius and stick radius (angstrom or Rasmol unit). The maximum parameter value is 3.0 and 2.0, respectively.

== cartoon ==
 cartoon {on/true}
Turns on the thick ribbons for the selected residues. When a chain does not have enough atoms to draw the ribbon model, a backbone will be shown instead.

 cartoon off/false
Turns off the thick ribbons for the selected residues.

 cartoon &lt;half_width&gt;
Turns on the thick ribbons for the selected residues with the specified half width (angstrom or Rasmol unit). The maximum parameter value is 4.0.

== center ==
 center {-r/-s} {&lt;atom_expression&gt;}
Sets the center of rotation and the center of the screen to the center of a group of atoms specified by the atom expression. When the option -r or -s is specified, only the center of rotation or the center of the screen is modified, respectively.

 center {-r} [x, y, z]
Moves the center of rotation and the center of the screen from the current position by the specified amount. When the option -r is specified, only the center of rotation is modified.

 center {-r} {x, y, z}
Sets the center of rotation and the center of the screen to the specified coordinates. When the option -r is specified, only the center of rotation is modified.

 center -s [x, y]
Moves the center of the screen from the current position by the specified amount.

 center -s {x, y}
Sets the center of the screen to the specified coordinates.

== color ==
 color {atoms} &lt;color&gt;
Sets the color of the selected atoms. The color may be given as RGB values [r,g,b], predefined color names, or predefined color schemes; amino, chain, charge, cpk, group, shapely, structure, and temperature.

 color bonds/backbone/ribbons/hbonds/ssbonds &lt;color&gt;
Sets the color of the specified object. The color may be given as RGB values [r,g,b] or predefined color names. For hydrogen bonds, color scheme 'type' can be specified.

 color bonds/backbone/ribbons/hbonds/ssbonds none
Resets the color of the specified object.

== colorvertex ==
 colorvertex &lt;color&gt;
Sets the color of the selected vertices. The color may be given as RGB values [r,g,b] or predefined color names.

 colorvertex none
Resets the color of the selected vertices.

== cpk ==
 cpk
A synonym of the [[#spacefill|spacefill]] command.

== define ==
 define &lt;name&gt; &lt;atom_expression&gt;
Associates an arbitrary set of atoms with a unique name.

== display ==
 display all
Displays the image of all files.

 display none
Turns off the image of all files.

 display {-a/-r} &lt;file_IDs&gt;
Displays the image of the specified files and turns off the others. More than one file IDs can be specified by putting commas as the delimiter. When the option -a or -r is specified, turns the image of the specified files on or off, respectively, and the others remain unchanged.

== displayatom ==
 displayatom {on/true}
Displays the selected atoms.

 displayatom off/false
Turns off the selected atoms.

== displayvertex ==
 displayvertex {on/true}
Displays the selected vertices.

 displayvertex off/false
Turns off the selected vertices.

== echo ==
 echo &lt;string&gt;
Echoes the specified message back to the message area.

== exit ==
 exit
Terminates the application.

== fit ==
 fit &lt;file1_ID&gt; &lt;file2_ID&gt;
Sets the transform matrix of file1 identical to that of file2. 

== fselect ==
 fselect all
Selects all files.

 fselect none
Selects no files.

 fselect {-a/-r} &lt;file_IDs&gt;
Selects the specified files and makes the others not selected. More than one file IDs can be specified by putting commas as the delimiter. When the option -a or -r is specified, only the selection status of the specified files are modified, selected or not selected, respectively, and the others remain unchanged.

== hbonds ==
 hbonds {on/true}
Turns on the selected hydrogen bonds.

 hbonds off/false
Turns off the selected hydrogen bonds.

 hbonds &lt;radius&gt;
Turns on the selected hydrogen bonds with the specified raidus (angstrom or Rasmol unit). The maximum parameter value is 2.0. 

== load ==
 load {pdbml} &lt;filename&gt; {fit &lt;file_ID&gt;}
Opens a PDBML file. URL can be used to open a remote file. On loading, the transform matrix can be set identical to that of the specified file.

 load pdb &lt;filename&gt; {fit &lt;file_ID&gt;}
Opens a PDB file. URL can be used to open a remote file. On loading, the transform matrix can be set identical to that of the specified file.

 load polygon &lt;filename&gt; {fit &lt;file_ID&gt;}
Opens a polygon file. URL can be used to open a remote file. On loading, the transform matrix can be set identical to that of the specified file.

 load animation &lt;filename&gt; {fit &lt;file_ID&gt;}
Opens an animation file. URL can be used to open a remote file. On loading, the transform matrix can be set identical to that of the specified file.

 load ftp &lt;PDB_code&gt; {fit &lt;file_ID&gt;}
Retrieves a PDBML file from the PDBj FTP site and opens it. On loading, the transform matrix can be set identical to that of the specified file. 

== pause ==
 pause
Stops the execution of a script file until any key is pressed to restart. 

== pdbj_describe ==
 pdbj_describe &lt;file_id&gt; {&lt;name&gt;} 
Shows the document for the jV_command in PDBMLplus specified by file ID and name. When the name is not specified, all available names are listed.

== pdbj_execute ==
 pdbj_execute &lt;file_id&gt; &lt;name&gt; 
Executes the jV_command in PDBMLplus specified by file ID and name.

== quit ==
 quit
A synonym of the [[#exit|exit]] command.

== refresh ==
 refresh
Redraws all images. 

== reset ==
=== default ===
 reset
Restores the original viewing transformation of all images, the center of rotation, and the view point. 

=== cartoon ===
 reset cartoon
Restores the thickness of the cartoon representation. 

=== line_width ===
 reset line_width
Restores the width of lines in polygon images. 

=== pickradius ===
 reset pickradius
Restores the mouse-pickable region of each atom. 

=== point_size ===
 reset point_size
Restores the size of points in polygon images. 

=== polyline_width ===
 reset polyline_width
Restores the width of polylines in polygon images. 

=== transparency ===
 reset transparency
Restores the transparency of polygon images.

 reset point_transparency
Restores the transparency of points in polygon images.

 reset line_transparency
Restores the transparency of lines in polygon images.

 reset triangle_transparency
Restores the transparency of triangles in polygon images.

 reset quad_transparency
Restores the transparency of quads in polygon images.

 reset polyline_transparency
Restores the transparency of polylines in polygon images. 

== ribbons ==
 ribbons {on/true}
Turns on the ribbon surfaces for the selected residues. When a chain does not have enough atoms to draw the ribbon model, a backbone will be shown instead.

 ribbons off/false
Turns off the ribbon surfaces for the selected residues.

 ribbons &lt;half_width&gt;
Turns on the ribbon surfaces for the selected residues with the specified half width (angstrom or Rasmol unit). The maximum parameter value is 4.0.

== rotate ==
 rotate x/y/z &lt;angle&gt;
Rotates images about the specified axis by the specified angle in degrees. 

== save ==
 save {pdb} &lt;filename&gt;
Saves the currently selected set of atoms in a PDB format file.

 save script &lt;filename&gt;
Creates a script file that reproduces the currently displayed image.

 save png &lt;filename&gt;
Creates a PNG image file of the currently displayed image.

 save jpeg &lt;filename&gt; {&lt;quality&gt;}
Creates a JPEG image file of the currently displayed image. The compression quality can be specified, 0 &lt; quality &lt;= 1, where 'quality = 1' means no compression. 

== script ==
 script &lt;filename&gt;
Opens and executes the specified script file. URL can be used to open a remote file. 

== select ==
 select
Selects all atoms. Whether hetero atoms and hydrogens are selected or not depends on the internal parameters, hetero and hydrogen, respectively.

 select all
Selects all atoms including hetero atoms and hydrogens.

 select none
Selects no atoms.

 select &lt;atom_expression&gt;
Selects a group of atoms specified by the atom expression. 

== selectvertex ==
 selectvertex {all}
Selects all vertices.

 selectvertex none
Selects no vertices.

 selectvertex &lt;vertex_expression&gt;
Selects a group of vertices specified by the vertex expression. 

== set ==
=== ambient ===
 set ambient {&lt;value&gt;}
Sets the amount of ambient light. The value must be between 0 and 100. When the parameter is not specified, it is restored to the default value 33.

=== adjustview ===
 set adjustview on
The view point is automatically adjusted when a new file is loaded.

 set adjustview off
The view point is kept unchanged when a new file is loaded. 

=== background ===
 set background &lt;color&gt;
Changes the background color. The color may be given as RGB values [r,g,b], or predefined color names. 

=== bondmode ===
 set bondmode and
Specifies how to select an individual bonds. A bond is selected when both atoms connected by the bond are selected.

 set bondmode or
Specifies how to select an individual bonds. A bond is selected when either of the connected atoms is selected. 

=== cartoon ===
 set cartoon {&lt;value&gt;}
Specifies the thickness of the cartoon representation (angstrom or Rasmol unit). The maximum parameter value is 2.0. When the parameter is not specified, it is restored to the default value. 

=== cartoon_loop_tube ===
 set cartoon_loop_tube on
The loop region is drawn as tube in the cartoon representation.

 set cartoon_loop_tube off
The loop region is drawn as square pillar in the cartoon representation.

=== cartoon_round ===
 set cartoon_round on
Square pillar with round edge is drawn in the cartoon representation (except beta strands). 

 set cartoon_round off
Square pillar is drawn in the cartoon representation.

=== center ===
 set center &lt;atom_expression&gt;
Sets the default center of the selected files to the center of the specified atoms.

 set center [x, y, z]
Sets the default center of the selected files to the specified coordinates. 

=== diffuse1 ===
 set diffuse1 {&lt;value&gt;}
Sets the amount of the first diffuse light. The value must be between 0 and 100. When the parameter is not specified, it is restored to the default value 50.

=== diffuse1_direction ===
 set diffuse1_direction {[x, y, z]}
Sets the direction of the first diffuse light. When the parameter is not specified, it is restored to the default value [-1, -1, -1].

=== diffuse2 ===
 set diffuse2 {&lt;value&gt;}
Sets the amount of the second diffuse light. The value must be between 0 and 100. When the parameter is not specified, it is restored to the default value 50.

=== diffuse2_direction ===
 set diffuse2_direction {[x, y, z]}
Sets the direction of the second diffuse light. When the parameter is not specified, it is restored to the default value [-1, -1, -1].

=== drawlevel ===
 set drawlevel &lt;value&gt;
Specifies precision of the rendering of spheres and cylinders. The value may be given as an integer (minimum 5) that stands for the number of straight line segments to represent an arc of 180 degrees. 

=== efsite_url ===
 set efsite_url &lt;URL&gt;
Sets the URL for eF-site.

=== ext_site_url ===
 set ext_site_url &lt;prefix&gt; &lt;URL&gt;
Sets the URL for an external database site.

=== hbonds ===
 set hbonds backbone
Hydrogen bonds are displayed between backbones.

 set hbonds sidechain
Hydrogen bonds are displayed between sidechains. 

=== hetero ===
 set hetero on
Sets the default behavior of the select command such that hetero atoms are selected.

 set hetero off
Sets the default behavior of the select command such that hetero atoms are not selected. 

=== hydrogen ===
 set hydrogen on
Sets the default behavior of the select command such that hydrogens are selected.

 set hydrogen off
Sets the default behavior of the select command such that hydrogens are not selected. 

=== imagesize ===
 set imagesize &lt;width&gt; &lt;height&gt;
Sets the size of the 3D-rendering panel in pixels. The size will be set within the screen size with the width being an even integer. 

=== line_width ===
 set line_width &lt;value&gt;
Sets the width of lines in polygon images. The &lt;value&gt; should be larger than 0. 

=== loadcenter ===
 set loadcenter on
When a file is opened, sets the default center of that file to the center of all files that have already opened.

 set loadcenter off
When a file is opened, sets the default center of that file according to its own coordiantes. 

=== pdbml_noatom_url ===
 set pdbml_noatom_url &lt;URL&gt;
Sets the URL for PDBML noatom files.

=== pdbml_extatom_url ===
 set pdbml_extatom_url &lt;URL&gt;
Sets the URL for PDBML extatom files.

=== pdbml_plus_url ===
 set pdbml_plus_url &lt;URL&gt;
Sets the URL for PDBMLplus files.

=== picking ===
 set picking off
Turns off the mouse picking.

 set picking ident
Sets the mouse picking behavior to show atom identification.

 set picking coord
Sets the mouse picking behavior to show atom coordinates with identification.

 set picking distance
Sets the mouse picking behavior to show the distance between atoms successively picked.

 set picking center
Sets the mouse picking behavior to specify the center of rotation and center of the screen.

 set picking select
Sets the mouse picking behavior to select the file that contains the atom picked. 

=== pickradius ===
 set pickradius &lt;value&gt;
Sets the mouse-pickable region of each atom to be the sphere centered to each atom with the specified radius (angstrom or Rasmol unit). 

=== point_size ===
 set point_size &lt;value&gt;
Sets the size of points in polygon images. The &lt;value&gt; should be larger than 0. 

=== polyline_width ===
 set polyline_width &lt;value&gt;
Sets the width of polylines in polygon images. The &lt;value&gt; should be larger than 0. 

=== projection ===
 set projection perspective
Sets the projection mode for a perspective projection.

 set projection parallel {&lt;size&gt;}
Sets the projection mode for a parallel projection. The size of image (fit to the height of the screen) can be specified (angstrom or Rasmol unit). 

=== ribbonback ===
 set ribbonback &lt;color&gt;
Sets the color of the back of ribbon models. The color may be given as RGB values [r,g,b] or predefined color names.

 set ribbonback none
Resets the color of the back of ribbon models.

=== specular ===
 set specular on/true
Enables the display of specular highlights on solid objects.

 set specular off/false
Disables the display of specular highlights on solid objects.

 set specular &lt;value&gt;
Enables the display of specular highlights on solid objects. The value between 0 and 100 specifies the specular color in gray scale with 0 and 100 being black and white, respectively. The default value is 50.0. 

=== specpower ===
 set specpower &lt;value&gt;
Sets the shininess of solid objects. The value between 0 and 100 specifies a material reflection coefficient with 0 being diffuse surfaces and 100 being shiny surfaces. 

=== ssbonds ===
 set ssbonds backbone
Disulfide bonds are displayed between backbones.

 set ssbonds sidechain
Disulfide bonds are displayed between sidechains. 

=== stereo ===
 set stereo
A synonym of the [[#stereo_2|stereo]] command.

=== transparency ===
 set transparency &lt;value&gt;
Sets the transparency of polygon images.

 set point_transparency &lt;value&gt;
Sets the transparency of points in polygon images.

 set line_transparency &lt;value&gt;
Sets the transparency of lines in polygon images.

 set triangle_transparency &lt;value&gt;
Sets the transparency of triangles in polygon images.

 set quad_transparency &lt;value&gt;
Sets the transparency of quads in polygon images.

 set polyline_transparency &lt;value&gt;
Sets the transparency of polylines in polygon images. 

=== viewpoint ===
 set viewpoint {x, y, z}
Sets the viewpoint to the specified coordinates. 

== show ==
 show godata
Displays gene ontology data of molecules.

 show imagesize
Displays the size of the 3D-rendering panel.

 show information
Displays a detail discription of molecules.

 show site {&lt;prefix&gt;:&lt;db&gt;:&lt;category&gt;}
Displays site information in an external database.

 show transform
Displays the transform matrix of molecules.

 show viewpoint
Displays the current viewpoint.

 show pdbj
Displays keywords available in PDBj expression.

== slab ==
 slab {on/true}
Enables the z-clipping plane of molecules and polygons.

 slab off/false
Disables the z-clipping plane of molecules and polygons.

 slab &lt;ratio&gt;
Sets the position of the z-clipping plane of molecules and polygons. The parameter may be given as a number from 0 to 100. The values 0 and 100 represent that image as a whole is completely invisible and visible, respectively.

 slab -v &lt;value&gt;
Sets the position of the z-clipping plane of molecules and polygons by specifying the z coordinate value. 

== spacefill ==
 spacefill {on/true}
Turns on the ball image of the selected atoms.

 spacefill off/false
Turns off the ball image of the selected atoms.

 spacefill &lt;radius&gt;
Turns on the ball image of the selected atoms with the specified radius (angstrom or Rasmol unit). The maximum parameter value is 3.0.

 spacefill temperature
Turns on the ball image of the selected atoms using the temperature factor as radius. 

== ssbonds ==
 ssbonds {on/true}
Turns on the selected disulfide bonds.

 ssbonds off/false
Turns off the selected disulfide bonds.

 ssbonds &lt;radius&gt;
Turns on the selected disulfide bonds with the specified raidus (angstrom or Rasmol unit). The maximum parameter value is 2.0. 

== stereo ==
 stereo {on/true}
Enables stereo display. This command without arguments cycles three state; 'stereo off', 'stereo on' in cross-eyed mode and 'stereo on' in parallel-eyed mode.

 stereo off/false
Disables stereo display.

 stereo &lt;angle&gt;
Enables stereo display with the specified separation angle. Positive and negative values represent cross-eyed and parallel-eyed viewing, respectively.


== structure ==
 structure
Estimates the secondary structure using Kabsch and Sander's DSSP algorithm. 

== trace ==
 trace {on/true}
Turns on a tube representation for the selected residues. When a chain does not have enough atoms to draw the tube model, a backbone will be shown instead.

 trace off/false
Turns off a tube representation for the selected residues.

 trace &lt;radius&gt;
Turns on a tube representation for the selected residues with the specified radius (angstrom or Rasmol unit). The maximum parameter value is 2.0.

== translate ==
 translate x/y/z &lt;value&gt;
Moves images along the specified axis by the specified amount (angstrom). 

== wireframe ==
 wireframe {on/true}
Turns on the selected bonds.

 wireframe off/false
Turns off the selected bonds.

 wireframe &lt;radius&gt;
Turns on the selected bonds with the specified raidus (angstrom or Rasmol unit). The maximum parameter value is 2.0. 

== write ==
 write
A synonym of the [[#save|save]] command.

== zap ==
 zap {&lt;file_IDs&gt;}
Closes the specified files. More than one file IDs can be specified by putting commas as the delimiter. When the paraneter is absent, all files are closed. 

== zoom ==
 zoom {&lt;value&gt;}
Sets the magnification of the image as a whole. The value stands for the magnification as a percentage of the current scale. The minimum parameter value is 10.0.</text>
    <sha1>90e841e1dc9befb3a384fd5509ab290a6f89985b</sha1>
  </revision>
  <revision>
    <id>420</id>
    <parentid>419</parentid>
    <timestamp>2010-12-03T04:44:08Z</timestamp>
    <contributor>
      <username>IMSsato</username>
      <id>4</id>
    </contributor>
    <comment>/* center */</comment>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="22089" xml:space="preserve"> {| style="float:right"
  |__TOC__
  |}
Command usage of jV follows that of [http://www.rasmol.org/ Rasmol] with some modifications. In the following part, command arguments that can take an arbitrary value are denoted as &lt;value&gt; for example, arguments restricted to several possible values are listed with / as a delimiter, and arguments that can be omitted are put in brackets {}. Commands, [[#exit|exit]], [[#load|load]], [[#quit|quit]], [[#save|save]], [[#script|script]], and [[#write|write]], are not available in applet circumstance.

== anim ==
 anim forward {&lt;value&gt;}
Starts animation forward. If the &lt;value&gt; is given, just move frames forward by the specified amount.

 anim backward {&lt;value&gt;}
Starts animation backward. If the &lt;value&gt; is given, just move frames backward by the specified amount.

 anim stop
Stops animation.

== animframe ==
 animframe &lt;frame&gt; {&lt;file_ID&gt;}
Sets the frame of all animation files for the specified value. When &lt;file_ID&gt; is given, only the specified file is processed.

== animmode ==
 animmode once
Sets the behavior of animation for 'once'. When the frame reaches the last one, animation is stopped.

 animmode loop
Sets the behavior of animation for 'loop'. When the frame reaches the last one, animation is reset to the first frame and continues playing.

 animmode swing
Sets the behavior of animation for 'swing'. When the frame reaches the last one, the direction of animation is reversed.

== animrange ==
 animrange &lt;init_frame&gt;-&lt;term_frame&gt; {&lt;file_IDs&gt;}
Sets the range of all animation files. When is given, only the specified file is processed.

== animselect ==
 animselect {-a/-r} &lt;file_IDs&gt;
Selects the specified files and makes the others not selected. More than one file IDs can be specified by putting commas as the delimiter. When the option -a or -r is specified, only the selection status of the specified files are modified, selected or not selected, respectively, and the others remain unchanged.

== animspeed ==
 animspeed &lt;speed&gt;
Sets the animation speed. The argument should be an integer value from 1 to 20.

== animstep ==
 animstep &lt;step&gt; {&lt;file_ID&gt;}
Sets the step of all animation files for the specified value. When &lt;file_ID&gt; is given, only the specified file is processed.

== backbone ==
 backbone {on/true}
Turns on the selected backbone bonds.

 backbone off/false
Turns off the selected backbone bonds.

 backbone &lt;radius&gt;
Turns on the selected backbone bonds with the specified raidus (angstrom or Rasmol unit). The maximum parameter value is 2.0.

== background ==
 background &lt;color&gt;
Changes the background color. The color may be given as RGB values [r,g,b], or predefined color names.

== ball_and_stick ==
 ball_and_stick {on/true}
Turns on the ball and stick image of the selected atoms with ball radius 0.5 and stick radius 0.2 in angstrom.

 ball_and_stick off/false
Turns off the ball and stick image of the selected atoms.

 ball_and_stick &lt;ball_radius&gt; &lt;stick_radius&gt;
Turns on the ball and stick image of the selected atoms with the specified ball radius and stick radius (angstrom or Rasmol unit). The maximum parameter value is 3.0 and 2.0, respectively.

== cartoon ==
 cartoon {on/true}
Turns on the thick ribbons for the selected residues. When a chain does not have enough atoms to draw the ribbon model, a backbone will be shown instead.

 cartoon off/false
Turns off the thick ribbons for the selected residues.

 cartoon &lt;half_width&gt;
Turns on the thick ribbons for the selected residues with the specified half width (angstrom or Rasmol unit). The maximum parameter value is 4.0.

== center ==
 center {-r/-s} {&lt;atom_expression&gt;}
Sets the center of rotation and the center of the screen to the center of a group of atoms specified by the [[Atom Expression|atom expression]]. When the option -r or -s is specified, only the center of rotation or the center of the screen is modified, respectively.

 center {-r} [x, y, z]
Moves the center of rotation and the center of the screen from the current position by the specified amount. When the option -r is specified, only the center of rotation is modified.

 center {-r} {x, y, z}
Sets the center of rotation and the center of the screen to the specified coordinates. When the option -r is specified, only the center of rotation is modified.

 center -s [x, y]
Moves the center of the screen from the current position by the specified amount.

 center -s {x, y}
Sets the center of the screen to the specified coordinates.

== color ==
 color {atoms} &lt;color&gt;
Sets the color of the selected atoms. The color may be given as RGB values [r,g,b], predefined color names, or predefined color schemes; amino, chain, charge, cpk, group, shapely, structure, and temperature.

 color bonds/backbone/ribbons/hbonds/ssbonds &lt;color&gt;
Sets the color of the specified object. The color may be given as RGB values [r,g,b] or predefined color names. For hydrogen bonds, color scheme 'type' can be specified.

 color bonds/backbone/ribbons/hbonds/ssbonds none
Resets the color of the specified object.

== colorvertex ==
 colorvertex &lt;color&gt;
Sets the color of the selected vertices. The color may be given as RGB values [r,g,b] or predefined color names.

 colorvertex none
Resets the color of the selected vertices.

== cpk ==
 cpk
A synonym of the [[#spacefill|spacefill]] command.

== define ==
 define &lt;name&gt; &lt;atom_expression&gt;
Associates an arbitrary set of atoms with a unique name.

== display ==
 display all
Displays the image of all files.

 display none
Turns off the image of all files.

 display {-a/-r} &lt;file_IDs&gt;
Displays the image of the specified files and turns off the others. More than one file IDs can be specified by putting commas as the delimiter. When the option -a or -r is specified, turns the image of the specified files on or off, respectively, and the others remain unchanged.

== displayatom ==
 displayatom {on/true}
Displays the selected atoms.

 displayatom off/false
Turns off the selected atoms.

== displayvertex ==
 displayvertex {on/true}
Displays the selected vertices.

 displayvertex off/false
Turns off the selected vertices.

== echo ==
 echo &lt;string&gt;
Echoes the specified message back to the message area.

== exit ==
 exit
Terminates the application.

== fit ==
 fit &lt;file1_ID&gt; &lt;file2_ID&gt;
Sets the transform matrix of file1 identical to that of file2. 

== fselect ==
 fselect all
Selects all files.

 fselect none
Selects no files.

 fselect {-a/-r} &lt;file_IDs&gt;
Selects the specified files and makes the others not selected. More than one file IDs can be specified by putting commas as the delimiter. When the option -a or -r is specified, only the selection status of the specified files are modified, selected or not selected, respectively, and the others remain unchanged.

== hbonds ==
 hbonds {on/true}
Turns on the selected hydrogen bonds.

 hbonds off/false
Turns off the selected hydrogen bonds.

 hbonds &lt;radius&gt;
Turns on the selected hydrogen bonds with the specified raidus (angstrom or Rasmol unit). The maximum parameter value is 2.0. 

== load ==
 load {pdbml} &lt;filename&gt; {fit &lt;file_ID&gt;}
Opens a PDBML file. URL can be used to open a remote file. On loading, the transform matrix can be set identical to that of the specified file.

 load pdb &lt;filename&gt; {fit &lt;file_ID&gt;}
Opens a PDB file. URL can be used to open a remote file. On loading, the transform matrix can be set identical to that of the specified file.

 load polygon &lt;filename&gt; {fit &lt;file_ID&gt;}
Opens a polygon file. URL can be used to open a remote file. On loading, the transform matrix can be set identical to that of the specified file.

 load animation &lt;filename&gt; {fit &lt;file_ID&gt;}
Opens an animation file. URL can be used to open a remote file. On loading, the transform matrix can be set identical to that of the specified file.

 load ftp &lt;PDB_code&gt; {fit &lt;file_ID&gt;}
Retrieves a PDBML file from the PDBj FTP site and opens it. On loading, the transform matrix can be set identical to that of the specified file. 

== pause ==
 pause
Stops the execution of a script file until any key is pressed to restart. 

== pdbj_describe ==
 pdbj_describe &lt;file_id&gt; {&lt;name&gt;} 
Shows the document for the jV_command in PDBMLplus specified by file ID and name. When the name is not specified, all available names are listed.

== pdbj_execute ==
 pdbj_execute &lt;file_id&gt; &lt;name&gt; 
Executes the jV_command in PDBMLplus specified by file ID and name.

== quit ==
 quit
A synonym of the [[#exit|exit]] command.

== refresh ==
 refresh
Redraws all images. 

== reset ==
=== default ===
 reset
Restores the original viewing transformation of all images, the center of rotation, and the view point. 

=== cartoon ===
 reset cartoon
Restores the thickness of the cartoon representation. 

=== line_width ===
 reset line_width
Restores the width of lines in polygon images. 

=== pickradius ===
 reset pickradius
Restores the mouse-pickable region of each atom. 

=== point_size ===
 reset point_size
Restores the size of points in polygon images. 

=== polyline_width ===
 reset polyline_width
Restores the width of polylines in polygon images. 

=== transparency ===
 reset transparency
Restores the transparency of polygon images.

 reset point_transparency
Restores the transparency of points in polygon images.

 reset line_transparency
Restores the transparency of lines in polygon images.

 reset triangle_transparency
Restores the transparency of triangles in polygon images.

 reset quad_transparency
Restores the transparency of quads in polygon images.

 reset polyline_transparency
Restores the transparency of polylines in polygon images. 

== ribbons ==
 ribbons {on/true}
Turns on the ribbon surfaces for the selected residues. When a chain does not have enough atoms to draw the ribbon model, a backbone will be shown instead.

 ribbons off/false
Turns off the ribbon surfaces for the selected residues.

 ribbons &lt;half_width&gt;
Turns on the ribbon surfaces for the selected residues with the specified half width (angstrom or Rasmol unit). The maximum parameter value is 4.0.

== rotate ==
 rotate x/y/z &lt;angle&gt;
Rotates images about the specified axis by the specified angle in degrees. 

== save ==
 save {pdb} &lt;filename&gt;
Saves the currently selected set of atoms in a PDB format file.

 save script &lt;filename&gt;
Creates a script file that reproduces the currently displayed image.

 save png &lt;filename&gt;
Creates a PNG image file of the currently displayed image.

 save jpeg &lt;filename&gt; {&lt;quality&gt;}
Creates a JPEG image file of the currently displayed image. The compression quality can be specified, 0 &lt; quality &lt;= 1, where 'quality = 1' means no compression. 

== script ==
 script &lt;filename&gt;
Opens and executes the specified script file. URL can be used to open a remote file. 

== select ==
 select
Selects all atoms. Whether hetero atoms and hydrogens are selected or not depends on the internal parameters, hetero and hydrogen, respectively.

 select all
Selects all atoms including hetero atoms and hydrogens.

 select none
Selects no atoms.

 select &lt;atom_expression&gt;
Selects a group of atoms specified by the atom expression. 

== selectvertex ==
 selectvertex {all}
Selects all vertices.

 selectvertex none
Selects no vertices.

 selectvertex &lt;vertex_expression&gt;
Selects a group of vertices specified by the vertex expression. 

== set ==
=== ambient ===
 set ambient {&lt;value&gt;}
Sets the amount of ambient light. The value must be between 0 and 100. When the parameter is not specified, it is restored to the default value 33.

=== adjustview ===
 set adjustview on
The view point is automatically adjusted when a new file is loaded.

 set adjustview off
The view point is kept unchanged when a new file is loaded. 

=== background ===
 set background &lt;color&gt;
Changes the background color. The color may be given as RGB values [r,g,b], or predefined color names. 

=== bondmode ===
 set bondmode and
Specifies how to select an individual bonds. A bond is selected when both atoms connected by the bond are selected.

 set bondmode or
Specifies how to select an individual bonds. A bond is selected when either of the connected atoms is selected. 

=== cartoon ===
 set cartoon {&lt;value&gt;}
Specifies the thickness of the cartoon representation (angstrom or Rasmol unit). The maximum parameter value is 2.0. When the parameter is not specified, it is restored to the default value. 

=== cartoon_loop_tube ===
 set cartoon_loop_tube on
The loop region is drawn as tube in the cartoon representation.

 set cartoon_loop_tube off
The loop region is drawn as square pillar in the cartoon representation.

=== cartoon_round ===
 set cartoon_round on
Square pillar with round edge is drawn in the cartoon representation (except beta strands). 

 set cartoon_round off
Square pillar is drawn in the cartoon representation.

=== center ===
 set center &lt;atom_expression&gt;
Sets the default center of the selected files to the center of the specified atoms.

 set center [x, y, z]
Sets the default center of the selected files to the specified coordinates. 

=== diffuse1 ===
 set diffuse1 {&lt;value&gt;}
Sets the amount of the first diffuse light. The value must be between 0 and 100. When the parameter is not specified, it is restored to the default value 50.

=== diffuse1_direction ===
 set diffuse1_direction {[x, y, z]}
Sets the direction of the first diffuse light. When the parameter is not specified, it is restored to the default value [-1, -1, -1].

=== diffuse2 ===
 set diffuse2 {&lt;value&gt;}
Sets the amount of the second diffuse light. The value must be between 0 and 100. When the parameter is not specified, it is restored to the default value 50.

=== diffuse2_direction ===
 set diffuse2_direction {[x, y, z]}
Sets the direction of the second diffuse light. When the parameter is not specified, it is restored to the default value [-1, -1, -1].

=== drawlevel ===
 set drawlevel &lt;value&gt;
Specifies precision of the rendering of spheres and cylinders. The value may be given as an integer (minimum 5) that stands for the number of straight line segments to represent an arc of 180 degrees. 

=== efsite_url ===
 set efsite_url &lt;URL&gt;
Sets the URL for eF-site.

=== ext_site_url ===
 set ext_site_url &lt;prefix&gt; &lt;URL&gt;
Sets the URL for an external database site.

=== hbonds ===
 set hbonds backbone
Hydrogen bonds are displayed between backbones.

 set hbonds sidechain
Hydrogen bonds are displayed between sidechains. 

=== hetero ===
 set hetero on
Sets the default behavior of the select command such that hetero atoms are selected.

 set hetero off
Sets the default behavior of the select command such that hetero atoms are not selected. 

=== hydrogen ===
 set hydrogen on
Sets the default behavior of the select command such that hydrogens are selected.

 set hydrogen off
Sets the default behavior of the select command such that hydrogens are not selected. 

=== imagesize ===
 set imagesize &lt;width&gt; &lt;height&gt;
Sets the size of the 3D-rendering panel in pixels. The size will be set within the screen size with the width being an even integer. 

=== line_width ===
 set line_width &lt;value&gt;
Sets the width of lines in polygon images. The &lt;value&gt; should be larger than 0. 

=== loadcenter ===
 set loadcenter on
When a file is opened, sets the default center of that file to the center of all files that have already opened.

 set loadcenter off
When a file is opened, sets the default center of that file according to its own coordiantes. 

=== pdbml_noatom_url ===
 set pdbml_noatom_url &lt;URL&gt;
Sets the URL for PDBML noatom files.

=== pdbml_extatom_url ===
 set pdbml_extatom_url &lt;URL&gt;
Sets the URL for PDBML extatom files.

=== pdbml_plus_url ===
 set pdbml_plus_url &lt;URL&gt;
Sets the URL for PDBMLplus files.

=== picking ===
 set picking off
Turns off the mouse picking.

 set picking ident
Sets the mouse picking behavior to show atom identification.

 set picking coord
Sets the mouse picking behavior to show atom coordinates with identification.

 set picking distance
Sets the mouse picking behavior to show the distance between atoms successively picked.

 set picking center
Sets the mouse picking behavior to specify the center of rotation and center of the screen.

 set picking select
Sets the mouse picking behavior to select the file that contains the atom picked. 

=== pickradius ===
 set pickradius &lt;value&gt;
Sets the mouse-pickable region of each atom to be the sphere centered to each atom with the specified radius (angstrom or Rasmol unit). 

=== point_size ===
 set point_size &lt;value&gt;
Sets the size of points in polygon images. The &lt;value&gt; should be larger than 0. 

=== polyline_width ===
 set polyline_width &lt;value&gt;
Sets the width of polylines in polygon images. The &lt;value&gt; should be larger than 0. 

=== projection ===
 set projection perspective
Sets the projection mode for a perspective projection.

 set projection parallel {&lt;size&gt;}
Sets the projection mode for a parallel projection. The size of image (fit to the height of the screen) can be specified (angstrom or Rasmol unit). 

=== ribbonback ===
 set ribbonback &lt;color&gt;
Sets the color of the back of ribbon models. The color may be given as RGB values [r,g,b] or predefined color names.

 set ribbonback none
Resets the color of the back of ribbon models.

=== specular ===
 set specular on/true
Enables the display of specular highlights on solid objects.

 set specular off/false
Disables the display of specular highlights on solid objects.

 set specular &lt;value&gt;
Enables the display of specular highlights on solid objects. The value between 0 and 100 specifies the specular color in gray scale with 0 and 100 being black and white, respectively. The default value is 50.0. 

=== specpower ===
 set specpower &lt;value&gt;
Sets the shininess of solid objects. The value between 0 and 100 specifies a material reflection coefficient with 0 being diffuse surfaces and 100 being shiny surfaces. 

=== ssbonds ===
 set ssbonds backbone
Disulfide bonds are displayed between backbones.

 set ssbonds sidechain
Disulfide bonds are displayed between sidechains. 

=== stereo ===
 set stereo
A synonym of the [[#stereo_2|stereo]] command.

=== transparency ===
 set transparency &lt;value&gt;
Sets the transparency of polygon images.

 set point_transparency &lt;value&gt;
Sets the transparency of points in polygon images.

 set line_transparency &lt;value&gt;
Sets the transparency of lines in polygon images.

 set triangle_transparency &lt;value&gt;
Sets the transparency of triangles in polygon images.

 set quad_transparency &lt;value&gt;
Sets the transparency of quads in polygon images.

 set polyline_transparency &lt;value&gt;
Sets the transparency of polylines in polygon images. 

=== viewpoint ===
 set viewpoint {x, y, z}
Sets the viewpoint to the specified coordinates. 

== show ==
 show godata
Displays gene ontology data of molecules.

 show imagesize
Displays the size of the 3D-rendering panel.

 show information
Displays a detail discription of molecules.

 show site {&lt;prefix&gt;:&lt;db&gt;:&lt;category&gt;}
Displays site information in an external database.

 show transform
Displays the transform matrix of molecules.

 show viewpoint
Displays the current viewpoint.

 show pdbj
Displays keywords available in PDBj expression.

== slab ==
 slab {on/true}
Enables the z-clipping plane of molecules and polygons.

 slab off/false
Disables the z-clipping plane of molecules and polygons.

 slab &lt;ratio&gt;
Sets the position of the z-clipping plane of molecules and polygons. The parameter may be given as a number from 0 to 100. The values 0 and 100 represent that image as a whole is completely invisible and visible, respectively.

 slab -v &lt;value&gt;
Sets the position of the z-clipping plane of molecules and polygons by specifying the z coordinate value. 

== spacefill ==
 spacefill {on/true}
Turns on the ball image of the selected atoms.

 spacefill off/false
Turns off the ball image of the selected atoms.

 spacefill &lt;radius&gt;
Turns on the ball image of the selected atoms with the specified radius (angstrom or Rasmol unit). The maximum parameter value is 3.0.

 spacefill temperature
Turns on the ball image of the selected atoms using the temperature factor as radius. 

== ssbonds ==
 ssbonds {on/true}
Turns on the selected disulfide bonds.

 ssbonds off/false
Turns off the selected disulfide bonds.

 ssbonds &lt;radius&gt;
Turns on the selected disulfide bonds with the specified raidus (angstrom or Rasmol unit). The maximum parameter value is 2.0. 

== stereo ==
 stereo {on/true}
Enables stereo display. This command without arguments cycles three state; 'stereo off', 'stereo on' in cross-eyed mode and 'stereo on' in parallel-eyed mode.

 stereo off/false
Disables stereo display.

 stereo &lt;angle&gt;
Enables stereo display with the specified separation angle. Positive and negative values represent cross-eyed and parallel-eyed viewing, respectively.


== structure ==
 structure
Estimates the secondary structure using Kabsch and Sander's DSSP algorithm. 

== trace ==
 trace {on/true}
Turns on a tube representation for the selected residues. When a chain does not have enough atoms to draw the tube model, a backbone will be shown instead.

 trace off/false
Turns off a tube representation for the selected residues.

 trace &lt;radius&gt;
Turns on a tube representation for the selected residues with the specified radius (angstrom or Rasmol unit). The maximum parameter value is 2.0.

== translate ==
 translate x/y/z &lt;value&gt;
Moves images along the specified axis by the specified amount (angstrom). 

== wireframe ==
 wireframe {on/true}
Turns on the selected bonds.

 wireframe off/false
Turns off the selected bonds.

 wireframe &lt;radius&gt;
Turns on the selected bonds with the specified raidus (angstrom or Rasmol unit). The maximum parameter value is 2.0. 

== write ==
 write
A synonym of the [[#save|save]] command.

== zap ==
 zap {&lt;file_IDs&gt;}
Closes the specified files. More than one file IDs can be specified by putting commas as the delimiter. When the paraneter is absent, all files are closed. 

== zoom ==
 zoom {&lt;value&gt;}
Sets the magnification of the image as a whole. The value stands for the magnification as a percentage of the current scale. The minimum parameter value is 10.0.</text>
    <sha1>ca0eb5bc4b65392d0cf7bf80b4762166d7198f01</sha1>
  </revision>
  <revision>
    <id>421</id>
    <parentid>420</parentid>
    <timestamp>2010-12-03T04:45:02Z</timestamp>
    <contributor>
      <username>IMSsato</username>
      <id>4</id>
    </contributor>
    <comment>/* define */</comment>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="22142" xml:space="preserve"> {| style="float:right"
  |__TOC__
  |}
Command usage of jV follows that of [http://www.rasmol.org/ Rasmol] with some modifications. In the following part, command arguments that can take an arbitrary value are denoted as &lt;value&gt; for example, arguments restricted to several possible values are listed with / as a delimiter, and arguments that can be omitted are put in brackets {}. Commands, [[#exit|exit]], [[#load|load]], [[#quit|quit]], [[#save|save]], [[#script|script]], and [[#write|write]], are not available in applet circumstance.

== anim ==
 anim forward {&lt;value&gt;}
Starts animation forward. If the &lt;value&gt; is given, just move frames forward by the specified amount.

 anim backward {&lt;value&gt;}
Starts animation backward. If the &lt;value&gt; is given, just move frames backward by the specified amount.

 anim stop
Stops animation.

== animframe ==
 animframe &lt;frame&gt; {&lt;file_ID&gt;}
Sets the frame of all animation files for the specified value. When &lt;file_ID&gt; is given, only the specified file is processed.

== animmode ==
 animmode once
Sets the behavior of animation for 'once'. When the frame reaches the last one, animation is stopped.

 animmode loop
Sets the behavior of animation for 'loop'. When the frame reaches the last one, animation is reset to the first frame and continues playing.

 animmode swing
Sets the behavior of animation for 'swing'. When the frame reaches the last one, the direction of animation is reversed.

== animrange ==
 animrange &lt;init_frame&gt;-&lt;term_frame&gt; {&lt;file_IDs&gt;}
Sets the range of all animation files. When is given, only the specified file is processed.

== animselect ==
 animselect {-a/-r} &lt;file_IDs&gt;
Selects the specified files and makes the others not selected. More than one file IDs can be specified by putting commas as the delimiter. When the option -a or -r is specified, only the selection status of the specified files are modified, selected or not selected, respectively, and the others remain unchanged.

== animspeed ==
 animspeed &lt;speed&gt;
Sets the animation speed. The argument should be an integer value from 1 to 20.

== animstep ==
 animstep &lt;step&gt; {&lt;file_ID&gt;}
Sets the step of all animation files for the specified value. When &lt;file_ID&gt; is given, only the specified file is processed.

== backbone ==
 backbone {on/true}
Turns on the selected backbone bonds.

 backbone off/false
Turns off the selected backbone bonds.

 backbone &lt;radius&gt;
Turns on the selected backbone bonds with the specified raidus (angstrom or Rasmol unit). The maximum parameter value is 2.0.

== background ==
 background &lt;color&gt;
Changes the background color. The color may be given as RGB values [r,g,b], or predefined color names.

== ball_and_stick ==
 ball_and_stick {on/true}
Turns on the ball and stick image of the selected atoms with ball radius 0.5 and stick radius 0.2 in angstrom.

 ball_and_stick off/false
Turns off the ball and stick image of the selected atoms.

 ball_and_stick &lt;ball_radius&gt; &lt;stick_radius&gt;
Turns on the ball and stick image of the selected atoms with the specified ball radius and stick radius (angstrom or Rasmol unit). The maximum parameter value is 3.0 and 2.0, respectively.

== cartoon ==
 cartoon {on/true}
Turns on the thick ribbons for the selected residues. When a chain does not have enough atoms to draw the ribbon model, a backbone will be shown instead.

 cartoon off/false
Turns off the thick ribbons for the selected residues.

 cartoon &lt;half_width&gt;
Turns on the thick ribbons for the selected residues with the specified half width (angstrom or Rasmol unit). The maximum parameter value is 4.0.

== center ==
 center {-r/-s} {&lt;atom_expression&gt;}
Sets the center of rotation and the center of the screen to the center of a group of atoms specified by the [[Atom Expression|atom expression]]. When the option -r or -s is specified, only the center of rotation or the center of the screen is modified, respectively.

 center {-r} [x, y, z]
Moves the center of rotation and the center of the screen from the current position by the specified amount. When the option -r is specified, only the center of rotation is modified.

 center {-r} {x, y, z}
Sets the center of rotation and the center of the screen to the specified coordinates. When the option -r is specified, only the center of rotation is modified.

 center -s [x, y]
Moves the center of the screen from the current position by the specified amount.

 center -s {x, y}
Sets the center of the screen to the specified coordinates.

== color ==
 color {atoms} &lt;color&gt;
Sets the color of the selected atoms. The color may be given as RGB values [r,g,b], predefined color names, or predefined color schemes; amino, chain, charge, cpk, group, shapely, structure, and temperature.

 color bonds/backbone/ribbons/hbonds/ssbonds &lt;color&gt;
Sets the color of the specified object. The color may be given as RGB values [r,g,b] or predefined color names. For hydrogen bonds, color scheme 'type' can be specified.

 color bonds/backbone/ribbons/hbonds/ssbonds none
Resets the color of the specified object.

== colorvertex ==
 colorvertex &lt;color&gt;
Sets the color of the selected vertices. The color may be given as RGB values [r,g,b] or predefined color names.

 colorvertex none
Resets the color of the selected vertices.

== cpk ==
 cpk
A synonym of the [[#spacefill|spacefill]] command.

== define ==
 define &lt;name&gt; &lt;atom_expression&gt;
Associates an arbitrary set of atoms specified by the [[Atom Expression|atom expression]] with a unique name.

== display ==
 display all
Displays the image of all files.

 display none
Turns off the image of all files.

 display {-a/-r} &lt;file_IDs&gt;
Displays the image of the specified files and turns off the others. More than one file IDs can be specified by putting commas as the delimiter. When the option -a or -r is specified, turns the image of the specified files on or off, respectively, and the others remain unchanged.

== displayatom ==
 displayatom {on/true}
Displays the selected atoms.

 displayatom off/false
Turns off the selected atoms.

== displayvertex ==
 displayvertex {on/true}
Displays the selected vertices.

 displayvertex off/false
Turns off the selected vertices.

== echo ==
 echo &lt;string&gt;
Echoes the specified message back to the message area.

== exit ==
 exit
Terminates the application.

== fit ==
 fit &lt;file1_ID&gt; &lt;file2_ID&gt;
Sets the transform matrix of file1 identical to that of file2. 

== fselect ==
 fselect all
Selects all files.

 fselect none
Selects no files.

 fselect {-a/-r} &lt;file_IDs&gt;
Selects the specified files and makes the others not selected. More than one file IDs can be specified by putting commas as the delimiter. When the option -a or -r is specified, only the selection status of the specified files are modified, selected or not selected, respectively, and the others remain unchanged.

== hbonds ==
 hbonds {on/true}
Turns on the selected hydrogen bonds.

 hbonds off/false
Turns off the selected hydrogen bonds.

 hbonds &lt;radius&gt;
Turns on the selected hydrogen bonds with the specified raidus (angstrom or Rasmol unit). The maximum parameter value is 2.0. 

== load ==
 load {pdbml} &lt;filename&gt; {fit &lt;file_ID&gt;}
Opens a PDBML file. URL can be used to open a remote file. On loading, the transform matrix can be set identical to that of the specified file.

 load pdb &lt;filename&gt; {fit &lt;file_ID&gt;}
Opens a PDB file. URL can be used to open a remote file. On loading, the transform matrix can be set identical to that of the specified file.

 load polygon &lt;filename&gt; {fit &lt;file_ID&gt;}
Opens a polygon file. URL can be used to open a remote file. On loading, the transform matrix can be set identical to that of the specified file.

 load animation &lt;filename&gt; {fit &lt;file_ID&gt;}
Opens an animation file. URL can be used to open a remote file. On loading, the transform matrix can be set identical to that of the specified file.

 load ftp &lt;PDB_code&gt; {fit &lt;file_ID&gt;}
Retrieves a PDBML file from the PDBj FTP site and opens it. On loading, the transform matrix can be set identical to that of the specified file. 

== pause ==
 pause
Stops the execution of a script file until any key is pressed to restart. 

== pdbj_describe ==
 pdbj_describe &lt;file_id&gt; {&lt;name&gt;} 
Shows the document for the jV_command in PDBMLplus specified by file ID and name. When the name is not specified, all available names are listed.

== pdbj_execute ==
 pdbj_execute &lt;file_id&gt; &lt;name&gt; 
Executes the jV_command in PDBMLplus specified by file ID and name.

== quit ==
 quit
A synonym of the [[#exit|exit]] command.

== refresh ==
 refresh
Redraws all images. 

== reset ==
=== default ===
 reset
Restores the original viewing transformation of all images, the center of rotation, and the view point. 

=== cartoon ===
 reset cartoon
Restores the thickness of the cartoon representation. 

=== line_width ===
 reset line_width
Restores the width of lines in polygon images. 

=== pickradius ===
 reset pickradius
Restores the mouse-pickable region of each atom. 

=== point_size ===
 reset point_size
Restores the size of points in polygon images. 

=== polyline_width ===
 reset polyline_width
Restores the width of polylines in polygon images. 

=== transparency ===
 reset transparency
Restores the transparency of polygon images.

 reset point_transparency
Restores the transparency of points in polygon images.

 reset line_transparency
Restores the transparency of lines in polygon images.

 reset triangle_transparency
Restores the transparency of triangles in polygon images.

 reset quad_transparency
Restores the transparency of quads in polygon images.

 reset polyline_transparency
Restores the transparency of polylines in polygon images. 

== ribbons ==
 ribbons {on/true}
Turns on the ribbon surfaces for the selected residues. When a chain does not have enough atoms to draw the ribbon model, a backbone will be shown instead.

 ribbons off/false
Turns off the ribbon surfaces for the selected residues.

 ribbons &lt;half_width&gt;
Turns on the ribbon surfaces for the selected residues with the specified half width (angstrom or Rasmol unit). The maximum parameter value is 4.0.

== rotate ==
 rotate x/y/z &lt;angle&gt;
Rotates images about the specified axis by the specified angle in degrees. 

== save ==
 save {pdb} &lt;filename&gt;
Saves the currently selected set of atoms in a PDB format file.

 save script &lt;filename&gt;
Creates a script file that reproduces the currently displayed image.

 save png &lt;filename&gt;
Creates a PNG image file of the currently displayed image.

 save jpeg &lt;filename&gt; {&lt;quality&gt;}
Creates a JPEG image file of the currently displayed image. The compression quality can be specified, 0 &lt; quality &lt;= 1, where 'quality = 1' means no compression. 

== script ==
 script &lt;filename&gt;
Opens and executes the specified script file. URL can be used to open a remote file. 

== select ==
 select
Selects all atoms. Whether hetero atoms and hydrogens are selected or not depends on the internal parameters, hetero and hydrogen, respectively.

 select all
Selects all atoms including hetero atoms and hydrogens.

 select none
Selects no atoms.

 select &lt;atom_expression&gt;
Selects a group of atoms specified by the atom expression. 

== selectvertex ==
 selectvertex {all}
Selects all vertices.

 selectvertex none
Selects no vertices.

 selectvertex &lt;vertex_expression&gt;
Selects a group of vertices specified by the vertex expression. 

== set ==
=== ambient ===
 set ambient {&lt;value&gt;}
Sets the amount of ambient light. The value must be between 0 and 100. When the parameter is not specified, it is restored to the default value 33.

=== adjustview ===
 set adjustview on
The view point is automatically adjusted when a new file is loaded.

 set adjustview off
The view point is kept unchanged when a new file is loaded. 

=== background ===
 set background &lt;color&gt;
Changes the background color. The color may be given as RGB values [r,g,b], or predefined color names. 

=== bondmode ===
 set bondmode and
Specifies how to select an individual bonds. A bond is selected when both atoms connected by the bond are selected.

 set bondmode or
Specifies how to select an individual bonds. A bond is selected when either of the connected atoms is selected. 

=== cartoon ===
 set cartoon {&lt;value&gt;}
Specifies the thickness of the cartoon representation (angstrom or Rasmol unit). The maximum parameter value is 2.0. When the parameter is not specified, it is restored to the default value. 

=== cartoon_loop_tube ===
 set cartoon_loop_tube on
The loop region is drawn as tube in the cartoon representation.

 set cartoon_loop_tube off
The loop region is drawn as square pillar in the cartoon representation.

=== cartoon_round ===
 set cartoon_round on
Square pillar with round edge is drawn in the cartoon representation (except beta strands). 

 set cartoon_round off
Square pillar is drawn in the cartoon representation.

=== center ===
 set center &lt;atom_expression&gt;
Sets the default center of the selected files to the center of the specified atoms.

 set center [x, y, z]
Sets the default center of the selected files to the specified coordinates. 

=== diffuse1 ===
 set diffuse1 {&lt;value&gt;}
Sets the amount of the first diffuse light. The value must be between 0 and 100. When the parameter is not specified, it is restored to the default value 50.

=== diffuse1_direction ===
 set diffuse1_direction {[x, y, z]}
Sets the direction of the first diffuse light. When the parameter is not specified, it is restored to the default value [-1, -1, -1].

=== diffuse2 ===
 set diffuse2 {&lt;value&gt;}
Sets the amount of the second diffuse light. The value must be between 0 and 100. When the parameter is not specified, it is restored to the default value 50.

=== diffuse2_direction ===
 set diffuse2_direction {[x, y, z]}
Sets the direction of the second diffuse light. When the parameter is not specified, it is restored to the default value [-1, -1, -1].

=== drawlevel ===
 set drawlevel &lt;value&gt;
Specifies precision of the rendering of spheres and cylinders. The value may be given as an integer (minimum 5) that stands for the number of straight line segments to represent an arc of 180 degrees. 

=== efsite_url ===
 set efsite_url &lt;URL&gt;
Sets the URL for eF-site.

=== ext_site_url ===
 set ext_site_url &lt;prefix&gt; &lt;URL&gt;
Sets the URL for an external database site.

=== hbonds ===
 set hbonds backbone
Hydrogen bonds are displayed between backbones.

 set hbonds sidechain
Hydrogen bonds are displayed between sidechains. 

=== hetero ===
 set hetero on
Sets the default behavior of the select command such that hetero atoms are selected.

 set hetero off
Sets the default behavior of the select command such that hetero atoms are not selected. 

=== hydrogen ===
 set hydrogen on
Sets the default behavior of the select command such that hydrogens are selected.

 set hydrogen off
Sets the default behavior of the select command such that hydrogens are not selected. 

=== imagesize ===
 set imagesize &lt;width&gt; &lt;height&gt;
Sets the size of the 3D-rendering panel in pixels. The size will be set within the screen size with the width being an even integer. 

=== line_width ===
 set line_width &lt;value&gt;
Sets the width of lines in polygon images. The &lt;value&gt; should be larger than 0. 

=== loadcenter ===
 set loadcenter on
When a file is opened, sets the default center of that file to the center of all files that have already opened.

 set loadcenter off
When a file is opened, sets the default center of that file according to its own coordiantes. 

=== pdbml_noatom_url ===
 set pdbml_noatom_url &lt;URL&gt;
Sets the URL for PDBML noatom files.

=== pdbml_extatom_url ===
 set pdbml_extatom_url &lt;URL&gt;
Sets the URL for PDBML extatom files.

=== pdbml_plus_url ===
 set pdbml_plus_url &lt;URL&gt;
Sets the URL for PDBMLplus files.

=== picking ===
 set picking off
Turns off the mouse picking.

 set picking ident
Sets the mouse picking behavior to show atom identification.

 set picking coord
Sets the mouse picking behavior to show atom coordinates with identification.

 set picking distance
Sets the mouse picking behavior to show the distance between atoms successively picked.

 set picking center
Sets the mouse picking behavior to specify the center of rotation and center of the screen.

 set picking select
Sets the mouse picking behavior to select the file that contains the atom picked. 

=== pickradius ===
 set pickradius &lt;value&gt;
Sets the mouse-pickable region of each atom to be the sphere centered to each atom with the specified radius (angstrom or Rasmol unit). 

=== point_size ===
 set point_size &lt;value&gt;
Sets the size of points in polygon images. The &lt;value&gt; should be larger than 0. 

=== polyline_width ===
 set polyline_width &lt;value&gt;
Sets the width of polylines in polygon images. The &lt;value&gt; should be larger than 0. 

=== projection ===
 set projection perspective
Sets the projection mode for a perspective projection.

 set projection parallel {&lt;size&gt;}
Sets the projection mode for a parallel projection. The size of image (fit to the height of the screen) can be specified (angstrom or Rasmol unit). 

=== ribbonback ===
 set ribbonback &lt;color&gt;
Sets the color of the back of ribbon models. The color may be given as RGB values [r,g,b] or predefined color names.

 set ribbonback none
Resets the color of the back of ribbon models.

=== specular ===
 set specular on/true
Enables the display of specular highlights on solid objects.

 set specular off/false
Disables the display of specular highlights on solid objects.

 set specular &lt;value&gt;
Enables the display of specular highlights on solid objects. The value between 0 and 100 specifies the specular color in gray scale with 0 and 100 being black and white, respectively. The default value is 50.0. 

=== specpower ===
 set specpower &lt;value&gt;
Sets the shininess of solid objects. The value between 0 and 100 specifies a material reflection coefficient with 0 being diffuse surfaces and 100 being shiny surfaces. 

=== ssbonds ===
 set ssbonds backbone
Disulfide bonds are displayed between backbones.

 set ssbonds sidechain
Disulfide bonds are displayed between sidechains. 

=== stereo ===
 set stereo
A synonym of the [[#stereo_2|stereo]] command.

=== transparency ===
 set transparency &lt;value&gt;
Sets the transparency of polygon images.

 set point_transparency &lt;value&gt;
Sets the transparency of points in polygon images.

 set line_transparency &lt;value&gt;
Sets the transparency of lines in polygon images.

 set triangle_transparency &lt;value&gt;
Sets the transparency of triangles in polygon images.

 set quad_transparency &lt;value&gt;
Sets the transparency of quads in polygon images.

 set polyline_transparency &lt;value&gt;
Sets the transparency of polylines in polygon images. 

=== viewpoint ===
 set viewpoint {x, y, z}
Sets the viewpoint to the specified coordinates. 

== show ==
 show godata
Displays gene ontology data of molecules.

 show imagesize
Displays the size of the 3D-rendering panel.

 show information
Displays a detail discription of molecules.

 show site {&lt;prefix&gt;:&lt;db&gt;:&lt;category&gt;}
Displays site information in an external database.

 show transform
Displays the transform matrix of molecules.

 show viewpoint
Displays the current viewpoint.

 show pdbj
Displays keywords available in PDBj expression.

== slab ==
 slab {on/true}
Enables the z-clipping plane of molecules and polygons.

 slab off/false
Disables the z-clipping plane of molecules and polygons.

 slab &lt;ratio&gt;
Sets the position of the z-clipping plane of molecules and polygons. The parameter may be given as a number from 0 to 100. The values 0 and 100 represent that image as a whole is completely invisible and visible, respectively.

 slab -v &lt;value&gt;
Sets the position of the z-clipping plane of molecules and polygons by specifying the z coordinate value. 

== spacefill ==
 spacefill {on/true}
Turns on the ball image of the selected atoms.

 spacefill off/false
Turns off the ball image of the selected atoms.

 spacefill &lt;radius&gt;
Turns on the ball image of the selected atoms with the specified radius (angstrom or Rasmol unit). The maximum parameter value is 3.0.

 spacefill temperature
Turns on the ball image of the selected atoms using the temperature factor as radius. 

== ssbonds ==
 ssbonds {on/true}
Turns on the selected disulfide bonds.

 ssbonds off/false
Turns off the selected disulfide bonds.

 ssbonds &lt;radius&gt;
Turns on the selected disulfide bonds with the specified raidus (angstrom or Rasmol unit). The maximum parameter value is 2.0. 

== stereo ==
 stereo {on/true}
Enables stereo display. This command without arguments cycles three state; 'stereo off', 'stereo on' in cross-eyed mode and 'stereo on' in parallel-eyed mode.

 stereo off/false
Disables stereo display.

 stereo &lt;angle&gt;
Enables stereo display with the specified separation angle. Positive and negative values represent cross-eyed and parallel-eyed viewing, respectively.


== structure ==
 structure
Estimates the secondary structure using Kabsch and Sander's DSSP algorithm. 

== trace ==
 trace {on/true}
Turns on a tube representation for the selected residues. When a chain does not have enough atoms to draw the tube model, a backbone will be shown instead.

 trace off/false
Turns off a tube representation for the selected residues.

 trace &lt;radius&gt;
Turns on a tube representation for the selected residues with the specified radius (angstrom or Rasmol unit). The maximum parameter value is 2.0.

== translate ==
 translate x/y/z &lt;value&gt;
Moves images along the specified axis by the specified amount (angstrom). 

== wireframe ==
 wireframe {on/true}
Turns on the selected bonds.

 wireframe off/false
Turns off the selected bonds.

 wireframe &lt;radius&gt;
Turns on the selected bonds with the specified raidus (angstrom or Rasmol unit). The maximum parameter value is 2.0. 

== write ==
 write
A synonym of the [[#save|save]] command.

== zap ==
 zap {&lt;file_IDs&gt;}
Closes the specified files. More than one file IDs can be specified by putting commas as the delimiter. When the paraneter is absent, all files are closed. 

== zoom ==
 zoom {&lt;value&gt;}
Sets the magnification of the image as a whole. The value stands for the magnification as a percentage of the current scale. The minimum parameter value is 10.0.</text>
    <sha1>700b33bc1524a942b6cbcc7b17caa65bc28643ed</sha1>
  </revision>
  <revision>
    <id>422</id>
    <parentid>421</parentid>
    <timestamp>2010-12-03T04:45:37Z</timestamp>
    <contributor>
      <username>IMSsato</username>
      <id>4</id>
    </contributor>
    <comment>/* select */</comment>
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    <format>text/x-wiki</format>
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  |__TOC__
  |}
Command usage of jV follows that of [http://www.rasmol.org/ Rasmol] with some modifications. In the following part, command arguments that can take an arbitrary value are denoted as &lt;value&gt; for example, arguments restricted to several possible values are listed with / as a delimiter, and arguments that can be omitted are put in brackets {}. Commands, [[#exit|exit]], [[#load|load]], [[#quit|quit]], [[#save|save]], [[#script|script]], and [[#write|write]], are not available in applet circumstance.

== anim ==
 anim forward {&lt;value&gt;}
Starts animation forward. If the &lt;value&gt; is given, just move frames forward by the specified amount.

 anim backward {&lt;value&gt;}
Starts animation backward. If the &lt;value&gt; is given, just move frames backward by the specified amount.

 anim stop
Stops animation.

== animframe ==
 animframe &lt;frame&gt; {&lt;file_ID&gt;}
Sets the frame of all animation files for the specified value. When &lt;file_ID&gt; is given, only the specified file is processed.

== animmode ==
 animmode once
Sets the behavior of animation for 'once'. When the frame reaches the last one, animation is stopped.

 animmode loop
Sets the behavior of animation for 'loop'. When the frame reaches the last one, animation is reset to the first frame and continues playing.

 animmode swing
Sets the behavior of animation for 'swing'. When the frame reaches the last one, the direction of animation is reversed.

== animrange ==
 animrange &lt;init_frame&gt;-&lt;term_frame&gt; {&lt;file_IDs&gt;}
Sets the range of all animation files. When is given, only the specified file is processed.

== animselect ==
 animselect {-a/-r} &lt;file_IDs&gt;
Selects the specified files and makes the others not selected. More than one file IDs can be specified by putting commas as the delimiter. When the option -a or -r is specified, only the selection status of the specified files are modified, selected or not selected, respectively, and the others remain unchanged.

== animspeed ==
 animspeed &lt;speed&gt;
Sets the animation speed. The argument should be an integer value from 1 to 20.

== animstep ==
 animstep &lt;step&gt; {&lt;file_ID&gt;}
Sets the step of all animation files for the specified value. When &lt;file_ID&gt; is given, only the specified file is processed.

== backbone ==
 backbone {on/true}
Turns on the selected backbone bonds.

 backbone off/false
Turns off the selected backbone bonds.

 backbone &lt;radius&gt;
Turns on the selected backbone bonds with the specified raidus (angstrom or Rasmol unit). The maximum parameter value is 2.0.

== background ==
 background &lt;color&gt;
Changes the background color. The color may be given as RGB values [r,g,b], or predefined color names.

== ball_and_stick ==
 ball_and_stick {on/true}
Turns on the ball and stick image of the selected atoms with ball radius 0.5 and stick radius 0.2 in angstrom.

 ball_and_stick off/false
Turns off the ball and stick image of the selected atoms.

 ball_and_stick &lt;ball_radius&gt; &lt;stick_radius&gt;
Turns on the ball and stick image of the selected atoms with the specified ball radius and stick radius (angstrom or Rasmol unit). The maximum parameter value is 3.0 and 2.0, respectively.

== cartoon ==
 cartoon {on/true}
Turns on the thick ribbons for the selected residues. When a chain does not have enough atoms to draw the ribbon model, a backbone will be shown instead.

 cartoon off/false
Turns off the thick ribbons for the selected residues.

 cartoon &lt;half_width&gt;
Turns on the thick ribbons for the selected residues with the specified half width (angstrom or Rasmol unit). The maximum parameter value is 4.0.

== center ==
 center {-r/-s} {&lt;atom_expression&gt;}
Sets the center of rotation and the center of the screen to the center of a group of atoms specified by the [[Atom Expression|atom expression]]. When the option -r or -s is specified, only the center of rotation or the center of the screen is modified, respectively.

 center {-r} [x, y, z]
Moves the center of rotation and the center of the screen from the current position by the specified amount. When the option -r is specified, only the center of rotation is modified.

 center {-r} {x, y, z}
Sets the center of rotation and the center of the screen to the specified coordinates. When the option -r is specified, only the center of rotation is modified.

 center -s [x, y]
Moves the center of the screen from the current position by the specified amount.

 center -s {x, y}
Sets the center of the screen to the specified coordinates.

== color ==
 color {atoms} &lt;color&gt;
Sets the color of the selected atoms. The color may be given as RGB values [r,g,b], predefined color names, or predefined color schemes; amino, chain, charge, cpk, group, shapely, structure, and temperature.

 color bonds/backbone/ribbons/hbonds/ssbonds &lt;color&gt;
Sets the color of the specified object. The color may be given as RGB values [r,g,b] or predefined color names. For hydrogen bonds, color scheme 'type' can be specified.

 color bonds/backbone/ribbons/hbonds/ssbonds none
Resets the color of the specified object.

== colorvertex ==
 colorvertex &lt;color&gt;
Sets the color of the selected vertices. The color may be given as RGB values [r,g,b] or predefined color names.

 colorvertex none
Resets the color of the selected vertices.

== cpk ==
 cpk
A synonym of the [[#spacefill|spacefill]] command.

== define ==
 define &lt;name&gt; &lt;atom_expression&gt;
Associates an arbitrary set of atoms specified by the [[Atom Expression|atom expression]] with a unique name.

== display ==
 display all
Displays the image of all files.

 display none
Turns off the image of all files.

 display {-a/-r} &lt;file_IDs&gt;
Displays the image of the specified files and turns off the others. More than one file IDs can be specified by putting commas as the delimiter. When the option -a or -r is specified, turns the image of the specified files on or off, respectively, and the others remain unchanged.

== displayatom ==
 displayatom {on/true}
Displays the selected atoms.

 displayatom off/false
Turns off the selected atoms.

== displayvertex ==
 displayvertex {on/true}
Displays the selected vertices.

 displayvertex off/false
Turns off the selected vertices.

== echo ==
 echo &lt;string&gt;
Echoes the specified message back to the message area.

== exit ==
 exit
Terminates the application.

== fit ==
 fit &lt;file1_ID&gt; &lt;file2_ID&gt;
Sets the transform matrix of file1 identical to that of file2. 

== fselect ==
 fselect all
Selects all files.

 fselect none
Selects no files.

 fselect {-a/-r} &lt;file_IDs&gt;
Selects the specified files and makes the others not selected. More than one file IDs can be specified by putting commas as the delimiter. When the option -a or -r is specified, only the selection status of the specified files are modified, selected or not selected, respectively, and the others remain unchanged.

== hbonds ==
 hbonds {on/true}
Turns on the selected hydrogen bonds.

 hbonds off/false
Turns off the selected hydrogen bonds.

 hbonds &lt;radius&gt;
Turns on the selected hydrogen bonds with the specified raidus (angstrom or Rasmol unit). The maximum parameter value is 2.0. 

== load ==
 load {pdbml} &lt;filename&gt; {fit &lt;file_ID&gt;}
Opens a PDBML file. URL can be used to open a remote file. On loading, the transform matrix can be set identical to that of the specified file.

 load pdb &lt;filename&gt; {fit &lt;file_ID&gt;}
Opens a PDB file. URL can be used to open a remote file. On loading, the transform matrix can be set identical to that of the specified file.

 load polygon &lt;filename&gt; {fit &lt;file_ID&gt;}
Opens a polygon file. URL can be used to open a remote file. On loading, the transform matrix can be set identical to that of the specified file.

 load animation &lt;filename&gt; {fit &lt;file_ID&gt;}
Opens an animation file. URL can be used to open a remote file. On loading, the transform matrix can be set identical to that of the specified file.

 load ftp &lt;PDB_code&gt; {fit &lt;file_ID&gt;}
Retrieves a PDBML file from the PDBj FTP site and opens it. On loading, the transform matrix can be set identical to that of the specified file. 

== pause ==
 pause
Stops the execution of a script file until any key is pressed to restart. 

== pdbj_describe ==
 pdbj_describe &lt;file_id&gt; {&lt;name&gt;} 
Shows the document for the jV_command in PDBMLplus specified by file ID and name. When the name is not specified, all available names are listed.

== pdbj_execute ==
 pdbj_execute &lt;file_id&gt; &lt;name&gt; 
Executes the jV_command in PDBMLplus specified by file ID and name.

== quit ==
 quit
A synonym of the [[#exit|exit]] command.

== refresh ==
 refresh
Redraws all images. 

== reset ==
=== default ===
 reset
Restores the original viewing transformation of all images, the center of rotation, and the view point. 

=== cartoon ===
 reset cartoon
Restores the thickness of the cartoon representation. 

=== line_width ===
 reset line_width
Restores the width of lines in polygon images. 

=== pickradius ===
 reset pickradius
Restores the mouse-pickable region of each atom. 

=== point_size ===
 reset point_size
Restores the size of points in polygon images. 

=== polyline_width ===
 reset polyline_width
Restores the width of polylines in polygon images. 

=== transparency ===
 reset transparency
Restores the transparency of polygon images.

 reset point_transparency
Restores the transparency of points in polygon images.

 reset line_transparency
Restores the transparency of lines in polygon images.

 reset triangle_transparency
Restores the transparency of triangles in polygon images.

 reset quad_transparency
Restores the transparency of quads in polygon images.

 reset polyline_transparency
Restores the transparency of polylines in polygon images. 

== ribbons ==
 ribbons {on/true}
Turns on the ribbon surfaces for the selected residues. When a chain does not have enough atoms to draw the ribbon model, a backbone will be shown instead.

 ribbons off/false
Turns off the ribbon surfaces for the selected residues.

 ribbons &lt;half_width&gt;
Turns on the ribbon surfaces for the selected residues with the specified half width (angstrom or Rasmol unit). The maximum parameter value is 4.0.

== rotate ==
 rotate x/y/z &lt;angle&gt;
Rotates images about the specified axis by the specified angle in degrees. 

== save ==
 save {pdb} &lt;filename&gt;
Saves the currently selected set of atoms in a PDB format file.

 save script &lt;filename&gt;
Creates a script file that reproduces the currently displayed image.

 save png &lt;filename&gt;
Creates a PNG image file of the currently displayed image.

 save jpeg &lt;filename&gt; {&lt;quality&gt;}
Creates a JPEG image file of the currently displayed image. The compression quality can be specified, 0 &lt; quality &lt;= 1, where 'quality = 1' means no compression. 

== script ==
 script &lt;filename&gt;
Opens and executes the specified script file. URL can be used to open a remote file. 

== select ==
 select
Selects all atoms. Whether hetero atoms and hydrogens are selected or not depends on the internal parameters, hetero and hydrogen, respectively.

 select all
Selects all atoms including hetero atoms and hydrogens.

 select none
Selects no atoms.

 select &lt;atom_expression&gt;
Selects a group of atoms specified by the [[Atom Expression|atom expression]].

== selectvertex ==
 selectvertex {all}
Selects all vertices.

 selectvertex none
Selects no vertices.

 selectvertex &lt;vertex_expression&gt;
Selects a group of vertices specified by the vertex expression. 

== set ==
=== ambient ===
 set ambient {&lt;value&gt;}
Sets the amount of ambient light. The value must be between 0 and 100. When the parameter is not specified, it is restored to the default value 33.

=== adjustview ===
 set adjustview on
The view point is automatically adjusted when a new file is loaded.

 set adjustview off
The view point is kept unchanged when a new file is loaded. 

=== background ===
 set background &lt;color&gt;
Changes the background color. The color may be given as RGB values [r,g,b], or predefined color names. 

=== bondmode ===
 set bondmode and
Specifies how to select an individual bonds. A bond is selected when both atoms connected by the bond are selected.

 set bondmode or
Specifies how to select an individual bonds. A bond is selected when either of the connected atoms is selected. 

=== cartoon ===
 set cartoon {&lt;value&gt;}
Specifies the thickness of the cartoon representation (angstrom or Rasmol unit). The maximum parameter value is 2.0. When the parameter is not specified, it is restored to the default value. 

=== cartoon_loop_tube ===
 set cartoon_loop_tube on
The loop region is drawn as tube in the cartoon representation.

 set cartoon_loop_tube off
The loop region is drawn as square pillar in the cartoon representation.

=== cartoon_round ===
 set cartoon_round on
Square pillar with round edge is drawn in the cartoon representation (except beta strands). 

 set cartoon_round off
Square pillar is drawn in the cartoon representation.

=== center ===
 set center &lt;atom_expression&gt;
Sets the default center of the selected files to the center of the specified atoms.

 set center [x, y, z]
Sets the default center of the selected files to the specified coordinates. 

=== diffuse1 ===
 set diffuse1 {&lt;value&gt;}
Sets the amount of the first diffuse light. The value must be between 0 and 100. When the parameter is not specified, it is restored to the default value 50.

=== diffuse1_direction ===
 set diffuse1_direction {[x, y, z]}
Sets the direction of the first diffuse light. When the parameter is not specified, it is restored to the default value [-1, -1, -1].

=== diffuse2 ===
 set diffuse2 {&lt;value&gt;}
Sets the amount of the second diffuse light. The value must be between 0 and 100. When the parameter is not specified, it is restored to the default value 50.

=== diffuse2_direction ===
 set diffuse2_direction {[x, y, z]}
Sets the direction of the second diffuse light. When the parameter is not specified, it is restored to the default value [-1, -1, -1].

=== drawlevel ===
 set drawlevel &lt;value&gt;
Specifies precision of the rendering of spheres and cylinders. The value may be given as an integer (minimum 5) that stands for the number of straight line segments to represent an arc of 180 degrees. 

=== efsite_url ===
 set efsite_url &lt;URL&gt;
Sets the URL for eF-site.

=== ext_site_url ===
 set ext_site_url &lt;prefix&gt; &lt;URL&gt;
Sets the URL for an external database site.

=== hbonds ===
 set hbonds backbone
Hydrogen bonds are displayed between backbones.

 set hbonds sidechain
Hydrogen bonds are displayed between sidechains. 

=== hetero ===
 set hetero on
Sets the default behavior of the select command such that hetero atoms are selected.

 set hetero off
Sets the default behavior of the select command such that hetero atoms are not selected. 

=== hydrogen ===
 set hydrogen on
Sets the default behavior of the select command such that hydrogens are selected.

 set hydrogen off
Sets the default behavior of the select command such that hydrogens are not selected. 

=== imagesize ===
 set imagesize &lt;width&gt; &lt;height&gt;
Sets the size of the 3D-rendering panel in pixels. The size will be set within the screen size with the width being an even integer. 

=== line_width ===
 set line_width &lt;value&gt;
Sets the width of lines in polygon images. The &lt;value&gt; should be larger than 0. 

=== loadcenter ===
 set loadcenter on
When a file is opened, sets the default center of that file to the center of all files that have already opened.

 set loadcenter off
When a file is opened, sets the default center of that file according to its own coordiantes. 

=== pdbml_noatom_url ===
 set pdbml_noatom_url &lt;URL&gt;
Sets the URL for PDBML noatom files.

=== pdbml_extatom_url ===
 set pdbml_extatom_url &lt;URL&gt;
Sets the URL for PDBML extatom files.

=== pdbml_plus_url ===
 set pdbml_plus_url &lt;URL&gt;
Sets the URL for PDBMLplus files.

=== picking ===
 set picking off
Turns off the mouse picking.

 set picking ident
Sets the mouse picking behavior to show atom identification.

 set picking coord
Sets the mouse picking behavior to show atom coordinates with identification.

 set picking distance
Sets the mouse picking behavior to show the distance between atoms successively picked.

 set picking center
Sets the mouse picking behavior to specify the center of rotation and center of the screen.

 set picking select
Sets the mouse picking behavior to select the file that contains the atom picked. 

=== pickradius ===
 set pickradius &lt;value&gt;
Sets the mouse-pickable region of each atom to be the sphere centered to each atom with the specified radius (angstrom or Rasmol unit). 

=== point_size ===
 set point_size &lt;value&gt;
Sets the size of points in polygon images. The &lt;value&gt; should be larger than 0. 

=== polyline_width ===
 set polyline_width &lt;value&gt;
Sets the width of polylines in polygon images. The &lt;value&gt; should be larger than 0. 

=== projection ===
 set projection perspective
Sets the projection mode for a perspective projection.

 set projection parallel {&lt;size&gt;}
Sets the projection mode for a parallel projection. The size of image (fit to the height of the screen) can be specified (angstrom or Rasmol unit). 

=== ribbonback ===
 set ribbonback &lt;color&gt;
Sets the color of the back of ribbon models. The color may be given as RGB values [r,g,b] or predefined color names.

 set ribbonback none
Resets the color of the back of ribbon models.

=== specular ===
 set specular on/true
Enables the display of specular highlights on solid objects.

 set specular off/false
Disables the display of specular highlights on solid objects.

 set specular &lt;value&gt;
Enables the display of specular highlights on solid objects. The value between 0 and 100 specifies the specular color in gray scale with 0 and 100 being black and white, respectively. The default value is 50.0. 

=== specpower ===
 set specpower &lt;value&gt;
Sets the shininess of solid objects. The value between 0 and 100 specifies a material reflection coefficient with 0 being diffuse surfaces and 100 being shiny surfaces. 

=== ssbonds ===
 set ssbonds backbone
Disulfide bonds are displayed between backbones.

 set ssbonds sidechain
Disulfide bonds are displayed between sidechains. 

=== stereo ===
 set stereo
A synonym of the [[#stereo_2|stereo]] command.

=== transparency ===
 set transparency &lt;value&gt;
Sets the transparency of polygon images.

 set point_transparency &lt;value&gt;
Sets the transparency of points in polygon images.

 set line_transparency &lt;value&gt;
Sets the transparency of lines in polygon images.

 set triangle_transparency &lt;value&gt;
Sets the transparency of triangles in polygon images.

 set quad_transparency &lt;value&gt;
Sets the transparency of quads in polygon images.

 set polyline_transparency &lt;value&gt;
Sets the transparency of polylines in polygon images. 

=== viewpoint ===
 set viewpoint {x, y, z}
Sets the viewpoint to the specified coordinates. 

== show ==
 show godata
Displays gene ontology data of molecules.

 show imagesize
Displays the size of the 3D-rendering panel.

 show information
Displays a detail discription of molecules.

 show site {&lt;prefix&gt;:&lt;db&gt;:&lt;category&gt;}
Displays site information in an external database.

 show transform
Displays the transform matrix of molecules.

 show viewpoint
Displays the current viewpoint.

 show pdbj
Displays keywords available in PDBj expression.

== slab ==
 slab {on/true}
Enables the z-clipping plane of molecules and polygons.

 slab off/false
Disables the z-clipping plane of molecules and polygons.

 slab &lt;ratio&gt;
Sets the position of the z-clipping plane of molecules and polygons. The parameter may be given as a number from 0 to 100. The values 0 and 100 represent that image as a whole is completely invisible and visible, respectively.

 slab -v &lt;value&gt;
Sets the position of the z-clipping plane of molecules and polygons by specifying the z coordinate value. 

== spacefill ==
 spacefill {on/true}
Turns on the ball image of the selected atoms.

 spacefill off/false
Turns off the ball image of the selected atoms.

 spacefill &lt;radius&gt;
Turns on the ball image of the selected atoms with the specified radius (angstrom or Rasmol unit). The maximum parameter value is 3.0.

 spacefill temperature
Turns on the ball image of the selected atoms using the temperature factor as radius. 

== ssbonds ==
 ssbonds {on/true}
Turns on the selected disulfide bonds.

 ssbonds off/false
Turns off the selected disulfide bonds.

 ssbonds &lt;radius&gt;
Turns on the selected disulfide bonds with the specified raidus (angstrom or Rasmol unit). The maximum parameter value is 2.0. 

== stereo ==
 stereo {on/true}
Enables stereo display. This command without arguments cycles three state; 'stereo off', 'stereo on' in cross-eyed mode and 'stereo on' in parallel-eyed mode.

 stereo off/false
Disables stereo display.

 stereo &lt;angle&gt;
Enables stereo display with the specified separation angle. Positive and negative values represent cross-eyed and parallel-eyed viewing, respectively.


== structure ==
 structure
Estimates the secondary structure using Kabsch and Sander's DSSP algorithm. 

== trace ==
 trace {on/true}
Turns on a tube representation for the selected residues. When a chain does not have enough atoms to draw the tube model, a backbone will be shown instead.

 trace off/false
Turns off a tube representation for the selected residues.

 trace &lt;radius&gt;
Turns on a tube representation for the selected residues with the specified radius (angstrom or Rasmol unit). The maximum parameter value is 2.0.

== translate ==
 translate x/y/z &lt;value&gt;
Moves images along the specified axis by the specified amount (angstrom). 

== wireframe ==
 wireframe {on/true}
Turns on the selected bonds.

 wireframe off/false
Turns off the selected bonds.

 wireframe &lt;radius&gt;
Turns on the selected bonds with the specified raidus (angstrom or Rasmol unit). The maximum parameter value is 2.0. 

== write ==
 write
A synonym of the [[#save|save]] command.

== zap ==
 zap {&lt;file_IDs&gt;}
Closes the specified files. More than one file IDs can be specified by putting commas as the delimiter. When the paraneter is absent, all files are closed. 

== zoom ==
 zoom {&lt;value&gt;}
Sets the magnification of the image as a whole. The value stands for the magnification as a percentage of the current scale. The minimum parameter value is 10.0.</text>
    <sha1>808890423f2efe6360321bff7ca4b4ebc1b5e1eb</sha1>
  </revision>
  <revision>
    <id>423</id>
    <parentid>422</parentid>
    <timestamp>2010-12-03T04:46:06Z</timestamp>
    <contributor>
      <username>IMSsato</username>
      <id>4</id>
    </contributor>
    <comment>/* selectvertex */</comment>
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    <format>text/x-wiki</format>
    <text bytes="22182" xml:space="preserve"> {| style="float:right"
  |__TOC__
  |}
Command usage of jV follows that of [http://www.rasmol.org/ Rasmol] with some modifications. In the following part, command arguments that can take an arbitrary value are denoted as &lt;value&gt; for example, arguments restricted to several possible values are listed with / as a delimiter, and arguments that can be omitted are put in brackets {}. Commands, [[#exit|exit]], [[#load|load]], [[#quit|quit]], [[#save|save]], [[#script|script]], and [[#write|write]], are not available in applet circumstance.

== anim ==
 anim forward {&lt;value&gt;}
Starts animation forward. If the &lt;value&gt; is given, just move frames forward by the specified amount.

 anim backward {&lt;value&gt;}
Starts animation backward. If the &lt;value&gt; is given, just move frames backward by the specified amount.

 anim stop
Stops animation.

== animframe ==
 animframe &lt;frame&gt; {&lt;file_ID&gt;}
Sets the frame of all animation files for the specified value. When &lt;file_ID&gt; is given, only the specified file is processed.

== animmode ==
 animmode once
Sets the behavior of animation for 'once'. When the frame reaches the last one, animation is stopped.

 animmode loop
Sets the behavior of animation for 'loop'. When the frame reaches the last one, animation is reset to the first frame and continues playing.

 animmode swing
Sets the behavior of animation for 'swing'. When the frame reaches the last one, the direction of animation is reversed.

== animrange ==
 animrange &lt;init_frame&gt;-&lt;term_frame&gt; {&lt;file_IDs&gt;}
Sets the range of all animation files. When is given, only the specified file is processed.

== animselect ==
 animselect {-a/-r} &lt;file_IDs&gt;
Selects the specified files and makes the others not selected. More than one file IDs can be specified by putting commas as the delimiter. When the option -a or -r is specified, only the selection status of the specified files are modified, selected or not selected, respectively, and the others remain unchanged.

== animspeed ==
 animspeed &lt;speed&gt;
Sets the animation speed. The argument should be an integer value from 1 to 20.

== animstep ==
 animstep &lt;step&gt; {&lt;file_ID&gt;}
Sets the step of all animation files for the specified value. When &lt;file_ID&gt; is given, only the specified file is processed.

== backbone ==
 backbone {on/true}
Turns on the selected backbone bonds.

 backbone off/false
Turns off the selected backbone bonds.

 backbone &lt;radius&gt;
Turns on the selected backbone bonds with the specified raidus (angstrom or Rasmol unit). The maximum parameter value is 2.0.

== background ==
 background &lt;color&gt;
Changes the background color. The color may be given as RGB values [r,g,b], or predefined color names.

== ball_and_stick ==
 ball_and_stick {on/true}
Turns on the ball and stick image of the selected atoms with ball radius 0.5 and stick radius 0.2 in angstrom.

 ball_and_stick off/false
Turns off the ball and stick image of the selected atoms.

 ball_and_stick &lt;ball_radius&gt; &lt;stick_radius&gt;
Turns on the ball and stick image of the selected atoms with the specified ball radius and stick radius (angstrom or Rasmol unit). The maximum parameter value is 3.0 and 2.0, respectively.

== cartoon ==
 cartoon {on/true}
Turns on the thick ribbons for the selected residues. When a chain does not have enough atoms to draw the ribbon model, a backbone will be shown instead.

 cartoon off/false
Turns off the thick ribbons for the selected residues.

 cartoon &lt;half_width&gt;
Turns on the thick ribbons for the selected residues with the specified half width (angstrom or Rasmol unit). The maximum parameter value is 4.0.

== center ==
 center {-r/-s} {&lt;atom_expression&gt;}
Sets the center of rotation and the center of the screen to the center of a group of atoms specified by the [[Atom Expression|atom expression]]. When the option -r or -s is specified, only the center of rotation or the center of the screen is modified, respectively.

 center {-r} [x, y, z]
Moves the center of rotation and the center of the screen from the current position by the specified amount. When the option -r is specified, only the center of rotation is modified.

 center {-r} {x, y, z}
Sets the center of rotation and the center of the screen to the specified coordinates. When the option -r is specified, only the center of rotation is modified.

 center -s [x, y]
Moves the center of the screen from the current position by the specified amount.

 center -s {x, y}
Sets the center of the screen to the specified coordinates.

== color ==
 color {atoms} &lt;color&gt;
Sets the color of the selected atoms. The color may be given as RGB values [r,g,b], predefined color names, or predefined color schemes; amino, chain, charge, cpk, group, shapely, structure, and temperature.

 color bonds/backbone/ribbons/hbonds/ssbonds &lt;color&gt;
Sets the color of the specified object. The color may be given as RGB values [r,g,b] or predefined color names. For hydrogen bonds, color scheme 'type' can be specified.

 color bonds/backbone/ribbons/hbonds/ssbonds none
Resets the color of the specified object.

== colorvertex ==
 colorvertex &lt;color&gt;
Sets the color of the selected vertices. The color may be given as RGB values [r,g,b] or predefined color names.

 colorvertex none
Resets the color of the selected vertices.

== cpk ==
 cpk
A synonym of the [[#spacefill|spacefill]] command.

== define ==
 define &lt;name&gt; &lt;atom_expression&gt;
Associates an arbitrary set of atoms specified by the [[Atom Expression|atom expression]] with a unique name.

== display ==
 display all
Displays the image of all files.

 display none
Turns off the image of all files.

 display {-a/-r} &lt;file_IDs&gt;
Displays the image of the specified files and turns off the others. More than one file IDs can be specified by putting commas as the delimiter. When the option -a or -r is specified, turns the image of the specified files on or off, respectively, and the others remain unchanged.

== displayatom ==
 displayatom {on/true}
Displays the selected atoms.

 displayatom off/false
Turns off the selected atoms.

== displayvertex ==
 displayvertex {on/true}
Displays the selected vertices.

 displayvertex off/false
Turns off the selected vertices.

== echo ==
 echo &lt;string&gt;
Echoes the specified message back to the message area.

== exit ==
 exit
Terminates the application.

== fit ==
 fit &lt;file1_ID&gt; &lt;file2_ID&gt;
Sets the transform matrix of file1 identical to that of file2. 

== fselect ==
 fselect all
Selects all files.

 fselect none
Selects no files.

 fselect {-a/-r} &lt;file_IDs&gt;
Selects the specified files and makes the others not selected. More than one file IDs can be specified by putting commas as the delimiter. When the option -a or -r is specified, only the selection status of the specified files are modified, selected or not selected, respectively, and the others remain unchanged.

== hbonds ==
 hbonds {on/true}
Turns on the selected hydrogen bonds.

 hbonds off/false
Turns off the selected hydrogen bonds.

 hbonds &lt;radius&gt;
Turns on the selected hydrogen bonds with the specified raidus (angstrom or Rasmol unit). The maximum parameter value is 2.0. 

== load ==
 load {pdbml} &lt;filename&gt; {fit &lt;file_ID&gt;}
Opens a PDBML file. URL can be used to open a remote file. On loading, the transform matrix can be set identical to that of the specified file.

 load pdb &lt;filename&gt; {fit &lt;file_ID&gt;}
Opens a PDB file. URL can be used to open a remote file. On loading, the transform matrix can be set identical to that of the specified file.

 load polygon &lt;filename&gt; {fit &lt;file_ID&gt;}
Opens a polygon file. URL can be used to open a remote file. On loading, the transform matrix can be set identical to that of the specified file.

 load animation &lt;filename&gt; {fit &lt;file_ID&gt;}
Opens an animation file. URL can be used to open a remote file. On loading, the transform matrix can be set identical to that of the specified file.

 load ftp &lt;PDB_code&gt; {fit &lt;file_ID&gt;}
Retrieves a PDBML file from the PDBj FTP site and opens it. On loading, the transform matrix can be set identical to that of the specified file. 

== pause ==
 pause
Stops the execution of a script file until any key is pressed to restart. 

== pdbj_describe ==
 pdbj_describe &lt;file_id&gt; {&lt;name&gt;} 
Shows the document for the jV_command in PDBMLplus specified by file ID and name. When the name is not specified, all available names are listed.

== pdbj_execute ==
 pdbj_execute &lt;file_id&gt; &lt;name&gt; 
Executes the jV_command in PDBMLplus specified by file ID and name.

== quit ==
 quit
A synonym of the [[#exit|exit]] command.

== refresh ==
 refresh
Redraws all images. 

== reset ==
=== default ===
 reset
Restores the original viewing transformation of all images, the center of rotation, and the view point. 

=== cartoon ===
 reset cartoon
Restores the thickness of the cartoon representation. 

=== line_width ===
 reset line_width
Restores the width of lines in polygon images. 

=== pickradius ===
 reset pickradius
Restores the mouse-pickable region of each atom. 

=== point_size ===
 reset point_size
Restores the size of points in polygon images. 

=== polyline_width ===
 reset polyline_width
Restores the width of polylines in polygon images. 

=== transparency ===
 reset transparency
Restores the transparency of polygon images.

 reset point_transparency
Restores the transparency of points in polygon images.

 reset line_transparency
Restores the transparency of lines in polygon images.

 reset triangle_transparency
Restores the transparency of triangles in polygon images.

 reset quad_transparency
Restores the transparency of quads in polygon images.

 reset polyline_transparency
Restores the transparency of polylines in polygon images. 

== ribbons ==
 ribbons {on/true}
Turns on the ribbon surfaces for the selected residues. When a chain does not have enough atoms to draw the ribbon model, a backbone will be shown instead.

 ribbons off/false
Turns off the ribbon surfaces for the selected residues.

 ribbons &lt;half_width&gt;
Turns on the ribbon surfaces for the selected residues with the specified half width (angstrom or Rasmol unit). The maximum parameter value is 4.0.

== rotate ==
 rotate x/y/z &lt;angle&gt;
Rotates images about the specified axis by the specified angle in degrees. 

== save ==
 save {pdb} &lt;filename&gt;
Saves the currently selected set of atoms in a PDB format file.

 save script &lt;filename&gt;
Creates a script file that reproduces the currently displayed image.

 save png &lt;filename&gt;
Creates a PNG image file of the currently displayed image.

 save jpeg &lt;filename&gt; {&lt;quality&gt;}
Creates a JPEG image file of the currently displayed image. The compression quality can be specified, 0 &lt; quality &lt;= 1, where 'quality = 1' means no compression. 

== script ==
 script &lt;filename&gt;
Opens and executes the specified script file. URL can be used to open a remote file. 

== select ==
 select
Selects all atoms. Whether hetero atoms and hydrogens are selected or not depends on the internal parameters, hetero and hydrogen, respectively.

 select all
Selects all atoms including hetero atoms and hydrogens.

 select none
Selects no atoms.

 select &lt;atom_expression&gt;
Selects a group of atoms specified by the [[Atom Expression|atom expression]].

== selectvertex ==
 selectvertex {all}
Selects all vertices.

 selectvertex none
Selects no vertices.

 selectvertex &lt;vertex_expression&gt;
Selects a group of vertices specified by the [[Vertex Expression|vertex expression]].

== set ==
=== ambient ===
 set ambient {&lt;value&gt;}
Sets the amount of ambient light. The value must be between 0 and 100. When the parameter is not specified, it is restored to the default value 33.

=== adjustview ===
 set adjustview on
The view point is automatically adjusted when a new file is loaded.

 set adjustview off
The view point is kept unchanged when a new file is loaded. 

=== background ===
 set background &lt;color&gt;
Changes the background color. The color may be given as RGB values [r,g,b], or predefined color names. 

=== bondmode ===
 set bondmode and
Specifies how to select an individual bonds. A bond is selected when both atoms connected by the bond are selected.

 set bondmode or
Specifies how to select an individual bonds. A bond is selected when either of the connected atoms is selected. 

=== cartoon ===
 set cartoon {&lt;value&gt;}
Specifies the thickness of the cartoon representation (angstrom or Rasmol unit). The maximum parameter value is 2.0. When the parameter is not specified, it is restored to the default value. 

=== cartoon_loop_tube ===
 set cartoon_loop_tube on
The loop region is drawn as tube in the cartoon representation.

 set cartoon_loop_tube off
The loop region is drawn as square pillar in the cartoon representation.

=== cartoon_round ===
 set cartoon_round on
Square pillar with round edge is drawn in the cartoon representation (except beta strands). 

 set cartoon_round off
Square pillar is drawn in the cartoon representation.

=== center ===
 set center &lt;atom_expression&gt;
Sets the default center of the selected files to the center of the specified atoms.

 set center [x, y, z]
Sets the default center of the selected files to the specified coordinates. 

=== diffuse1 ===
 set diffuse1 {&lt;value&gt;}
Sets the amount of the first diffuse light. The value must be between 0 and 100. When the parameter is not specified, it is restored to the default value 50.

=== diffuse1_direction ===
 set diffuse1_direction {[x, y, z]}
Sets the direction of the first diffuse light. When the parameter is not specified, it is restored to the default value [-1, -1, -1].

=== diffuse2 ===
 set diffuse2 {&lt;value&gt;}
Sets the amount of the second diffuse light. The value must be between 0 and 100. When the parameter is not specified, it is restored to the default value 50.

=== diffuse2_direction ===
 set diffuse2_direction {[x, y, z]}
Sets the direction of the second diffuse light. When the parameter is not specified, it is restored to the default value [-1, -1, -1].

=== drawlevel ===
 set drawlevel &lt;value&gt;
Specifies precision of the rendering of spheres and cylinders. The value may be given as an integer (minimum 5) that stands for the number of straight line segments to represent an arc of 180 degrees. 

=== efsite_url ===
 set efsite_url &lt;URL&gt;
Sets the URL for eF-site.

=== ext_site_url ===
 set ext_site_url &lt;prefix&gt; &lt;URL&gt;
Sets the URL for an external database site.

=== hbonds ===
 set hbonds backbone
Hydrogen bonds are displayed between backbones.

 set hbonds sidechain
Hydrogen bonds are displayed between sidechains. 

=== hetero ===
 set hetero on
Sets the default behavior of the select command such that hetero atoms are selected.

 set hetero off
Sets the default behavior of the select command such that hetero atoms are not selected. 

=== hydrogen ===
 set hydrogen on
Sets the default behavior of the select command such that hydrogens are selected.

 set hydrogen off
Sets the default behavior of the select command such that hydrogens are not selected. 

=== imagesize ===
 set imagesize &lt;width&gt; &lt;height&gt;
Sets the size of the 3D-rendering panel in pixels. The size will be set within the screen size with the width being an even integer. 

=== line_width ===
 set line_width &lt;value&gt;
Sets the width of lines in polygon images. The &lt;value&gt; should be larger than 0. 

=== loadcenter ===
 set loadcenter on
When a file is opened, sets the default center of that file to the center of all files that have already opened.

 set loadcenter off
When a file is opened, sets the default center of that file according to its own coordiantes. 

=== pdbml_noatom_url ===
 set pdbml_noatom_url &lt;URL&gt;
Sets the URL for PDBML noatom files.

=== pdbml_extatom_url ===
 set pdbml_extatom_url &lt;URL&gt;
Sets the URL for PDBML extatom files.

=== pdbml_plus_url ===
 set pdbml_plus_url &lt;URL&gt;
Sets the URL for PDBMLplus files.

=== picking ===
 set picking off
Turns off the mouse picking.

 set picking ident
Sets the mouse picking behavior to show atom identification.

 set picking coord
Sets the mouse picking behavior to show atom coordinates with identification.

 set picking distance
Sets the mouse picking behavior to show the distance between atoms successively picked.

 set picking center
Sets the mouse picking behavior to specify the center of rotation and center of the screen.

 set picking select
Sets the mouse picking behavior to select the file that contains the atom picked. 

=== pickradius ===
 set pickradius &lt;value&gt;
Sets the mouse-pickable region of each atom to be the sphere centered to each atom with the specified radius (angstrom or Rasmol unit). 

=== point_size ===
 set point_size &lt;value&gt;
Sets the size of points in polygon images. The &lt;value&gt; should be larger than 0. 

=== polyline_width ===
 set polyline_width &lt;value&gt;
Sets the width of polylines in polygon images. The &lt;value&gt; should be larger than 0. 

=== projection ===
 set projection perspective
Sets the projection mode for a perspective projection.

 set projection parallel {&lt;size&gt;}
Sets the projection mode for a parallel projection. The size of image (fit to the height of the screen) can be specified (angstrom or Rasmol unit). 

=== ribbonback ===
 set ribbonback &lt;color&gt;
Sets the color of the back of ribbon models. The color may be given as RGB values [r,g,b] or predefined color names.

 set ribbonback none
Resets the color of the back of ribbon models.

=== specular ===
 set specular on/true
Enables the display of specular highlights on solid objects.

 set specular off/false
Disables the display of specular highlights on solid objects.

 set specular &lt;value&gt;
Enables the display of specular highlights on solid objects. The value between 0 and 100 specifies the specular color in gray scale with 0 and 100 being black and white, respectively. The default value is 50.0. 

=== specpower ===
 set specpower &lt;value&gt;
Sets the shininess of solid objects. The value between 0 and 100 specifies a material reflection coefficient with 0 being diffuse surfaces and 100 being shiny surfaces. 

=== ssbonds ===
 set ssbonds backbone
Disulfide bonds are displayed between backbones.

 set ssbonds sidechain
Disulfide bonds are displayed between sidechains. 

=== stereo ===
 set stereo
A synonym of the [[#stereo_2|stereo]] command.

=== transparency ===
 set transparency &lt;value&gt;
Sets the transparency of polygon images.

 set point_transparency &lt;value&gt;
Sets the transparency of points in polygon images.

 set line_transparency &lt;value&gt;
Sets the transparency of lines in polygon images.

 set triangle_transparency &lt;value&gt;
Sets the transparency of triangles in polygon images.

 set quad_transparency &lt;value&gt;
Sets the transparency of quads in polygon images.

 set polyline_transparency &lt;value&gt;
Sets the transparency of polylines in polygon images. 

=== viewpoint ===
 set viewpoint {x, y, z}
Sets the viewpoint to the specified coordinates. 

== show ==
 show godata
Displays gene ontology data of molecules.

 show imagesize
Displays the size of the 3D-rendering panel.

 show information
Displays a detail discription of molecules.

 show site {&lt;prefix&gt;:&lt;db&gt;:&lt;category&gt;}
Displays site information in an external database.

 show transform
Displays the transform matrix of molecules.

 show viewpoint
Displays the current viewpoint.

 show pdbj
Displays keywords available in PDBj expression.

== slab ==
 slab {on/true}
Enables the z-clipping plane of molecules and polygons.

 slab off/false
Disables the z-clipping plane of molecules and polygons.

 slab &lt;ratio&gt;
Sets the position of the z-clipping plane of molecules and polygons. The parameter may be given as a number from 0 to 100. The values 0 and 100 represent that image as a whole is completely invisible and visible, respectively.

 slab -v &lt;value&gt;
Sets the position of the z-clipping plane of molecules and polygons by specifying the z coordinate value. 

== spacefill ==
 spacefill {on/true}
Turns on the ball image of the selected atoms.

 spacefill off/false
Turns off the ball image of the selected atoms.

 spacefill &lt;radius&gt;
Turns on the ball image of the selected atoms with the specified radius (angstrom or Rasmol unit). The maximum parameter value is 3.0.

 spacefill temperature
Turns on the ball image of the selected atoms using the temperature factor as radius. 

== ssbonds ==
 ssbonds {on/true}
Turns on the selected disulfide bonds.

 ssbonds off/false
Turns off the selected disulfide bonds.

 ssbonds &lt;radius&gt;
Turns on the selected disulfide bonds with the specified raidus (angstrom or Rasmol unit). The maximum parameter value is 2.0. 

== stereo ==
 stereo {on/true}
Enables stereo display. This command without arguments cycles three state; 'stereo off', 'stereo on' in cross-eyed mode and 'stereo on' in parallel-eyed mode.

 stereo off/false
Disables stereo display.

 stereo &lt;angle&gt;
Enables stereo display with the specified separation angle. Positive and negative values represent cross-eyed and parallel-eyed viewing, respectively.


== structure ==
 structure
Estimates the secondary structure using Kabsch and Sander's DSSP algorithm. 

== trace ==
 trace {on/true}
Turns on a tube representation for the selected residues. When a chain does not have enough atoms to draw the tube model, a backbone will be shown instead.

 trace off/false
Turns off a tube representation for the selected residues.

 trace &lt;radius&gt;
Turns on a tube representation for the selected residues with the specified radius (angstrom or Rasmol unit). The maximum parameter value is 2.0.

== translate ==
 translate x/y/z &lt;value&gt;
Moves images along the specified axis by the specified amount (angstrom). 

== wireframe ==
 wireframe {on/true}
Turns on the selected bonds.

 wireframe off/false
Turns off the selected bonds.

 wireframe &lt;radius&gt;
Turns on the selected bonds with the specified raidus (angstrom or Rasmol unit). The maximum parameter value is 2.0. 

== write ==
 write
A synonym of the [[#save|save]] command.

== zap ==
 zap {&lt;file_IDs&gt;}
Closes the specified files. More than one file IDs can be specified by putting commas as the delimiter. When the paraneter is absent, all files are closed. 

== zoom ==
 zoom {&lt;value&gt;}
Sets the magnification of the image as a whole. The value stands for the magnification as a percentage of the current scale. The minimum parameter value is 10.0.</text>
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Command usage of jV follows that of [http://www.rasmol.org/ Rasmol] with some modifications. In the following part, command arguments that can take an arbitrary value are denoted as &lt;value&gt; for example, arguments restricted to several possible values are listed with / as a delimiter, and arguments that can be omitted are put in brackets {}. Commands, [[#exit|exit]], [[#load|load]], [[#quit|quit]], [[#save|save]], [[#script|script]], and [[#write|write]], are not available in applet circumstance.

== anim ==
 anim forward {&lt;value&gt;}
Starts animation forward. If the &lt;value&gt; is given, just move frames forward by the specified amount.

 anim backward {&lt;value&gt;}
Starts animation backward. If the &lt;value&gt; is given, just move frames backward by the specified amount.

 anim stop
Stops animation.

== animframe ==
 animframe &lt;frame&gt; {&lt;file_ID&gt;}
Sets the frame of all animation files for the specified value. When &lt;file_ID&gt; is given, only the specified file is processed.

== animmode ==
 animmode once
Sets the behavior of animation for 'once'. When the frame reaches the last one, animation is stopped.

 animmode loop
Sets the behavior of animation for 'loop'. When the frame reaches the last one, animation is reset to the first frame and continues playing.

 animmode swing
Sets the behavior of animation for 'swing'. When the frame reaches the last one, the direction of animation is reversed.

== animrange ==
 animrange &lt;init_frame&gt;-&lt;term_frame&gt; {&lt;file_IDs&gt;}
Sets the range of all animation files. When is given, only the specified file is processed.

== animselect ==
 animselect {-a/-r} &lt;file_IDs&gt;
Selects the specified files and makes the others not selected. More than one file IDs can be specified by putting commas as the delimiter. When the option -a or -r is specified, only the selection status of the specified files are modified, selected or not selected, respectively, and the others remain unchanged.

== animspeed ==
 animspeed &lt;speed&gt;
Sets the animation speed. The argument should be an integer value from 1 to 20.

== animstep ==
 animstep &lt;step&gt; {&lt;file_ID&gt;}
Sets the step of all animation files for the specified value. When &lt;file_ID&gt; is given, only the specified file is processed.

== backbone ==
 backbone {on/true}
Turns on the selected backbone bonds.

 backbone off/false
Turns off the selected backbone bonds.

 backbone &lt;radius&gt;
Turns on the selected backbone bonds with the specified raidus (angstrom or Rasmol unit). The maximum parameter value is 2.0.

== background ==
 background &lt;color&gt;
Changes the background color. The color may be given as RGB values [r,g,b], or predefined color names.

== ball_and_stick ==
 ball_and_stick {on/true}
Turns on the ball and stick image of the selected atoms with ball radius 0.5 and stick radius 0.2 in angstrom.

 ball_and_stick off/false
Turns off the ball and stick image of the selected atoms.

 ball_and_stick &lt;ball_radius&gt; &lt;stick_radius&gt;
Turns on the ball and stick image of the selected atoms with the specified ball radius and stick radius (angstrom or Rasmol unit). The maximum parameter value is 3.0 and 2.0, respectively.

== cartoon ==
 cartoon {on/true}
Turns on the thick ribbons for the selected residues. When a chain does not have enough atoms to draw the ribbon model, a backbone will be shown instead.

 cartoon off/false
Turns off the thick ribbons for the selected residues.

 cartoon &lt;half_width&gt;
Turns on the thick ribbons for the selected residues with the specified half width (angstrom or Rasmol unit). The maximum parameter value is 4.0.

== center ==
 center {-r/-s} {&lt;atom_expression&gt;}
Sets the center of rotation and the center of the screen to the center of a group of atoms specified by the [[Atom Expression|atom expression]]. When the option -r or -s is specified, only the center of rotation or the center of the screen is modified, respectively.

 center {-r} [x, y, z]
Moves the center of rotation and the center of the screen from the current position by the specified amount. When the option -r is specified, only the center of rotation is modified.

 center {-r} {x, y, z}
Sets the center of rotation and the center of the screen to the specified coordinates. When the option -r is specified, only the center of rotation is modified.

 center -s [x, y]
Moves the center of the screen from the current position by the specified amount.

 center -s {x, y}
Sets the center of the screen to the specified coordinates.

== color ==
 color {atoms} &lt;color&gt;
Sets the color of the selected atoms. The color may be given as RGB values [r,g,b], predefined color names, or predefined color schemes; amino, chain, charge, cpk, group, shapely, structure, and temperature.

 color bonds/backbone/ribbons/hbonds/ssbonds &lt;color&gt;
Sets the color of the specified object. The color may be given as RGB values [r,g,b] or predefined color names. For hydrogen bonds, color scheme 'type' can be specified.

 color bonds/backbone/ribbons/hbonds/ssbonds none
Resets the color of the specified object.

== colorvertex ==
 colorvertex &lt;color&gt;
Sets the color of the selected vertices. The color may be given as RGB values [r,g,b] or predefined color names.

 colorvertex none
Resets the color of the selected vertices.

== cpk ==
 cpk
A synonym of the [[#spacefill|spacefill]] command.

== define ==
 define &lt;name&gt; &lt;atom_expression&gt;
Associates an arbitrary set of atoms specified by the [[Atom Expression|atom expression]] with a unique name.

== display ==
 display all
Displays the image of all files.

 display none
Turns off the image of all files.

 display {-a/-r} &lt;file_IDs&gt;
Displays the image of the specified files and turns off the others. More than one file IDs can be specified by putting commas as the delimiter. When the option -a or -r is specified, turns the image of the specified files on or off, respectively, and the others remain unchanged.

== displayatom ==
 displayatom {on/true}
Displays the selected atoms.

 displayatom off/false
Turns off the selected atoms.

== displayvertex ==
 displayvertex {on/true}
Displays the selected vertices.

 displayvertex off/false
Turns off the selected vertices.

== echo ==
 echo &lt;string&gt;
Echoes the specified message back to the message area.

== exit ==
 exit
Terminates the application.

== fit ==
 fit &lt;file1_ID&gt; &lt;file2_ID&gt;
Sets the transform matrix of file1 identical to that of file2. 

== fselect ==
 fselect all
Selects all files.

 fselect none
Selects no files.

 fselect {-a/-r} &lt;file_IDs&gt;
Selects the specified files and makes the others not selected. More than one file IDs can be specified by putting commas as the delimiter. When the option -a or -r is specified, only the selection status of the specified files are modified, selected or not selected, respectively, and the others remain unchanged.

== hbonds ==
 hbonds {on/true}
Turns on the selected hydrogen bonds.

 hbonds off/false
Turns off the selected hydrogen bonds.

 hbonds &lt;radius&gt;
Turns on the selected hydrogen bonds with the specified raidus (angstrom or Rasmol unit). The maximum parameter value is 2.0. 

== load ==
 load {pdbml} &lt;filename&gt; {fit &lt;file_ID&gt;}
Opens a PDBML file. URL can be used to open a remote file. On loading, the transform matrix can be set identical to that of the specified file.

 load pdb &lt;filename&gt; {fit &lt;file_ID&gt;}
Opens a PDB file. URL can be used to open a remote file. On loading, the transform matrix can be set identical to that of the specified file.

 load polygon &lt;filename&gt; {fit &lt;file_ID&gt;}
Opens a polygon file. URL can be used to open a remote file. On loading, the transform matrix can be set identical to that of the specified file.

 load animation &lt;filename&gt; {fit &lt;file_ID&gt;}
Opens an animation file. URL can be used to open a remote file. On loading, the transform matrix can be set identical to that of the specified file.

 load ftp &lt;PDB_code&gt; {fit &lt;file_ID&gt;}
Retrieves a PDBML file from the PDBj FTP site and opens it. On loading, the transform matrix can be set identical to that of the specified file. 

== pause ==
 pause
Stops the execution of a script file until any key is pressed to restart. 

== pdbj_describe ==
 pdbj_describe &lt;file_id&gt; {&lt;name&gt;} 
Shows the document for the jV_command in PDBMLplus specified by file ID and name. When the name is not specified, all available names are listed.

== pdbj_execute ==
 pdbj_execute &lt;file_id&gt; &lt;name&gt; 
Executes the jV_command in PDBMLplus specified by file ID and name.

== quit ==
 quit
A synonym of the [[#exit|exit]] command.

== refresh ==
 refresh
Redraws all images. 

== reset ==
=== default ===
 reset
Restores the original viewing transformation of all images, the center of rotation, and the view point. 

=== cartoon ===
 reset cartoon
Restores the thickness of the cartoon representation. 

=== line_width ===
 reset line_width
Restores the width of lines in polygon images. 

=== pickradius ===
 reset pickradius
Restores the mouse-pickable region of each atom. 

=== point_size ===
 reset point_size
Restores the size of points in polygon images. 

=== polyline_width ===
 reset polyline_width
Restores the width of polylines in polygon images. 

=== transparency ===
 reset transparency
Restores the transparency of polygon images.

 reset point_transparency
Restores the transparency of points in polygon images.

 reset line_transparency
Restores the transparency of lines in polygon images.

 reset triangle_transparency
Restores the transparency of triangles in polygon images.

 reset quad_transparency
Restores the transparency of quads in polygon images.

 reset polyline_transparency
Restores the transparency of polylines in polygon images. 

== ribbons ==
 ribbons {on/true}
Turns on the ribbon surfaces for the selected residues. When a chain does not have enough atoms to draw the ribbon model, a backbone will be shown instead.

 ribbons off/false
Turns off the ribbon surfaces for the selected residues.

 ribbons &lt;half_width&gt;
Turns on the ribbon surfaces for the selected residues with the specified half width (angstrom or Rasmol unit). The maximum parameter value is 4.0.

== rotate ==
 rotate x/y/z &lt;angle&gt;
Rotates images about the specified axis by the specified angle in degrees. 

== save ==
 save {pdb} &lt;filename&gt;
Saves the currently selected set of atoms in a PDB format file.

 save script &lt;filename&gt;
Creates a script file that reproduces the currently displayed image.

 save png &lt;filename&gt;
Creates a PNG image file of the currently displayed image.

 save jpeg &lt;filename&gt; {&lt;quality&gt;}
Creates a JPEG image file of the currently displayed image. The compression quality can be specified, 0 &lt; quality &lt;= 1, where 'quality = 1' means no compression. 

== script ==
 script &lt;filename&gt;
Opens and executes the specified script file. URL can be used to open a remote file. 

== select ==
 select
Selects all atoms. Whether hetero atoms and hydrogens are selected or not depends on the internal parameters, hetero and hydrogen, respectively.

 select all
Selects all atoms including hetero atoms and hydrogens.

 select none
Selects no atoms.

 select &lt;atom_expression&gt;
Selects a group of atoms specified by the [[Atom Expression|atom expression]].

== selectvertex ==
 selectvertex {all}
Selects all vertices.

 selectvertex none
Selects no vertices.

 selectvertex &lt;vertex_expression&gt;
Selects a group of vertices specified by the [[Vertex Expression|vertex expression]].

== set ==
=== ambient ===
 set ambient {&lt;value&gt;}
Sets the amount of ambient light. The value must be between 0 and 100. When the parameter is not specified, it is restored to the default value 33.

=== adjustview ===
 set adjustview on
The view point is automatically adjusted when a new file is loaded.

 set adjustview off
The view point is kept unchanged when a new file is loaded. 

=== background ===
 set background &lt;color&gt;
Changes the background color. The color may be given as RGB values [r,g,b], or predefined color names. 

=== bondmode ===
 set bondmode and
Specifies how to select an individual bonds. A bond is selected when both atoms connected by the bond are selected.

 set bondmode or
Specifies how to select an individual bonds. A bond is selected when either of the connected atoms is selected. 

=== cartoon ===
 set cartoon {&lt;value&gt;}
Specifies the thickness of the cartoon representation (angstrom or Rasmol unit). The maximum parameter value is 2.0. When the parameter is not specified, it is restored to the default value. 

=== cartoon_loop_tube ===
 set cartoon_loop_tube on
The loop region is drawn as tube in the cartoon representation.

 set cartoon_loop_tube off
The loop region is drawn as square pillar in the cartoon representation.

=== cartoon_round ===
 set cartoon_round on
Square pillar with round edge is drawn in the cartoon representation (except beta strands). 

 set cartoon_round off
Square pillar is drawn in the cartoon representation.

=== center ===
 set center &lt;atom_expression&gt;
Sets the default center of the selected files to the center of a group of atoms specified by the [[Atom Expression|atom expression]].

 set center [x, y, z]
Sets the default center of the selected files to the specified coordinates.

=== diffuse1 ===
 set diffuse1 {&lt;value&gt;}
Sets the amount of the first diffuse light. The value must be between 0 and 100. When the parameter is not specified, it is restored to the default value 50.

=== diffuse1_direction ===
 set diffuse1_direction {[x, y, z]}
Sets the direction of the first diffuse light. When the parameter is not specified, it is restored to the default value [-1, -1, -1].

=== diffuse2 ===
 set diffuse2 {&lt;value&gt;}
Sets the amount of the second diffuse light. The value must be between 0 and 100. When the parameter is not specified, it is restored to the default value 50.

=== diffuse2_direction ===
 set diffuse2_direction {[x, y, z]}
Sets the direction of the second diffuse light. When the parameter is not specified, it is restored to the default value [-1, -1, -1].

=== drawlevel ===
 set drawlevel &lt;value&gt;
Specifies precision of the rendering of spheres and cylinders. The value may be given as an integer (minimum 5) that stands for the number of straight line segments to represent an arc of 180 degrees. 

=== efsite_url ===
 set efsite_url &lt;URL&gt;
Sets the URL for eF-site.

=== ext_site_url ===
 set ext_site_url &lt;prefix&gt; &lt;URL&gt;
Sets the URL for an external database site.

=== hbonds ===
 set hbonds backbone
Hydrogen bonds are displayed between backbones.

 set hbonds sidechain
Hydrogen bonds are displayed between sidechains. 

=== hetero ===
 set hetero on
Sets the default behavior of the select command such that hetero atoms are selected.

 set hetero off
Sets the default behavior of the select command such that hetero atoms are not selected. 

=== hydrogen ===
 set hydrogen on
Sets the default behavior of the select command such that hydrogens are selected.

 set hydrogen off
Sets the default behavior of the select command such that hydrogens are not selected. 

=== imagesize ===
 set imagesize &lt;width&gt; &lt;height&gt;
Sets the size of the 3D-rendering panel in pixels. The size will be set within the screen size with the width being an even integer. 

=== line_width ===
 set line_width &lt;value&gt;
Sets the width of lines in polygon images. The &lt;value&gt; should be larger than 0. 

=== loadcenter ===
 set loadcenter on
When a file is opened, sets the default center of that file to the center of all files that have already opened.

 set loadcenter off
When a file is opened, sets the default center of that file according to its own coordiantes. 

=== pdbml_noatom_url ===
 set pdbml_noatom_url &lt;URL&gt;
Sets the URL for PDBML noatom files.

=== pdbml_extatom_url ===
 set pdbml_extatom_url &lt;URL&gt;
Sets the URL for PDBML extatom files.

=== pdbml_plus_url ===
 set pdbml_plus_url &lt;URL&gt;
Sets the URL for PDBMLplus files.

=== picking ===
 set picking off
Turns off the mouse picking.

 set picking ident
Sets the mouse picking behavior to show atom identification.

 set picking coord
Sets the mouse picking behavior to show atom coordinates with identification.

 set picking distance
Sets the mouse picking behavior to show the distance between atoms successively picked.

 set picking center
Sets the mouse picking behavior to specify the center of rotation and center of the screen.

 set picking select
Sets the mouse picking behavior to select the file that contains the atom picked. 

=== pickradius ===
 set pickradius &lt;value&gt;
Sets the mouse-pickable region of each atom to be the sphere centered to each atom with the specified radius (angstrom or Rasmol unit). 

=== point_size ===
 set point_size &lt;value&gt;
Sets the size of points in polygon images. The &lt;value&gt; should be larger than 0. 

=== polyline_width ===
 set polyline_width &lt;value&gt;
Sets the width of polylines in polygon images. The &lt;value&gt; should be larger than 0. 

=== projection ===
 set projection perspective
Sets the projection mode for a perspective projection.

 set projection parallel {&lt;size&gt;}
Sets the projection mode for a parallel projection. The size of image (fit to the height of the screen) can be specified (angstrom or Rasmol unit). 

=== ribbonback ===
 set ribbonback &lt;color&gt;
Sets the color of the back of ribbon models. The color may be given as RGB values [r,g,b] or predefined color names.

 set ribbonback none
Resets the color of the back of ribbon models.

=== specular ===
 set specular on/true
Enables the display of specular highlights on solid objects.

 set specular off/false
Disables the display of specular highlights on solid objects.

 set specular &lt;value&gt;
Enables the display of specular highlights on solid objects. The value between 0 and 100 specifies the specular color in gray scale with 0 and 100 being black and white, respectively. The default value is 50.0. 

=== specpower ===
 set specpower &lt;value&gt;
Sets the shininess of solid objects. The value between 0 and 100 specifies a material reflection coefficient with 0 being diffuse surfaces and 100 being shiny surfaces. 

=== ssbonds ===
 set ssbonds backbone
Disulfide bonds are displayed between backbones.

 set ssbonds sidechain
Disulfide bonds are displayed between sidechains. 

=== stereo ===
 set stereo
A synonym of the [[#stereo_2|stereo]] command.

=== transparency ===
 set transparency &lt;value&gt;
Sets the transparency of polygon images.

 set point_transparency &lt;value&gt;
Sets the transparency of points in polygon images.

 set line_transparency &lt;value&gt;
Sets the transparency of lines in polygon images.

 set triangle_transparency &lt;value&gt;
Sets the transparency of triangles in polygon images.

 set quad_transparency &lt;value&gt;
Sets the transparency of quads in polygon images.

 set polyline_transparency &lt;value&gt;
Sets the transparency of polylines in polygon images. 

=== viewpoint ===
 set viewpoint {x, y, z}
Sets the viewpoint to the specified coordinates. 

== show ==
 show godata
Displays gene ontology data of molecules.

 show imagesize
Displays the size of the 3D-rendering panel.

 show information
Displays a detail discription of molecules.

 show site {&lt;prefix&gt;:&lt;db&gt;:&lt;category&gt;}
Displays site information in an external database.

 show transform
Displays the transform matrix of molecules.

 show viewpoint
Displays the current viewpoint.

 show pdbj
Displays keywords available in PDBj expression.

== slab ==
 slab {on/true}
Enables the z-clipping plane of molecules and polygons.

 slab off/false
Disables the z-clipping plane of molecules and polygons.

 slab &lt;ratio&gt;
Sets the position of the z-clipping plane of molecules and polygons. The parameter may be given as a number from 0 to 100. The values 0 and 100 represent that image as a whole is completely invisible and visible, respectively.

 slab -v &lt;value&gt;
Sets the position of the z-clipping plane of molecules and polygons by specifying the z coordinate value. 

== spacefill ==
 spacefill {on/true}
Turns on the ball image of the selected atoms.

 spacefill off/false
Turns off the ball image of the selected atoms.

 spacefill &lt;radius&gt;
Turns on the ball image of the selected atoms with the specified radius (angstrom or Rasmol unit). The maximum parameter value is 3.0.

 spacefill temperature
Turns on the ball image of the selected atoms using the temperature factor as radius. 

== ssbonds ==
 ssbonds {on/true}
Turns on the selected disulfide bonds.

 ssbonds off/false
Turns off the selected disulfide bonds.

 ssbonds &lt;radius&gt;
Turns on the selected disulfide bonds with the specified raidus (angstrom or Rasmol unit). The maximum parameter value is 2.0. 

== stereo ==
 stereo {on/true}
Enables stereo display. This command without arguments cycles three state; 'stereo off', 'stereo on' in cross-eyed mode and 'stereo on' in parallel-eyed mode.

 stereo off/false
Disables stereo display.

 stereo &lt;angle&gt;
Enables stereo display with the specified separation angle. Positive and negative values represent cross-eyed and parallel-eyed viewing, respectively.


== structure ==
 structure
Estimates the secondary structure using Kabsch and Sander's DSSP algorithm. 

== trace ==
 trace {on/true}
Turns on a tube representation for the selected residues. When a chain does not have enough atoms to draw the tube model, a backbone will be shown instead.

 trace off/false
Turns off a tube representation for the selected residues.

 trace &lt;radius&gt;
Turns on a tube representation for the selected residues with the specified radius (angstrom or Rasmol unit). The maximum parameter value is 2.0.

== translate ==
 translate x/y/z &lt;value&gt;
Moves images along the specified axis by the specified amount (angstrom). 

== wireframe ==
 wireframe {on/true}
Turns on the selected bonds.

 wireframe off/false
Turns off the selected bonds.

 wireframe &lt;radius&gt;
Turns on the selected bonds with the specified raidus (angstrom or Rasmol unit). The maximum parameter value is 2.0. 

== write ==
 write
A synonym of the [[#save|save]] command.

== zap ==
 zap {&lt;file_IDs&gt;}
Closes the specified files. More than one file IDs can be specified by putting commas as the delimiter. When the paraneter is absent, all files are closed. 

== zoom ==
 zoom {&lt;value&gt;}
Sets the magnification of the image as a whole. The value stands for the magnification as a percentage of the current scale. The minimum parameter value is 10.0.</text>
    <sha1>1c12d449ea80fb9337ded5262f8d3c3ec0e0b254</sha1>
  </revision>
  <revision>
    <id>425</id>
    <parentid>424</parentid>
    <timestamp>2010-12-03T04:53:37Z</timestamp>
    <contributor>
      <username>IMSsato</username>
      <id>4</id>
    </contributor>
    <comment>/* show */</comment>
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    <format>text/x-wiki</format>
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  |__TOC__
  |}
Command usage of jV follows that of [http://www.rasmol.org/ Rasmol] with some modifications. In the following part, command arguments that can take an arbitrary value are denoted as &lt;value&gt; for example, arguments restricted to several possible values are listed with / as a delimiter, and arguments that can be omitted are put in brackets {}. Commands, [[#exit|exit]], [[#load|load]], [[#quit|quit]], [[#save|save]], [[#script|script]], and [[#write|write]], are not available in applet circumstance.

== anim ==
 anim forward {&lt;value&gt;}
Starts animation forward. If the &lt;value&gt; is given, just move frames forward by the specified amount.

 anim backward {&lt;value&gt;}
Starts animation backward. If the &lt;value&gt; is given, just move frames backward by the specified amount.

 anim stop
Stops animation.

== animframe ==
 animframe &lt;frame&gt; {&lt;file_ID&gt;}
Sets the frame of all animation files for the specified value. When &lt;file_ID&gt; is given, only the specified file is processed.

== animmode ==
 animmode once
Sets the behavior of animation for 'once'. When the frame reaches the last one, animation is stopped.

 animmode loop
Sets the behavior of animation for 'loop'. When the frame reaches the last one, animation is reset to the first frame and continues playing.

 animmode swing
Sets the behavior of animation for 'swing'. When the frame reaches the last one, the direction of animation is reversed.

== animrange ==
 animrange &lt;init_frame&gt;-&lt;term_frame&gt; {&lt;file_IDs&gt;}
Sets the range of all animation files. When is given, only the specified file is processed.

== animselect ==
 animselect {-a/-r} &lt;file_IDs&gt;
Selects the specified files and makes the others not selected. More than one file IDs can be specified by putting commas as the delimiter. When the option -a or -r is specified, only the selection status of the specified files are modified, selected or not selected, respectively, and the others remain unchanged.

== animspeed ==
 animspeed &lt;speed&gt;
Sets the animation speed. The argument should be an integer value from 1 to 20.

== animstep ==
 animstep &lt;step&gt; {&lt;file_ID&gt;}
Sets the step of all animation files for the specified value. When &lt;file_ID&gt; is given, only the specified file is processed.

== backbone ==
 backbone {on/true}
Turns on the selected backbone bonds.

 backbone off/false
Turns off the selected backbone bonds.

 backbone &lt;radius&gt;
Turns on the selected backbone bonds with the specified raidus (angstrom or Rasmol unit). The maximum parameter value is 2.0.

== background ==
 background &lt;color&gt;
Changes the background color. The color may be given as RGB values [r,g,b], or predefined color names.

== ball_and_stick ==
 ball_and_stick {on/true}
Turns on the ball and stick image of the selected atoms with ball radius 0.5 and stick radius 0.2 in angstrom.

 ball_and_stick off/false
Turns off the ball and stick image of the selected atoms.

 ball_and_stick &lt;ball_radius&gt; &lt;stick_radius&gt;
Turns on the ball and stick image of the selected atoms with the specified ball radius and stick radius (angstrom or Rasmol unit). The maximum parameter value is 3.0 and 2.0, respectively.

== cartoon ==
 cartoon {on/true}
Turns on the thick ribbons for the selected residues. When a chain does not have enough atoms to draw the ribbon model, a backbone will be shown instead.

 cartoon off/false
Turns off the thick ribbons for the selected residues.

 cartoon &lt;half_width&gt;
Turns on the thick ribbons for the selected residues with the specified half width (angstrom or Rasmol unit). The maximum parameter value is 4.0.

== center ==
 center {-r/-s} {&lt;atom_expression&gt;}
Sets the center of rotation and the center of the screen to the center of a group of atoms specified by the [[Atom Expression|atom expression]]. When the option -r or -s is specified, only the center of rotation or the center of the screen is modified, respectively.

 center {-r} [x, y, z]
Moves the center of rotation and the center of the screen from the current position by the specified amount. When the option -r is specified, only the center of rotation is modified.

 center {-r} {x, y, z}
Sets the center of rotation and the center of the screen to the specified coordinates. When the option -r is specified, only the center of rotation is modified.

 center -s [x, y]
Moves the center of the screen from the current position by the specified amount.

 center -s {x, y}
Sets the center of the screen to the specified coordinates.

== color ==
 color {atoms} &lt;color&gt;
Sets the color of the selected atoms. The color may be given as RGB values [r,g,b], predefined color names, or predefined color schemes; amino, chain, charge, cpk, group, shapely, structure, and temperature.

 color bonds/backbone/ribbons/hbonds/ssbonds &lt;color&gt;
Sets the color of the specified object. The color may be given as RGB values [r,g,b] or predefined color names. For hydrogen bonds, color scheme 'type' can be specified.

 color bonds/backbone/ribbons/hbonds/ssbonds none
Resets the color of the specified object.

== colorvertex ==
 colorvertex &lt;color&gt;
Sets the color of the selected vertices. The color may be given as RGB values [r,g,b] or predefined color names.

 colorvertex none
Resets the color of the selected vertices.

== cpk ==
 cpk
A synonym of the [[#spacefill|spacefill]] command.

== define ==
 define &lt;name&gt; &lt;atom_expression&gt;
Associates an arbitrary set of atoms specified by the [[Atom Expression|atom expression]] with a unique name.

== display ==
 display all
Displays the image of all files.

 display none
Turns off the image of all files.

 display {-a/-r} &lt;file_IDs&gt;
Displays the image of the specified files and turns off the others. More than one file IDs can be specified by putting commas as the delimiter. When the option -a or -r is specified, turns the image of the specified files on or off, respectively, and the others remain unchanged.

== displayatom ==
 displayatom {on/true}
Displays the selected atoms.

 displayatom off/false
Turns off the selected atoms.

== displayvertex ==
 displayvertex {on/true}
Displays the selected vertices.

 displayvertex off/false
Turns off the selected vertices.

== echo ==
 echo &lt;string&gt;
Echoes the specified message back to the message area.

== exit ==
 exit
Terminates the application.

== fit ==
 fit &lt;file1_ID&gt; &lt;file2_ID&gt;
Sets the transform matrix of file1 identical to that of file2. 

== fselect ==
 fselect all
Selects all files.

 fselect none
Selects no files.

 fselect {-a/-r} &lt;file_IDs&gt;
Selects the specified files and makes the others not selected. More than one file IDs can be specified by putting commas as the delimiter. When the option -a or -r is specified, only the selection status of the specified files are modified, selected or not selected, respectively, and the others remain unchanged.

== hbonds ==
 hbonds {on/true}
Turns on the selected hydrogen bonds.

 hbonds off/false
Turns off the selected hydrogen bonds.

 hbonds &lt;radius&gt;
Turns on the selected hydrogen bonds with the specified raidus (angstrom or Rasmol unit). The maximum parameter value is 2.0. 

== load ==
 load {pdbml} &lt;filename&gt; {fit &lt;file_ID&gt;}
Opens a PDBML file. URL can be used to open a remote file. On loading, the transform matrix can be set identical to that of the specified file.

 load pdb &lt;filename&gt; {fit &lt;file_ID&gt;}
Opens a PDB file. URL can be used to open a remote file. On loading, the transform matrix can be set identical to that of the specified file.

 load polygon &lt;filename&gt; {fit &lt;file_ID&gt;}
Opens a polygon file. URL can be used to open a remote file. On loading, the transform matrix can be set identical to that of the specified file.

 load animation &lt;filename&gt; {fit &lt;file_ID&gt;}
Opens an animation file. URL can be used to open a remote file. On loading, the transform matrix can be set identical to that of the specified file.

 load ftp &lt;PDB_code&gt; {fit &lt;file_ID&gt;}
Retrieves a PDBML file from the PDBj FTP site and opens it. On loading, the transform matrix can be set identical to that of the specified file. 

== pause ==
 pause
Stops the execution of a script file until any key is pressed to restart. 

== pdbj_describe ==
 pdbj_describe &lt;file_id&gt; {&lt;name&gt;} 
Shows the document for the jV_command in PDBMLplus specified by file ID and name. When the name is not specified, all available names are listed.

== pdbj_execute ==
 pdbj_execute &lt;file_id&gt; &lt;name&gt; 
Executes the jV_command in PDBMLplus specified by file ID and name.

== quit ==
 quit
A synonym of the [[#exit|exit]] command.

== refresh ==
 refresh
Redraws all images. 

== reset ==
=== default ===
 reset
Restores the original viewing transformation of all images, the center of rotation, and the view point. 

=== cartoon ===
 reset cartoon
Restores the thickness of the cartoon representation. 

=== line_width ===
 reset line_width
Restores the width of lines in polygon images. 

=== pickradius ===
 reset pickradius
Restores the mouse-pickable region of each atom. 

=== point_size ===
 reset point_size
Restores the size of points in polygon images. 

=== polyline_width ===
 reset polyline_width
Restores the width of polylines in polygon images. 

=== transparency ===
 reset transparency
Restores the transparency of polygon images.

 reset point_transparency
Restores the transparency of points in polygon images.

 reset line_transparency
Restores the transparency of lines in polygon images.

 reset triangle_transparency
Restores the transparency of triangles in polygon images.

 reset quad_transparency
Restores the transparency of quads in polygon images.

 reset polyline_transparency
Restores the transparency of polylines in polygon images. 

== ribbons ==
 ribbons {on/true}
Turns on the ribbon surfaces for the selected residues. When a chain does not have enough atoms to draw the ribbon model, a backbone will be shown instead.

 ribbons off/false
Turns off the ribbon surfaces for the selected residues.

 ribbons &lt;half_width&gt;
Turns on the ribbon surfaces for the selected residues with the specified half width (angstrom or Rasmol unit). The maximum parameter value is 4.0.

== rotate ==
 rotate x/y/z &lt;angle&gt;
Rotates images about the specified axis by the specified angle in degrees. 

== save ==
 save {pdb} &lt;filename&gt;
Saves the currently selected set of atoms in a PDB format file.

 save script &lt;filename&gt;
Creates a script file that reproduces the currently displayed image.

 save png &lt;filename&gt;
Creates a PNG image file of the currently displayed image.

 save jpeg &lt;filename&gt; {&lt;quality&gt;}
Creates a JPEG image file of the currently displayed image. The compression quality can be specified, 0 &lt; quality &lt;= 1, where 'quality = 1' means no compression. 

== script ==
 script &lt;filename&gt;
Opens and executes the specified script file. URL can be used to open a remote file. 

== select ==
 select
Selects all atoms. Whether hetero atoms and hydrogens are selected or not depends on the internal parameters, hetero and hydrogen, respectively.

 select all
Selects all atoms including hetero atoms and hydrogens.

 select none
Selects no atoms.

 select &lt;atom_expression&gt;
Selects a group of atoms specified by the [[Atom Expression|atom expression]].

== selectvertex ==
 selectvertex {all}
Selects all vertices.

 selectvertex none
Selects no vertices.

 selectvertex &lt;vertex_expression&gt;
Selects a group of vertices specified by the [[Vertex Expression|vertex expression]].

== set ==
=== ambient ===
 set ambient {&lt;value&gt;}
Sets the amount of ambient light. The value must be between 0 and 100. When the parameter is not specified, it is restored to the default value 33.

=== adjustview ===
 set adjustview on
The view point is automatically adjusted when a new file is loaded.

 set adjustview off
The view point is kept unchanged when a new file is loaded. 

=== background ===
 set background &lt;color&gt;
Changes the background color. The color may be given as RGB values [r,g,b], or predefined color names. 

=== bondmode ===
 set bondmode and
Specifies how to select an individual bonds. A bond is selected when both atoms connected by the bond are selected.

 set bondmode or
Specifies how to select an individual bonds. A bond is selected when either of the connected atoms is selected. 

=== cartoon ===
 set cartoon {&lt;value&gt;}
Specifies the thickness of the cartoon representation (angstrom or Rasmol unit). The maximum parameter value is 2.0. When the parameter is not specified, it is restored to the default value. 

=== cartoon_loop_tube ===
 set cartoon_loop_tube on
The loop region is drawn as tube in the cartoon representation.

 set cartoon_loop_tube off
The loop region is drawn as square pillar in the cartoon representation.

=== cartoon_round ===
 set cartoon_round on
Square pillar with round edge is drawn in the cartoon representation (except beta strands). 

 set cartoon_round off
Square pillar is drawn in the cartoon representation.

=== center ===
 set center &lt;atom_expression&gt;
Sets the default center of the selected files to the center of a group of atoms specified by the [[Atom Expression|atom expression]].

 set center [x, y, z]
Sets the default center of the selected files to the specified coordinates.

=== diffuse1 ===
 set diffuse1 {&lt;value&gt;}
Sets the amount of the first diffuse light. The value must be between 0 and 100. When the parameter is not specified, it is restored to the default value 50.

=== diffuse1_direction ===
 set diffuse1_direction {[x, y, z]}
Sets the direction of the first diffuse light. When the parameter is not specified, it is restored to the default value [-1, -1, -1].

=== diffuse2 ===
 set diffuse2 {&lt;value&gt;}
Sets the amount of the second diffuse light. The value must be between 0 and 100. When the parameter is not specified, it is restored to the default value 50.

=== diffuse2_direction ===
 set diffuse2_direction {[x, y, z]}
Sets the direction of the second diffuse light. When the parameter is not specified, it is restored to the default value [-1, -1, -1].

=== drawlevel ===
 set drawlevel &lt;value&gt;
Specifies precision of the rendering of spheres and cylinders. The value may be given as an integer (minimum 5) that stands for the number of straight line segments to represent an arc of 180 degrees. 

=== efsite_url ===
 set efsite_url &lt;URL&gt;
Sets the URL for eF-site.

=== ext_site_url ===
 set ext_site_url &lt;prefix&gt; &lt;URL&gt;
Sets the URL for an external database site.

=== hbonds ===
 set hbonds backbone
Hydrogen bonds are displayed between backbones.

 set hbonds sidechain
Hydrogen bonds are displayed between sidechains. 

=== hetero ===
 set hetero on
Sets the default behavior of the select command such that hetero atoms are selected.

 set hetero off
Sets the default behavior of the select command such that hetero atoms are not selected. 

=== hydrogen ===
 set hydrogen on
Sets the default behavior of the select command such that hydrogens are selected.

 set hydrogen off
Sets the default behavior of the select command such that hydrogens are not selected. 

=== imagesize ===
 set imagesize &lt;width&gt; &lt;height&gt;
Sets the size of the 3D-rendering panel in pixels. The size will be set within the screen size with the width being an even integer. 

=== line_width ===
 set line_width &lt;value&gt;
Sets the width of lines in polygon images. The &lt;value&gt; should be larger than 0. 

=== loadcenter ===
 set loadcenter on
When a file is opened, sets the default center of that file to the center of all files that have already opened.

 set loadcenter off
When a file is opened, sets the default center of that file according to its own coordiantes. 

=== pdbml_noatom_url ===
 set pdbml_noatom_url &lt;URL&gt;
Sets the URL for PDBML noatom files.

=== pdbml_extatom_url ===
 set pdbml_extatom_url &lt;URL&gt;
Sets the URL for PDBML extatom files.

=== pdbml_plus_url ===
 set pdbml_plus_url &lt;URL&gt;
Sets the URL for PDBMLplus files.

=== picking ===
 set picking off
Turns off the mouse picking.

 set picking ident
Sets the mouse picking behavior to show atom identification.

 set picking coord
Sets the mouse picking behavior to show atom coordinates with identification.

 set picking distance
Sets the mouse picking behavior to show the distance between atoms successively picked.

 set picking center
Sets the mouse picking behavior to specify the center of rotation and center of the screen.

 set picking select
Sets the mouse picking behavior to select the file that contains the atom picked. 

=== pickradius ===
 set pickradius &lt;value&gt;
Sets the mouse-pickable region of each atom to be the sphere centered to each atom with the specified radius (angstrom or Rasmol unit). 

=== point_size ===
 set point_size &lt;value&gt;
Sets the size of points in polygon images. The &lt;value&gt; should be larger than 0. 

=== polyline_width ===
 set polyline_width &lt;value&gt;
Sets the width of polylines in polygon images. The &lt;value&gt; should be larger than 0. 

=== projection ===
 set projection perspective
Sets the projection mode for a perspective projection.

 set projection parallel {&lt;size&gt;}
Sets the projection mode for a parallel projection. The size of image (fit to the height of the screen) can be specified (angstrom or Rasmol unit). 

=== ribbonback ===
 set ribbonback &lt;color&gt;
Sets the color of the back of ribbon models. The color may be given as RGB values [r,g,b] or predefined color names.

 set ribbonback none
Resets the color of the back of ribbon models.

=== specular ===
 set specular on/true
Enables the display of specular highlights on solid objects.

 set specular off/false
Disables the display of specular highlights on solid objects.

 set specular &lt;value&gt;
Enables the display of specular highlights on solid objects. The value between 0 and 100 specifies the specular color in gray scale with 0 and 100 being black and white, respectively. The default value is 50.0. 

=== specpower ===
 set specpower &lt;value&gt;
Sets the shininess of solid objects. The value between 0 and 100 specifies a material reflection coefficient with 0 being diffuse surfaces and 100 being shiny surfaces. 

=== ssbonds ===
 set ssbonds backbone
Disulfide bonds are displayed between backbones.

 set ssbonds sidechain
Disulfide bonds are displayed between sidechains. 

=== stereo ===
 set stereo
A synonym of the [[#stereo_2|stereo]] command.

=== transparency ===
 set transparency &lt;value&gt;
Sets the transparency of polygon images.

 set point_transparency &lt;value&gt;
Sets the transparency of points in polygon images.

 set line_transparency &lt;value&gt;
Sets the transparency of lines in polygon images.

 set triangle_transparency &lt;value&gt;
Sets the transparency of triangles in polygon images.

 set quad_transparency &lt;value&gt;
Sets the transparency of quads in polygon images.

 set polyline_transparency &lt;value&gt;
Sets the transparency of polylines in polygon images. 

=== viewpoint ===
 set viewpoint {x, y, z}
Sets the viewpoint to the specified coordinates. 

== show ==
 show godata
Displays gene ontology data of molecules.

 show imagesize
Displays the size of the 3D-rendering panel.

 show information
Displays a detail discription of molecules.

 show site {&lt;prefix&gt;:&lt;db&gt;:&lt;category&gt;}
Displays site information in an external database.

 show transform
Displays the transform matrix of molecules.

 show viewpoint
Displays the current viewpoint.

 show pdbj
Displays keywords available in [[Atom Expression#PDBj expression|PDBj expression]].

== slab ==
 slab {on/true}
Enables the z-clipping plane of molecules and polygons.

 slab off/false
Disables the z-clipping plane of molecules and polygons.

 slab &lt;ratio&gt;
Sets the position of the z-clipping plane of molecules and polygons. The parameter may be given as a number from 0 to 100. The values 0 and 100 represent that image as a whole is completely invisible and visible, respectively.

 slab -v &lt;value&gt;
Sets the position of the z-clipping plane of molecules and polygons by specifying the z coordinate value. 

== spacefill ==
 spacefill {on/true}
Turns on the ball image of the selected atoms.

 spacefill off/false
Turns off the ball image of the selected atoms.

 spacefill &lt;radius&gt;
Turns on the ball image of the selected atoms with the specified radius (angstrom or Rasmol unit). The maximum parameter value is 3.0.

 spacefill temperature
Turns on the ball image of the selected atoms using the temperature factor as radius. 

== ssbonds ==
 ssbonds {on/true}
Turns on the selected disulfide bonds.

 ssbonds off/false
Turns off the selected disulfide bonds.

 ssbonds &lt;radius&gt;
Turns on the selected disulfide bonds with the specified raidus (angstrom or Rasmol unit). The maximum parameter value is 2.0. 

== stereo ==
 stereo {on/true}
Enables stereo display. This command without arguments cycles three state; 'stereo off', 'stereo on' in cross-eyed mode and 'stereo on' in parallel-eyed mode.

 stereo off/false
Disables stereo display.

 stereo &lt;angle&gt;
Enables stereo display with the specified separation angle. Positive and negative values represent cross-eyed and parallel-eyed viewing, respectively.


== structure ==
 structure
Estimates the secondary structure using Kabsch and Sander's DSSP algorithm. 

== trace ==
 trace {on/true}
Turns on a tube representation for the selected residues. When a chain does not have enough atoms to draw the tube model, a backbone will be shown instead.

 trace off/false
Turns off a tube representation for the selected residues.

 trace &lt;radius&gt;
Turns on a tube representation for the selected residues with the specified radius (angstrom or Rasmol unit). The maximum parameter value is 2.0.

== translate ==
 translate x/y/z &lt;value&gt;
Moves images along the specified axis by the specified amount (angstrom). 

== wireframe ==
 wireframe {on/true}
Turns on the selected bonds.

 wireframe off/false
Turns off the selected bonds.

 wireframe &lt;radius&gt;
Turns on the selected bonds with the specified raidus (angstrom or Rasmol unit). The maximum parameter value is 2.0. 

== write ==
 write
A synonym of the [[#save|save]] command.

== zap ==
 zap {&lt;file_IDs&gt;}
Closes the specified files. More than one file IDs can be specified by putting commas as the delimiter. When the paraneter is absent, all files are closed. 

== zoom ==
 zoom {&lt;value&gt;}
Sets the magnification of the image as a whole. The value stands for the magnification as a percentage of the current scale. The minimum parameter value is 10.0.</text>
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</page>
<page arvcontinue="20100805022053|404">
  <title>Vertex Expression</title>
  <ns>0</ns>
  <id>22</id>
  <revision>
    <id>426</id>
    <parentid>164</parentid>
    <timestamp>2010-12-03T04:54:30Z</timestamp>
    <contributor>
      <username>IMSsato</username>
      <id>4</id>
    </contributor>
    <comment>/* within expression */</comment>
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    <format>text/x-wiki</format>
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 |__TOC__
 |}
In order to specify a group of vertices in a polygon, the following three expressions are available.

The standard boolean connectives 'and', 'or' and 'not', and brackets can be used to construct a complex expression. The boolean connectives may be abbreviated as '&amp;', '|', and '|', respectively. 

== comparison operators ==
Parts of a polygon can be selected using equality and inequality operators on the ID numbers assigned to each vertex; for example, id &gt;= 100. Possible operators are =, ==, &lt;&gt;, !=, /=, &lt;, &lt;=, &gt; and &gt;=. When each vertex element has a user_data element, every attributes in the user_data element can be used to select vertices with equality and inequality operators. 

== within expression ==
A within expression selects vertices that exist within a specified distance from a set of atoms specified by the [[Atom Expression|atom expression]].
# within( &lt;distance&gt;, &lt;atom_expression&gt; )&lt;br /&gt;Instead of a set of atoms, a single point coordinates, from which the distance is measured, can be specified.
# within( &lt;distance&gt;, [x, y, z] )
# within( &lt;distance&gt;, {x, y, z} )
In case 2), vertices are selected according to their current coordinates displayed in the screen. On the other hand, coordinates written in the original polygon file are used in case 3).

== box expression ==
A box expression selects vertices that exist in some cubes, where each cube is centered to each atom in a specified set of atoms. The syntax is similar to that of the within expression.
# box( &lt;size&gt;, &lt;atom_expression&gt; )&lt;br /&gt;When a single point coordinates is given in the second argument, vertices that exist in a single cube, whose center is set to the passed coordinates, are selected.
# box( &lt;size&gt;, [x, y, z] )
# box( &lt;size&gt;, {x, y, z} )
In every cases, the length of an edge of the cubes is twice as the specified value.</text>
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In order to specify a group of vertices in a polygon, the following three expressions are available.

The standard boolean connectives 'and', 'or' and 'not', and brackets can be used to construct a complex expression. The boolean connectives may be abbreviated as '&amp;', '|', and '|', respectively. 

== comparison operators ==
Parts of a polygon can be selected using equality and inequality operators on the ID numbers assigned to each vertex; for example, id &gt;= 100. Possible operators are =, ==, &lt;&gt;, !=, /=, &lt;, &lt;=, &gt; and &gt;=. When each vertex element has a user_data element, every attributes in the user_data element can be used to select vertices with equality and inequality operators. 

== within expression ==
A within expression selects vertices that exist within a specified distance from a set of atoms specified by the [[Atom Expression|atom expression]].
# within( &lt;distance&gt;, &lt;atom_expression&gt; )&lt;br /&gt;Instead of a set of atoms, a single point coordinates, from which the distance is measured, can be specified.
# within( &lt;distance&gt;, [x, y, z] )
# within( &lt;distance&gt;, {x, y, z} )
In case 2), vertices are selected according to their current coordinates displayed in the screen. On the other hand, coordinates written in the original polygon file are used in case 3).

== box expression ==
A box expression selects vertices that exist in some cubes, where each cube is centered to each atom in a set of atoms specified by the [[Atom Expression|atom expression]]. The syntax is similar to that of the within expression.
# box( &lt;size&gt;, &lt;atom_expression&gt; )&lt;br /&gt;When a single point coordinates is given in the second argument, vertices that exist in a single cube, whose center is set to the passed coordinates, are selected.
# box( &lt;size&gt;, [x, y, z] )
# box( &lt;size&gt;, {x, y, z} )
In every cases, the length of an edge of the cubes is twice as the specified value.</text>
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In order to specify a group of vertices in a polygon, the following three expressions are available.

The standard boolean connectives 'and', 'or' and 'not', and brackets can be used to construct a complex expression. The boolean connectives may be abbreviated as '&amp;', '|', and '!', respectively. 

== comparison operators ==
Parts of a polygon can be selected using equality and inequality operators on the ID numbers assigned to each vertex; for example, id &gt;= 100. Possible operators are =, ==, &lt;&gt;, !=, /=, &lt;, &lt;=, &gt; and &gt;=. When each vertex element has a user_data element, every attributes in the user_data element can be used to select vertices with equality and inequality operators. 

== within expression ==
A within expression selects vertices that exist within a specified distance from a set of atoms specified by the [[Atom Expression|atom expression]].
# within( &lt;distance&gt;, &lt;atom_expression&gt; )&lt;br /&gt;Instead of a set of atoms, a single point coordinates, from which the distance is measured, can be specified.
# within( &lt;distance&gt;, [x, y, z] )
# within( &lt;distance&gt;, {x, y, z} )
In case 2), vertices are selected according to their current coordinates displayed in the screen. On the other hand, coordinates written in the original polygon file are used in case 3).

== box expression ==
A box expression selects vertices that exist in some cubes, where each cube is centered to each atom in a set of atoms specified by the [[Atom Expression|atom expression]]. The syntax is similar to that of the within expression.
# box( &lt;size&gt;, &lt;atom_expression&gt; )&lt;br /&gt;When a single point coordinates is given in the second argument, vertices that exist in a single cube, whose center is set to the passed coordinates, are selected.
# box( &lt;size&gt;, [x, y, z] )
# box( &lt;size&gt;, {x, y, z} )
In every cases, the length of an edge of the cubes is twice as the specified value.</text>
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== Starting up ==
It is assumed that Java Runtime Environment and JOGL have been appropriately installed. Once you extract the binary distribution file of jV3, the directory of the name, jV_(version), is generated (Ex. jV_3_6_2). The version is assumed to be 3_6_x hereafter. The application starts up by double-clicking the file ‘jv_3_6_x.jar’ in the jV_3_6_x directory or executing the following command from the command line interface.
 java –jar jv_3_6_x.jar
Figure 1 shows the start-up screen. The window has a 3-panel structure, and the upper-left panel with the black background is a 3D image display area. The status of files that have been loaded to the application is shown in the upper-right panel and the lower panel is a command-input and a message-output area.
[[File:Tutorial_fig1.jpg|thumb|Figure 1: Start-up screen|center|500px]]

== Displaying molecules ==
If you are working in the environment that is getting on the Internet and know the PDB ID of the molecule that you want to display, the simplest way is as follows. A dialog shown in Figure 2 is opened by selecting the [File] – [Open – Remote] – [PDB ID] menu item. Enter a PDB ID '12as', for example, to the text field and click the 'OK' button, then the PDBML file is read through the Internet and the molecule is displayed. The URL where the PDBML file is retrieved from is specified in the 'properties.txt' file in the jV_3_3_x directory. A molecule is displayed in a wire frame model with colored by atom type in the initial state.

[[File:Fig2.jpg|thumb|Figure 2: Dialog to open the molecule specified by PDB ID|center|200px]]

Let us next attempt to load an arbitrary file on the Internet. Here we use 'http://ef-site.hgc.jp/eF-site/jV/1yec.pdb' as an example. The file is a conventional PDB file whose PDB ID is 1yec. In this case we choose the [File] – [Open – Remote] – [PDB] menu item. Then the open-remote dialog is appeared. Enter the above URL to the text field at the top of the dialog and click the 'OK' button and the molecule is read in and displayed. In jV3, each molecule is displayed according to the space coordination described in its file. Therefore, when loading and displaying more than one molecule together, they can be viewed with an appropriate separation in some cases; however, they may be displayed far separately or may be overlapped depending on the combination. In any case, when adding a new file, the position of the viewpoint is automatically controlled for the whole to be displayed.

The coordinate system is the right hand system with the x-y plane being on the screen (the x-axis is a horizontal line with positive values to the right and the y-axis is a vertical line with positive values up). Although, the above examples are about operations for remote files, a PDB file on your local hard disk can also be opened from the [File] – [Open – Local] – [PDB] menu item.

== Operating molecules ==
Interactive mouse operations are possible for 3D images. By left-dragging the mouse on the 3D-display panel, molecules are rotated around the x-axis or y-axis. By left-dragging the mouse while holding the Shift key or Alt key on the keyboard, molecules are translated along the z-axis. All mouse operations are as follows (as for the Macintosh environment, the Command key + left-drag substitutes for the right-drag).

{| border="1"
 ! Mouse operations !! Actions
 |-
 | Left-drag || The image is rotated around the x (for a vertical motion) and y (for a horizontal motion) axes.
 |-
 | Right-drag || The image is translated on the x-y plane.
 |-
 | [Alt or Shift] + left-drag || The image is translated along the z-axis.
 |-
 | [Alt or Shift] + right-drag || The image is rotated around the z-axis.
 |-
 | [Ctrl] + left-drag || The z-clipping plane is shifted when [Option]-[Slab] is checked.
 |-
 | Left-click || An atom of the molecule displayed on the screen is picked.
 |}

In the upper-right panel in the application window (see Figure 3), the file names that have been loaded to the application are listed, where sequential integers are automatically assigned to the individual file. Each integer is a file ID that can be used to specify the file in the command line interface. In addition, two checkboxes are attached to each file. If you change the status of a ‘display’ checkbox, the corresponding molecule is switched to be displayed or not to be displayed. If you change the status of a ‘select’ checkbox, the corresponding molecule is switched to be a target of the mouse operations or not. For example, set the both ‘display’ checkboxes on, and the both ‘select’ checkboxes off. In this case, either molecule does not move against mouse operations. 

Subsequently set the ‘select’ checkbox of file 1 on. In this case, mouse operations work for the molecule 1. Thus, each file is assigned either selected or not selected, and transform operations, such as rotation or translation, act only on selected files. On the other hand, every atom in a molecule is also assigned either selected or not selected, independently of whether the molecule itself is selected or not. Operations that modify display models or colors work for selected atoms. To see this, choose the [Display] – [Spacefill] menu item. Then the both molecules are displayed with the space fill model because all atoms are initially selected. In the same way, if you choose the [Colors] – [Monochrome] menu item, the both molecules are colored white. These operations are independent of the status of ‘select’ checkboxes mentioned above. 

Let us next try a more detailed operation. Type ‘select *@2’ in the command line area and press Enter key. This command means to select all atoms contained in the file 2 (the usage of the select command is summarized in the reference manual included in the binary distribution of jV3). Subsequently, choose the [Display] – [Cartoon] menu item. As a result, only the molecule 2 is displayed in the cartoon model. Furthermore select the [Colors] – [Structure] menu item, and each residue of the molecule 2 is colored according to its secondary structure type (see Figure 3). 

In order to reproduce the same view as that in Figure 3, first execute ‘reset’ command. It restores the position of the viewpoint and the transform of every file to the initial state. Note that the command line interface tries to complement a command word when the Tab key is pressed. If you enter ‘res’ to the command line and subsequently press the Tab key, the command ‘reset’ is automatically entered. Next set the both ‘select’ checkboxes on, and execute ‘translate z 100’ command. This command means to translate the molecules along the z-axis by 100 angstroms.

[[File:Tutorial_fig3.jpg|thumb|Figure 3: An example of molecular images.|center|500px]]

== Displaying polygons ==
In addition to molecules, arbitrary shapes described by polygons can be read in and displayed together, where the polygon file is an XML file, whose document type is described in the section 6. Here, we use ’http://ef-site.hgc.jp/eF-site/jV/1yec.surface.gz’ as an example. This polygon file represents a molecular surface of the molecule 2 (1yec) and the surface is colored according to the electrostatic potential and the hydrophobicity. It is assumed that the current image is the same as that in Figure 3. Then, open the open-remote dialog by choosing the [File] – [Open – Remote] – [Polygon] menu item, enter the above URL to the text field at the top of the dialog, and click the 'OK' button. As a result, the polygon is loaded, displayed and assigned file ID 3. 

Note that the polygon is displayed at the different position from the molecule 2 since the molecule 2 is translated. However, because the polygon and the molecule 2 are described by the same coordinates in their files, their images can be exactly superposed by executing ‘fit 3 2’ from the command line, where the ‘fit’ command performs the copy of the transform matrix. Finally, the image in Figure 4 appears.

[[File:Tutorial_fig4.jpg|thumb|Figure4: An example of polygon images.|center|500px]]

You can control the transparency rate of polygons. Try ’set transparency 0.5’ from the command line, where 0.5 stands for 50% transparency. To restore the image, execute ‘reset transparency’ or ‘set transparency 0’. In the same sense as each atom of a molecule, each vertex of a polygon is assigned either selected or not selected. All vertices are selected in the initial state. Execute a command ’displayvertex off’ and all vertices become invisible. Next execute ’selectvertex within(10.0, 1&amp;*H@2)’, where this means to select vertices that exist within 10 angstroms from each atom that belongs to the first residue of the ‘H’ chain of the molecule 2. Subsequently execute ’displayvertex on’. As a result, only the selected vertices are appeared. The usage of the selectvertex command is summarized in the [[Command List]].

== Working with xPSSS ==
Functional site information on a molecule stored at xPSSS (xml-based Protein Structure Search Service) is available in jV3. Before trying this, let us close the molecule 2 and the polygon 3 to make the situation simple. Select the [File] – [Close] – [2. 1yec.pdb] and [File] – [Close] – [3. 1yec.surface.gz] menu items sequentially. Then execute a ‘reset’ command and the transform of the molecule 1 and the position of the viewpoint are initialized. 

Next, confirm that the ‘select’ checkbox of the file 1 is checked, and try a ‘show xps3’ command. The functional site information of the molecule ‘12as’ is read from the xPSSS and ‘type’ and ‘subtype’ keywords for each functional site are listed. These keywords can be used to select a set of atoms. For example, if a keyword ‘CATRES’ exists (probably it does), the command ‘select xps3:CATRES’ selects the corresponding atoms. 

In addition, gene ontology information can be obtained from the xPSSS. The gene ontology information for the molecule 12as is displayed by the command ’show godata’. Similar operations can be applied to other external databases on the Internet provided that the external database supports the interface that jV3 requires. See the [[Functional site information for molecules]] for details.

== Animation ==
The animation of molecules can be performed in jV3. The animation file takes the PDB format, where the MODEL line divides each frame. Let us open an animation file ’http://ef-site.hgc.jp/eF-site/jV/anim.pdb.gz’ as an example from the open-remote dialog shown by selecting the [File] – [Open – Remote] – [Animation] menu item. When an animation file is loaded to the application, the first frame is automatically displayed in the wire frame model. You can start the animation by using the animation-control dialog that is shown by choosing the [Options] – [Animation] menu item. The dialog provides operations such as start and stop of the animation, selection of the animation mode, and adjustment of the speed. Some sample figures of the dialog are shown in the [[GUI#Animation_control_dialog]]

== Saving your work ==
While in your work, you can create a script file that contains a set of commands that reproduces the current work by using the [File] – [Save] – [Script] menu item. The script file can be loaded by the [File] – [Open – Local] – [Script] menu item. On the other hand, the [File] – [Save] – [PDB] menu item enables to save a molecule to a PDB format file with the coordinates of the atoms being transformed according to the current image. Here, only one molecule must be selected and only selected atoms in the molecule are saved. The other two menu items in the [File] – [Save] menu, [PNG] and [JPEG], save the current screen image to an image file in the PNG and JPEG format, respectively. The created image file has the same size as that of the 3D-display panel in the application.

== Terminating the application ==
The application is terminated when the [File] – [Exit] menu item is chosen or the application window is closed by the way your operation system provides. You can also quit the application by executing ‘exit’ or ‘quit’ command.</text>
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== Starting up ==
It is assumed that Java Runtime Environment and JOGL have been appropriately installed. Once you extract the binary distribution file of jV3, the directory of the name, jV_(version), is generated (Ex. jV_3_6_2). The version is assumed to be 3_6_x hereafter. The application starts up by double-clicking the file ‘jv_3_6_x.jar’ in the jV_3_6_x directory or executing the following command from the command line interface.
 java –jar jv_3_6_x.jar
Figure 1 shows the start-up screen. The window has a 3-panel structure, and the upper-left panel with the black background is a 3D image display area. The status of files that have been loaded to the application is shown in the upper-right panel and the lower panel is a command-input and a message-output area.
[[File:Tutorial_fig1.jpg|thumb|Figure 1: Start-up screen|center|500px]]

== Displaying molecules ==
If you are working in the environment that is getting on the Internet and know the PDB ID of the molecule that you want to display, the simplest way is as follows. A dialog shown in Figure 2 is opened by selecting the [File] – [Open – Remote] – [PDB ID] menu item. Enter a PDB ID '12as', for example, to the text field and click the 'OK' button, then the PDBML file is read through the Internet and the molecule is displayed. A molecule is displayed in a wire frame model with colored by atom type in the initial state.

[[File:Fig2.jpg|thumb|Figure 2: Dialog to open the molecule specified by PDB ID|center|200px]]

Let us next attempt to load an arbitrary file on the Internet. Here we use 'http://ef-site.hgc.jp/eF-site/jV/1yec.pdb' as an example. The file is a conventional PDB file whose PDB ID is 1yec. In this case we choose the [File] – [Open – Remote] – [PDB] menu item. Then the open-remote dialog appears. Enter the above URL to the text field at the top of the dialog and click the 'OK' button and the molecule is read in and displayed. In jV3, each molecule is displayed according to the space coordination described in its file. Therefore, when loading and displaying more than one molecule together, they can be viewed with an appropriate separation in some cases; however, they may be displayed far separately or may be overlapped depending on the combination. In any case, when adding a new file, the position of the viewpoint is automatically controlled for the whole to be displayed.

The coordinate system is the right hand system with the x-y plane being on the screen (the x-axis is a horizontal line with positive values to the right and the y-axis is a vertical line with positive values up). Although, the above examples are about operations for remote files, a PDB file on your local hard disk can also be opened from the [File] – [Open – Local] – [PDB] menu item.

== Operating molecules ==
Interactive mouse operations are possible for 3D images. By left-dragging the mouse on the 3D-display panel, molecules are rotated around the x-axis or y-axis. By left-dragging the mouse while holding the Shift key or Alt key on the keyboard, molecules are translated along the z-axis. All mouse operations are as follows (as for the Macintosh environment, the Command key + left-drag substitutes for the right-drag).

{| border="1"
 ! Mouse operations !! Actions
 |-
 | Left-drag || The image is rotated around the x (for a vertical motion) and y (for a horizontal motion) axes.
 |-
 | Right-drag || The image is translated on the x-y plane.
 |-
 | [Alt or Shift] + left-drag || The image is translated along the z-axis.
 |-
 | [Alt or Shift] + right-drag || The image is rotated around the z-axis.
 |-
 | [Ctrl] + left-drag || The z-clipping plane is shifted when [Option]-[Slab] is checked.
 |-
 | Left-click || An atom of the molecule displayed on the screen is picked.
 |}

In the upper-right panel in the application window (see Figure 3), the file names that have been loaded to the application are listed, where sequential integers are automatically assigned to the individual file. Each integer is a file ID that can be used to specify the file in the command line interface. In addition, two checkboxes are attached to each file. If you change the status of a ‘display’ checkbox, the corresponding molecule is switched to be displayed or not to be displayed. If you change the status of a ‘select’ checkbox, the corresponding molecule is switched to be a target of the mouse operations or not. For example, set the both ‘display’ checkboxes on, and the both ‘select’ checkboxes off. In this case, either molecule does not move against mouse operations. 

Subsequently set the ‘select’ checkbox of file 1 on. In this case, mouse operations work for the molecule 1. Thus, each file is assigned either selected or not selected, and transform operations, such as rotation or translation, act only on selected files. On the other hand, every atom in a molecule is also assigned either selected or not selected, independently of whether the molecule itself is selected or not. Operations that modify display models or colors work for selected atoms. To see this, choose the [Display] – [Spacefill] menu item. Then the both molecules are displayed with the space fill model because all atoms are initially selected. In the same way, if you choose the [Colors] – [Monochrome] menu item, the both molecules are colored white. These operations are independent of the status of ‘select’ checkboxes mentioned above. 

Let us next try a more detailed operation. Type ‘select *@2’ in the command line area and press Enter key. This command means to select all atoms contained in the file 2 (the usage of the select command is summarized in the reference manual included in the binary distribution of jV3). Subsequently, choose the [Display] – [Cartoon] menu item. As a result, only the molecule 2 is displayed in the cartoon model. Furthermore select the [Colors] – [Structure] menu item, and each residue of the molecule 2 is colored according to its secondary structure type (see Figure 3). 

In order to reproduce the same view as that in Figure 3, first execute ‘reset’ command. It restores the position of the viewpoint and the transform of every file to the initial state. Note that the command line interface tries to complement a command word when the Tab key is pressed. If you enter ‘res’ to the command line and subsequently press the Tab key, the command ‘reset’ is automatically entered. Next set the both ‘select’ checkboxes on, and execute ‘translate z 100’ command. This command means to translate the molecules along the z-axis by 100 angstroms.

[[File:Tutorial_fig3.jpg|thumb|Figure 3: An example of molecular images.|center|500px]]

== Displaying polygons ==
In addition to molecules, arbitrary shapes described by polygons can be read in and displayed together, where the polygon file is an XML file, whose document type is described in the section 6. Here, we use ’http://ef-site.hgc.jp/eF-site/jV/1yec.surface.gz’ as an example. This polygon file represents a molecular surface of the molecule 2 (1yec) and the surface is colored according to the electrostatic potential and the hydrophobicity. It is assumed that the current image is the same as that in Figure 3. Then, open the open-remote dialog by choosing the [File] – [Open – Remote] – [Polygon] menu item, enter the above URL to the text field at the top of the dialog, and click the 'OK' button. As a result, the polygon is loaded, displayed and assigned file ID 3. 

Note that the polygon is displayed at the different position from the molecule 2 since the molecule 2 is translated. However, because the polygon and the molecule 2 are described by the same coordinates in their files, their images can be exactly superposed by executing ‘fit 3 2’ from the command line, where the ‘fit’ command performs the copy of the transform matrix. Finally, the image in Figure 4 appears.

[[File:Tutorial_fig4.jpg|thumb|Figure4: An example of polygon images.|center|500px]]

You can control the transparency rate of polygons. Try ’set transparency 0.5’ from the command line, where 0.5 stands for 50% transparency. To restore the image, execute ‘reset transparency’ or ‘set transparency 0’. In the same sense as each atom of a molecule, each vertex of a polygon is assigned either selected or not selected. All vertices are selected in the initial state. Execute a command ’displayvertex off’ and all vertices become invisible. Next execute ’selectvertex within(10.0, 1&amp;*H@2)’, where this means to select vertices that exist within 10 angstroms from each atom that belongs to the first residue of the ‘H’ chain of the molecule 2. Subsequently execute ’displayvertex on’. As a result, only the selected vertices are appeared. The usage of the selectvertex command is summarized in the [[Command List]].

== Working with xPSSS ==
Functional site information on a molecule stored at xPSSS (xml-based Protein Structure Search Service) is available in jV3. Before trying this, let us close the molecule 2 and the polygon 3 to make the situation simple. Select the [File] – [Close] – [2. 1yec.pdb] and [File] – [Close] – [3. 1yec.surface.gz] menu items sequentially. Then execute a ‘reset’ command and the transform of the molecule 1 and the position of the viewpoint are initialized. 

Next, confirm that the ‘select’ checkbox of the file 1 is checked, and try a ‘show xps3’ command. The functional site information of the molecule ‘12as’ is read from the xPSSS and ‘type’ and ‘subtype’ keywords for each functional site are listed. These keywords can be used to select a set of atoms. For example, if a keyword ‘CATRES’ exists (probably it does), the command ‘select xps3:CATRES’ selects the corresponding atoms. 

In addition, gene ontology information can be obtained from the xPSSS. The gene ontology information for the molecule 12as is displayed by the command ’show godata’. Similar operations can be applied to other external databases on the Internet provided that the external database supports the interface that jV3 requires. See the [[Functional site information for molecules]] for details.

== Animation ==
The animation of molecules can be performed in jV3. The animation file takes the PDB format, where the MODEL line divides each frame. Let us open an animation file ’http://ef-site.hgc.jp/eF-site/jV/anim.pdb.gz’ as an example from the open-remote dialog shown by selecting the [File] – [Open – Remote] – [Animation] menu item. When an animation file is loaded to the application, the first frame is automatically displayed in the wire frame model. You can start the animation by using the animation-control dialog that is shown by choosing the [Options] – [Animation] menu item. The dialog provides operations such as start and stop of the animation, selection of the animation mode, and adjustment of the speed. Some sample figures of the dialog are shown in the [[GUI#Animation_control_dialog]]

== Saving your work ==
While in your work, you can create a script file that contains a set of commands that reproduces the current work by using the [File] – [Save] – [Script] menu item. The script file can be loaded by the [File] – [Open – Local] – [Script] menu item. On the other hand, the [File] – [Save] – [PDB] menu item enables to save a molecule to a PDB format file with the coordinates of the atoms being transformed according to the current image. Here, only one molecule must be selected and only selected atoms in the molecule are saved. The other two menu items in the [File] – [Save] menu, [PNG] and [JPEG], save the current screen image to an image file in the PNG and JPEG format, respectively. The created image file has the same size as that of the 3D-display panel in the application.

== Terminating the application ==
The application is terminated when the [File] – [Exit] menu item is chosen or the application window is closed by the way your operation system provides. You can also quit the application by executing ‘exit’ or ‘quit’ command.</text>
    <sha1>c371c0090b42832c102fc4c0cbbdb54744d45b5c</sha1>
  </revision>
  <revision>
    <id>441</id>
    <parentid>440</parentid>
    <timestamp>2010-12-15T02:48:18Z</timestamp>
    <contributor>
      <username>IMSsato</username>
      <id>4</id>
    </contributor>
    <comment>/* Operating molecules */</comment>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="12111" xml:space="preserve">{| style="float:right"
 |__TOC__
 |}
== Starting up ==
It is assumed that Java Runtime Environment and JOGL have been appropriately installed. Once you extract the binary distribution file of jV3, the directory of the name, jV_(version), is generated (Ex. jV_3_6_2). The version is assumed to be 3_6_x hereafter. The application starts up by double-clicking the file ‘jv_3_6_x.jar’ in the jV_3_6_x directory or executing the following command from the command line interface.
 java –jar jv_3_6_x.jar
Figure 1 shows the start-up screen. The window has a 3-panel structure, and the upper-left panel with the black background is a 3D image display area. The status of files that have been loaded to the application is shown in the upper-right panel and the lower panel is a command-input and a message-output area.
[[File:Tutorial_fig1.jpg|thumb|Figure 1: Start-up screen|center|500px]]

== Displaying molecules ==
If you are working in the environment that is getting on the Internet and know the PDB ID of the molecule that you want to display, the simplest way is as follows. A dialog shown in Figure 2 is opened by selecting the [File] – [Open – Remote] – [PDB ID] menu item. Enter a PDB ID '12as', for example, to the text field and click the 'OK' button, then the PDBML file is read through the Internet and the molecule is displayed. A molecule is displayed in a wire frame model with colored by atom type in the initial state.

[[File:Fig2.jpg|thumb|Figure 2: Dialog to open the molecule specified by PDB ID|center|200px]]

Let us next attempt to load an arbitrary file on the Internet. Here we use 'http://ef-site.hgc.jp/eF-site/jV/1yec.pdb' as an example. The file is a conventional PDB file whose PDB ID is 1yec. In this case we choose the [File] – [Open – Remote] – [PDB] menu item. Then the open-remote dialog appears. Enter the above URL to the text field at the top of the dialog and click the 'OK' button and the molecule is read in and displayed. In jV3, each molecule is displayed according to the space coordination described in its file. Therefore, when loading and displaying more than one molecule together, they can be viewed with an appropriate separation in some cases; however, they may be displayed far separately or may be overlapped depending on the combination. In any case, when adding a new file, the position of the viewpoint is automatically controlled for the whole to be displayed.

The coordinate system is the right hand system with the x-y plane being on the screen (the x-axis is a horizontal line with positive values to the right and the y-axis is a vertical line with positive values up). Although, the above examples are about operations for remote files, a PDB file on your local hard disk can also be opened from the [File] – [Open – Local] – [PDB] menu item.

== Operating molecules ==
Interactive mouse operations are possible for 3D images. By left-dragging the mouse on the 3D-display panel, molecules are rotated around the x-axis or y-axis. By left-dragging the mouse while holding the Shift key on the keyboard, molecules are translated along the z-axis. All mouse operations are as follows (as for the Macintosh environment, the Command key + left-drag substitutes for the right-drag).

{| border="1"
 ! Mouse operations !! Actions
 |-
 | Left-drag || The image is rotated around the x (for a vertical motion) and y (for a horizontal motion) axes.
 |-
 | Right-drag || The image is translated on the x-y plane.
 |-
 | [Shift] + left-drag || The image is translated along the z-axis.
 |-
 | [Shift] + right-drag || The image is rotated around the z-axis.
 |-
 | [Ctrl] + left-drag || The z-clipping plane is shifted when [Option]-[Slab] is checked.
 |-
 | Left-click || An atom of the molecule displayed on the screen is picked.
 |}

In the upper-right panel in the application window (see Figure 3), the file names that have been loaded to the application are listed, where sequential integers are automatically assigned to the individual file. Each integer is a file ID that can be used to specify the file in the command line interface. In addition, three checkboxes are attached to each file. If you change the status of a ‘Disp’ checkbox, the corresponding molecule is switched to be displayed or not to be displayed. If you change the status of a ‘Mouse’ checkbox, the corresponding molecule is switched to be a target of the mouse operations or not. For example, set the both ‘Disp’ checkboxes on, and the both ‘Mouse’ checkboxes off. In this case, either molecule does not move against mouse operations. 

Subsequently set the ‘Mouse’ checkbox of file 1 on. In this case, mouse operations work for the molecule 1. Thus, each file is assigned either selected or not selected, and transform operations, such as rotation or translation, act only on selected files. On the other hand, every atom in a molecule is also assigned either selected or not selected, independently of whether the molecule itself is selected or not. Operations that modify display models or colors work for selected atoms. To see this, choose the [Display] – [Spacefill] menu item. Then the both molecules are displayed with the space fill model because all atoms are initially selected. In the same way, if you choose the [Colors] – [Monochrome] menu item, the both molecules are colored white. A ‘Sel’ checkbox selects or disselects all atoms in each file. 

Let us next try a more detailed operation. Type ‘select *@2’ in the command line area and press Enter key. This command means to select all atoms contained in the file 2 (the usage of the [[Command_List#select|select command]] is summarized in the reference manual). Subsequently, choose the [Display] – [Cartoon] menu item. As a result, only the molecule 2 is displayed in the cartoon model. Furthermore select the [Colors] – [Structure] menu item, and each residue of the molecule 2 is colored according to its secondary structure type (see Figure 3). 

In order to reproduce the same view as that in Figure 3, first execute ‘reset’ command. It restores the position of the viewpoint and the transform of every file to the initial state. Note that the command line interface tries to complement a command word when the Tab key is pressed. If you enter ‘res’ to the command line and subsequently press the Tab key, the command ‘reset’ is automatically entered. Next set the both ‘Mouse’ checkboxes on, and execute ‘translate z 100’ command. This command means to translate the molecules along the z-axis by 100 angstroms.

[[File:Tutorial_fig3.jpg|thumb|Figure 3: An example of molecular images.|center|500px]]

== Displaying polygons ==
In addition to molecules, arbitrary shapes described by polygons can be read in and displayed together, where the polygon file is an XML file, whose document type is described in the section 6. Here, we use ’http://ef-site.hgc.jp/eF-site/jV/1yec.surface.gz’ as an example. This polygon file represents a molecular surface of the molecule 2 (1yec) and the surface is colored according to the electrostatic potential and the hydrophobicity. It is assumed that the current image is the same as that in Figure 3. Then, open the open-remote dialog by choosing the [File] – [Open – Remote] – [Polygon] menu item, enter the above URL to the text field at the top of the dialog, and click the 'OK' button. As a result, the polygon is loaded, displayed and assigned file ID 3. 

Note that the polygon is displayed at the different position from the molecule 2 since the molecule 2 is translated. However, because the polygon and the molecule 2 are described by the same coordinates in their files, their images can be exactly superposed by executing ‘fit 3 2’ from the command line, where the ‘fit’ command performs the copy of the transform matrix. Finally, the image in Figure 4 appears.

[[File:Tutorial_fig4.jpg|thumb|Figure4: An example of polygon images.|center|500px]]

You can control the transparency rate of polygons. Try ’set transparency 0.5’ from the command line, where 0.5 stands for 50% transparency. To restore the image, execute ‘reset transparency’ or ‘set transparency 0’. In the same sense as each atom of a molecule, each vertex of a polygon is assigned either selected or not selected. All vertices are selected in the initial state. Execute a command ’displayvertex off’ and all vertices become invisible. Next execute ’selectvertex within(10.0, 1&amp;*H@2)’, where this means to select vertices that exist within 10 angstroms from each atom that belongs to the first residue of the ‘H’ chain of the molecule 2. Subsequently execute ’displayvertex on’. As a result, only the selected vertices are appeared. The usage of the selectvertex command is summarized in the [[Command List]].

== Working with xPSSS ==
Functional site information on a molecule stored at xPSSS (xml-based Protein Structure Search Service) is available in jV3. Before trying this, let us close the molecule 2 and the polygon 3 to make the situation simple. Select the [File] – [Close] – [2. 1yec.pdb] and [File] – [Close] – [3. 1yec.surface.gz] menu items sequentially. Then execute a ‘reset’ command and the transform of the molecule 1 and the position of the viewpoint are initialized. 

Next, confirm that the ‘select’ checkbox of the file 1 is checked, and try a ‘show xps3’ command. The functional site information of the molecule ‘12as’ is read from the xPSSS and ‘type’ and ‘subtype’ keywords for each functional site are listed. These keywords can be used to select a set of atoms. For example, if a keyword ‘CATRES’ exists (probably it does), the command ‘select xps3:CATRES’ selects the corresponding atoms. 

In addition, gene ontology information can be obtained from the xPSSS. The gene ontology information for the molecule 12as is displayed by the command ’show godata’. Similar operations can be applied to other external databases on the Internet provided that the external database supports the interface that jV3 requires. See the [[Functional site information for molecules]] for details.

== Animation ==
The animation of molecules can be performed in jV3. The animation file takes the PDB format, where the MODEL line divides each frame. Let us open an animation file ’http://ef-site.hgc.jp/eF-site/jV/anim.pdb.gz’ as an example from the open-remote dialog shown by selecting the [File] – [Open – Remote] – [Animation] menu item. When an animation file is loaded to the application, the first frame is automatically displayed in the wire frame model. You can start the animation by using the animation-control dialog that is shown by choosing the [Options] – [Animation] menu item. The dialog provides operations such as start and stop of the animation, selection of the animation mode, and adjustment of the speed. Some sample figures of the dialog are shown in the [[GUI#Animation_control_dialog]]

== Saving your work ==
While in your work, you can create a script file that contains a set of commands that reproduces the current work by using the [File] – [Save] – [Script] menu item. The script file can be loaded by the [File] – [Open – Local] – [Script] menu item. On the other hand, the [File] – [Save] – [PDB] menu item enables to save a molecule to a PDB format file with the coordinates of the atoms being transformed according to the current image. Here, only one molecule must be selected and only selected atoms in the molecule are saved. The other two menu items in the [File] – [Save] menu, [PNG] and [JPEG], save the current screen image to an image file in the PNG and JPEG format, respectively. The created image file has the same size as that of the 3D-display panel in the application.

== Terminating the application ==
The application is terminated when the [File] – [Exit] menu item is chosen or the application window is closed by the way your operation system provides. You can also quit the application by executing ‘exit’ or ‘quit’ command.</text>
    <sha1>074e831b8ba1a0c79e7e8053505070a08e8357dd</sha1>
  </revision>
  <revision>
    <id>442</id>
    <parentid>441</parentid>
    <timestamp>2010-12-15T02:52:55Z</timestamp>
    <contributor>
      <username>IMSsato</username>
      <id>4</id>
    </contributor>
    <comment>/* Displaying polygons */</comment>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="12135" xml:space="preserve">{| style="float:right"
 |__TOC__
 |}
== Starting up ==
It is assumed that Java Runtime Environment and JOGL have been appropriately installed. Once you extract the binary distribution file of jV3, the directory of the name, jV_(version), is generated (Ex. jV_3_6_2). The version is assumed to be 3_6_x hereafter. The application starts up by double-clicking the file ‘jv_3_6_x.jar’ in the jV_3_6_x directory or executing the following command from the command line interface.
 java –jar jv_3_6_x.jar
Figure 1 shows the start-up screen. The window has a 3-panel structure, and the upper-left panel with the black background is a 3D image display area. The status of files that have been loaded to the application is shown in the upper-right panel and the lower panel is a command-input and a message-output area.
[[File:Tutorial_fig1.jpg|thumb|Figure 1: Start-up screen|center|500px]]

== Displaying molecules ==
If you are working in the environment that is getting on the Internet and know the PDB ID of the molecule that you want to display, the simplest way is as follows. A dialog shown in Figure 2 is opened by selecting the [File] – [Open – Remote] – [PDB ID] menu item. Enter a PDB ID '12as', for example, to the text field and click the 'OK' button, then the PDBML file is read through the Internet and the molecule is displayed. A molecule is displayed in a wire frame model with colored by atom type in the initial state.

[[File:Fig2.jpg|thumb|Figure 2: Dialog to open the molecule specified by PDB ID|center|200px]]

Let us next attempt to load an arbitrary file on the Internet. Here we use 'http://ef-site.hgc.jp/eF-site/jV/1yec.pdb' as an example. The file is a conventional PDB file whose PDB ID is 1yec. In this case we choose the [File] – [Open – Remote] – [PDB] menu item. Then the open-remote dialog appears. Enter the above URL to the text field at the top of the dialog and click the 'OK' button and the molecule is read in and displayed. In jV3, each molecule is displayed according to the space coordination described in its file. Therefore, when loading and displaying more than one molecule together, they can be viewed with an appropriate separation in some cases; however, they may be displayed far separately or may be overlapped depending on the combination. In any case, when adding a new file, the position of the viewpoint is automatically controlled for the whole to be displayed.

The coordinate system is the right hand system with the x-y plane being on the screen (the x-axis is a horizontal line with positive values to the right and the y-axis is a vertical line with positive values up). Although, the above examples are about operations for remote files, a PDB file on your local hard disk can also be opened from the [File] – [Open – Local] – [PDB] menu item.

== Operating molecules ==
Interactive mouse operations are possible for 3D images. By left-dragging the mouse on the 3D-display panel, molecules are rotated around the x-axis or y-axis. By left-dragging the mouse while holding the Shift key on the keyboard, molecules are translated along the z-axis. All mouse operations are as follows (as for the Macintosh environment, the Command key + left-drag substitutes for the right-drag).

{| border="1"
 ! Mouse operations !! Actions
 |-
 | Left-drag || The image is rotated around the x (for a vertical motion) and y (for a horizontal motion) axes.
 |-
 | Right-drag || The image is translated on the x-y plane.
 |-
 | [Shift] + left-drag || The image is translated along the z-axis.
 |-
 | [Shift] + right-drag || The image is rotated around the z-axis.
 |-
 | [Ctrl] + left-drag || The z-clipping plane is shifted when [Option]-[Slab] is checked.
 |-
 | Left-click || An atom of the molecule displayed on the screen is picked.
 |}

In the upper-right panel in the application window (see Figure 3), the file names that have been loaded to the application are listed, where sequential integers are automatically assigned to the individual file. Each integer is a file ID that can be used to specify the file in the command line interface. In addition, three checkboxes are attached to each file. If you change the status of a ‘Disp’ checkbox, the corresponding molecule is switched to be displayed or not to be displayed. If you change the status of a ‘Mouse’ checkbox, the corresponding molecule is switched to be a target of the mouse operations or not. For example, set the both ‘Disp’ checkboxes on, and the both ‘Mouse’ checkboxes off. In this case, either molecule does not move against mouse operations. 

Subsequently set the ‘Mouse’ checkbox of file 1 on. In this case, mouse operations work for the molecule 1. Thus, each file is assigned either selected or not selected, and transform operations, such as rotation or translation, act only on selected files. On the other hand, every atom in a molecule is also assigned either selected or not selected, independently of whether the molecule itself is selected or not. Operations that modify display models or colors work for selected atoms. To see this, choose the [Display] – [Spacefill] menu item. Then the both molecules are displayed with the space fill model because all atoms are initially selected. In the same way, if you choose the [Colors] – [Monochrome] menu item, the both molecules are colored white. A ‘Sel’ checkbox selects or disselects all atoms in each file. 

Let us next try a more detailed operation. Type ‘select *@2’ in the command line area and press Enter key. This command means to select all atoms contained in the file 2 (the usage of the [[Command_List#select|select command]] is summarized in the reference manual). Subsequently, choose the [Display] – [Cartoon] menu item. As a result, only the molecule 2 is displayed in the cartoon model. Furthermore select the [Colors] – [Structure] menu item, and each residue of the molecule 2 is colored according to its secondary structure type (see Figure 3). 

In order to reproduce the same view as that in Figure 3, first execute ‘reset’ command. It restores the position of the viewpoint and the transform of every file to the initial state. Note that the command line interface tries to complement a command word when the Tab key is pressed. If you enter ‘res’ to the command line and subsequently press the Tab key, the command ‘reset’ is automatically entered. Next set the both ‘Mouse’ checkboxes on, and execute ‘translate z 100’ command. This command means to translate the molecules along the z-axis by 100 angstroms.

[[File:Tutorial_fig3.jpg|thumb|Figure 3: An example of molecular images.|center|500px]]

== Displaying polygons ==
In addition to molecules, arbitrary shapes described by polygons can be read in and displayed together, where the polygon file is an XML file, whose document type is described in the section 6. Here, we use ’http://ef-site.hgc.jp/eF-site/jV/1yec.surface.gz’ as an example. This polygon file represents a molecular surface of the molecule 2 (1yec) and the surface is colored according to the electrostatic potential and the hydrophobicity. It is assumed that the current image is the same as that in Figure 3. Then, open the open-remote dialog by choosing the [File] – [Open – Remote] – [Polygon] menu item, enter the above URL to the text field at the top of the dialog, and click the 'OK' button. As a result, the polygon is loaded, displayed and assigned file ID 3. 

Note that the polygon is displayed at the different position from the molecule 2 since the molecule 2 is translated. However, because the polygon and the molecule 2 are described by the same coordinates in their files, their images can be exactly superposed by executing ‘fit 3 2’ from the command line, where the ‘fit’ command performs the copy of the transform matrix. Finally, the image in Figure 4 appears.

[[File:Tutorial_fig4.jpg|thumb|Figure4: An example of polygon images.|center|500px]]

You can control the transparency rate of polygons. Try ’set transparency 0.5’ from the command line, where 0.5 stands for 50% transparency. To restore the image, execute ‘reset transparency’ or ‘set transparency 0’. In the same sense as each atom of a molecule, each vertex of a polygon is assigned either selected or not selected. All vertices are selected in the initial state. Execute a command ’displayvertex off’ and all vertices become invisible. Next execute ’selectvertex within(10.0, 1&amp;*H@2)’, where this means to select vertices that exist within 10 angstroms from each atom that belongs to the first residue of the ‘H’ chain of the molecule 2. Subsequently execute ’displayvertex on’. As a result, only the selected vertices appear. The usage of the [[Command List#selectvertex|selectvertex command]] is summarized in the reference manual.

== Working with xPSSS ==
Functional site information on a molecule stored at xPSSS (xml-based Protein Structure Search Service) is available in jV3. Before trying this, let us close the molecule 2 and the polygon 3 to make the situation simple. Select the [File] – [Close] – [2. 1yec.pdb] and [File] – [Close] – [3. 1yec.surface.gz] menu items sequentially. Then execute a ‘reset’ command and the transform of the molecule 1 and the position of the viewpoint are initialized. 

Next, confirm that the ‘select’ checkbox of the file 1 is checked, and try a ‘show xps3’ command. The functional site information of the molecule ‘12as’ is read from the xPSSS and ‘type’ and ‘subtype’ keywords for each functional site are listed. These keywords can be used to select a set of atoms. For example, if a keyword ‘CATRES’ exists (probably it does), the command ‘select xps3:CATRES’ selects the corresponding atoms. 

In addition, gene ontology information can be obtained from the xPSSS. The gene ontology information for the molecule 12as is displayed by the command ’show godata’. Similar operations can be applied to other external databases on the Internet provided that the external database supports the interface that jV3 requires. See the [[Functional site information for molecules]] for details.

== Animation ==
The animation of molecules can be performed in jV3. The animation file takes the PDB format, where the MODEL line divides each frame. Let us open an animation file ’http://ef-site.hgc.jp/eF-site/jV/anim.pdb.gz’ as an example from the open-remote dialog shown by selecting the [File] – [Open – Remote] – [Animation] menu item. When an animation file is loaded to the application, the first frame is automatically displayed in the wire frame model. You can start the animation by using the animation-control dialog that is shown by choosing the [Options] – [Animation] menu item. The dialog provides operations such as start and stop of the animation, selection of the animation mode, and adjustment of the speed. Some sample figures of the dialog are shown in the [[GUI#Animation_control_dialog]]

== Saving your work ==
While in your work, you can create a script file that contains a set of commands that reproduces the current work by using the [File] – [Save] – [Script] menu item. The script file can be loaded by the [File] – [Open – Local] – [Script] menu item. On the other hand, the [File] – [Save] – [PDB] menu item enables to save a molecule to a PDB format file with the coordinates of the atoms being transformed according to the current image. Here, only one molecule must be selected and only selected atoms in the molecule are saved. The other two menu items in the [File] – [Save] menu, [PNG] and [JPEG], save the current screen image to an image file in the PNG and JPEG format, respectively. The created image file has the same size as that of the 3D-display panel in the application.

== Terminating the application ==
The application is terminated when the [File] – [Exit] menu item is chosen or the application window is closed by the way your operation system provides. You can also quit the application by executing ‘exit’ or ‘quit’ command.</text>
    <sha1>0db0130d9ec1720a815886892c60578e253d5fcd</sha1>
  </revision>
  <revision>
    <id>443</id>
    <parentid>442</parentid>
    <timestamp>2010-12-15T02:59:56Z</timestamp>
    <contributor>
      <username>IMSsato</username>
      <id>4</id>
    </contributor>
    <comment>/* Working with xPSSS */</comment>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="12115" xml:space="preserve">{| style="float:right"
 |__TOC__
 |}
== Starting up ==
It is assumed that Java Runtime Environment and JOGL have been appropriately installed. Once you extract the binary distribution file of jV3, the directory of the name, jV_(version), is generated (Ex. jV_3_6_2). The version is assumed to be 3_6_x hereafter. The application starts up by double-clicking the file ‘jv_3_6_x.jar’ in the jV_3_6_x directory or executing the following command from the command line interface.
 java –jar jv_3_6_x.jar
Figure 1 shows the start-up screen. The window has a 3-panel structure, and the upper-left panel with the black background is a 3D image display area. The status of files that have been loaded to the application is shown in the upper-right panel and the lower panel is a command-input and a message-output area.
[[File:Tutorial_fig1.jpg|thumb|Figure 1: Start-up screen|center|500px]]

== Displaying molecules ==
If you are working in the environment that is getting on the Internet and know the PDB ID of the molecule that you want to display, the simplest way is as follows. A dialog shown in Figure 2 is opened by selecting the [File] – [Open – Remote] – [PDB ID] menu item. Enter a PDB ID '12as', for example, to the text field and click the 'OK' button, then the PDBML file is read through the Internet and the molecule is displayed. A molecule is displayed in a wire frame model with colored by atom type in the initial state.

[[File:Fig2.jpg|thumb|Figure 2: Dialog to open the molecule specified by PDB ID|center|200px]]

Let us next attempt to load an arbitrary file on the Internet. Here we use 'http://ef-site.hgc.jp/eF-site/jV/1yec.pdb' as an example. The file is a conventional PDB file whose PDB ID is 1yec. In this case we choose the [File] – [Open – Remote] – [PDB] menu item. Then the open-remote dialog appears. Enter the above URL to the text field at the top of the dialog and click the 'OK' button and the molecule is read in and displayed. In jV3, each molecule is displayed according to the space coordination described in its file. Therefore, when loading and displaying more than one molecule together, they can be viewed with an appropriate separation in some cases; however, they may be displayed far separately or may be overlapped depending on the combination. In any case, when adding a new file, the position of the viewpoint is automatically controlled for the whole to be displayed.

The coordinate system is the right hand system with the x-y plane being on the screen (the x-axis is a horizontal line with positive values to the right and the y-axis is a vertical line with positive values up). Although, the above examples are about operations for remote files, a PDB file on your local hard disk can also be opened from the [File] – [Open – Local] – [PDB] menu item.

== Operating molecules ==
Interactive mouse operations are possible for 3D images. By left-dragging the mouse on the 3D-display panel, molecules are rotated around the x-axis or y-axis. By left-dragging the mouse while holding the Shift key on the keyboard, molecules are translated along the z-axis. All mouse operations are as follows (as for the Macintosh environment, the Command key + left-drag substitutes for the right-drag).

{| border="1"
 ! Mouse operations !! Actions
 |-
 | Left-drag || The image is rotated around the x (for a vertical motion) and y (for a horizontal motion) axes.
 |-
 | Right-drag || The image is translated on the x-y plane.
 |-
 | [Shift] + left-drag || The image is translated along the z-axis.
 |-
 | [Shift] + right-drag || The image is rotated around the z-axis.
 |-
 | [Ctrl] + left-drag || The z-clipping plane is shifted when [Option]-[Slab] is checked.
 |-
 | Left-click || An atom of the molecule displayed on the screen is picked.
 |}

In the upper-right panel in the application window (see Figure 3), the file names that have been loaded to the application are listed, where sequential integers are automatically assigned to the individual file. Each integer is a file ID that can be used to specify the file in the command line interface. In addition, three checkboxes are attached to each file. If you change the status of a ‘Disp’ checkbox, the corresponding molecule is switched to be displayed or not to be displayed. If you change the status of a ‘Mouse’ checkbox, the corresponding molecule is switched to be a target of the mouse operations or not. For example, set the both ‘Disp’ checkboxes on, and the both ‘Mouse’ checkboxes off. In this case, either molecule does not move against mouse operations. 

Subsequently set the ‘Mouse’ checkbox of file 1 on. In this case, mouse operations work for the molecule 1. Thus, each file is assigned either selected or not selected, and transform operations, such as rotation or translation, act only on selected files. On the other hand, every atom in a molecule is also assigned either selected or not selected, independently of whether the molecule itself is selected or not. Operations that modify display models or colors work for selected atoms. To see this, choose the [Display] – [Spacefill] menu item. Then the both molecules are displayed with the space fill model because all atoms are initially selected. In the same way, if you choose the [Colors] – [Monochrome] menu item, the both molecules are colored white. A ‘Sel’ checkbox selects or disselects all atoms in each file. 

Let us next try a more detailed operation. Type ‘select *@2’ in the command line area and press Enter key. This command means to select all atoms contained in the file 2 (the usage of the [[Command_List#select|select command]] is summarized in the reference manual). Subsequently, choose the [Display] – [Cartoon] menu item. As a result, only the molecule 2 is displayed in the cartoon model. Furthermore select the [Colors] – [Structure] menu item, and each residue of the molecule 2 is colored according to its secondary structure type (see Figure 3). 

In order to reproduce the same view as that in Figure 3, first execute ‘reset’ command. It restores the position of the viewpoint and the transform of every file to the initial state. Note that the command line interface tries to complement a command word when the Tab key is pressed. If you enter ‘res’ to the command line and subsequently press the Tab key, the command ‘reset’ is automatically entered. Next set the both ‘Mouse’ checkboxes on, and execute ‘translate z 100’ command. This command means to translate the molecules along the z-axis by 100 angstroms.

[[File:Tutorial_fig3.jpg|thumb|Figure 3: An example of molecular images.|center|500px]]

== Displaying polygons ==
In addition to molecules, arbitrary shapes described by polygons can be read in and displayed together, where the polygon file is an XML file, whose document type is described in the section 6. Here, we use ’http://ef-site.hgc.jp/eF-site/jV/1yec.surface.gz’ as an example. This polygon file represents a molecular surface of the molecule 2 (1yec) and the surface is colored according to the electrostatic potential and the hydrophobicity. It is assumed that the current image is the same as that in Figure 3. Then, open the open-remote dialog by choosing the [File] – [Open – Remote] – [Polygon] menu item, enter the above URL to the text field at the top of the dialog, and click the 'OK' button. As a result, the polygon is loaded, displayed and assigned file ID 3. 

Note that the polygon is displayed at the different position from the molecule 2 since the molecule 2 is translated. However, because the polygon and the molecule 2 are described by the same coordinates in their files, their images can be exactly superposed by executing ‘fit 3 2’ from the command line, where the ‘fit’ command performs the copy of the transform matrix. Finally, the image in Figure 4 appears.

[[File:Tutorial_fig4.jpg|thumb|Figure4: An example of polygon images.|center|500px]]

You can control the transparency rate of polygons. Try ’set transparency 0.5’ from the command line, where 0.5 stands for 50% transparency. To restore the image, execute ‘reset transparency’ or ‘set transparency 0’. In the same sense as each atom of a molecule, each vertex of a polygon is assigned either selected or not selected. All vertices are selected in the initial state. Execute a command ’displayvertex off’ and all vertices become invisible. Next execute ’selectvertex within(10.0, 1&amp;*H@2)’, where this means to select vertices that exist within 10 angstroms from each atom that belongs to the first residue of the ‘H’ chain of the molecule 2. Subsequently execute ’displayvertex on’. As a result, only the selected vertices appear. The usage of the [[Command List#selectvertex|selectvertex command]] is summarized in the reference manual.

== Working with PDBMLplus ==
Functional site information on a molecule stored in PDBMLplus is available in jV3. Before trying this, let us close the molecule 2 and the polygon 3 to make the situation simple. Select the [File] – [Close] – [2. 1yec.pdb] and [File] – [Close] – [3. 1yec.surface.gz] menu items sequentially. Then execute a ‘reset’ command and the transform of the molecule 1 and the position of the viewpoint are initialized. 

Next, confirm that the ‘Mouse’ checkbox of the file 1 is checked, and try a ‘show pdbj’ command. The functional site information of the molecule ‘12as’ is read from the PDBMLplus and ‘type’ and ‘subtype’ keywords for each functional site are listed. These keywords can be used to select a set of atoms. For example, if a keyword ‘CATRES’ exists (probably it does), the command ‘select pdbj:CATRES’ selects the corresponding atoms. 

In addition, gene ontology information can be obtained from the PDBMLplus. The gene ontology information for the molecule 12as is displayed by the command ’show godata’. Similar operations can be applied to other external databases on the Internet provided that the external database supports the interface that jV3 requires. See the '[[Functional site information for molecules]]' section for details.

== Animation ==
The animation of molecules can be performed in jV3. The animation file takes the PDB format, where the MODEL line divides each frame. Let us open an animation file ’http://ef-site.hgc.jp/eF-site/jV/anim.pdb.gz’ as an example from the open-remote dialog shown by selecting the [File] – [Open – Remote] – [Animation] menu item. When an animation file is loaded to the application, the first frame is automatically displayed in the wire frame model. You can start the animation by using the animation-control dialog that is shown by choosing the [Options] – [Animation] menu item. The dialog provides operations such as start and stop of the animation, selection of the animation mode, and adjustment of the speed. Some sample figures of the dialog are shown in the [[GUI#Animation_control_dialog]]

== Saving your work ==
While in your work, you can create a script file that contains a set of commands that reproduces the current work by using the [File] – [Save] – [Script] menu item. The script file can be loaded by the [File] – [Open – Local] – [Script] menu item. On the other hand, the [File] – [Save] – [PDB] menu item enables to save a molecule to a PDB format file with the coordinates of the atoms being transformed according to the current image. Here, only one molecule must be selected and only selected atoms in the molecule are saved. The other two menu items in the [File] – [Save] menu, [PNG] and [JPEG], save the current screen image to an image file in the PNG and JPEG format, respectively. The created image file has the same size as that of the 3D-display panel in the application.

== Terminating the application ==
The application is terminated when the [File] – [Exit] menu item is chosen or the application window is closed by the way your operation system provides. You can also quit the application by executing ‘exit’ or ‘quit’ command.</text>
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    <id>444</id>
    <parentid>443</parentid>
    <timestamp>2010-12-15T03:02:53Z</timestamp>
    <contributor>
      <username>IMSsato</username>
      <id>4</id>
    </contributor>
    <comment>/* Animation */</comment>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="12128" xml:space="preserve">{| style="float:right"
 |__TOC__
 |}
== Starting up ==
It is assumed that Java Runtime Environment and JOGL have been appropriately installed. Once you extract the binary distribution file of jV3, the directory of the name, jV_(version), is generated (Ex. jV_3_6_2). The version is assumed to be 3_6_x hereafter. The application starts up by double-clicking the file ‘jv_3_6_x.jar’ in the jV_3_6_x directory or executing the following command from the command line interface.
 java –jar jv_3_6_x.jar
Figure 1 shows the start-up screen. The window has a 3-panel structure, and the upper-left panel with the black background is a 3D image display area. The status of files that have been loaded to the application is shown in the upper-right panel and the lower panel is a command-input and a message-output area.
[[File:Tutorial_fig1.jpg|thumb|Figure 1: Start-up screen|center|500px]]

== Displaying molecules ==
If you are working in the environment that is getting on the Internet and know the PDB ID of the molecule that you want to display, the simplest way is as follows. A dialog shown in Figure 2 is opened by selecting the [File] – [Open – Remote] – [PDB ID] menu item. Enter a PDB ID '12as', for example, to the text field and click the 'OK' button, then the PDBML file is read through the Internet and the molecule is displayed. A molecule is displayed in a wire frame model with colored by atom type in the initial state.

[[File:Fig2.jpg|thumb|Figure 2: Dialog to open the molecule specified by PDB ID|center|200px]]

Let us next attempt to load an arbitrary file on the Internet. Here we use 'http://ef-site.hgc.jp/eF-site/jV/1yec.pdb' as an example. The file is a conventional PDB file whose PDB ID is 1yec. In this case we choose the [File] – [Open – Remote] – [PDB] menu item. Then the open-remote dialog appears. Enter the above URL to the text field at the top of the dialog and click the 'OK' button and the molecule is read in and displayed. In jV3, each molecule is displayed according to the space coordination described in its file. Therefore, when loading and displaying more than one molecule together, they can be viewed with an appropriate separation in some cases; however, they may be displayed far separately or may be overlapped depending on the combination. In any case, when adding a new file, the position of the viewpoint is automatically controlled for the whole to be displayed.

The coordinate system is the right hand system with the x-y plane being on the screen (the x-axis is a horizontal line with positive values to the right and the y-axis is a vertical line with positive values up). Although, the above examples are about operations for remote files, a PDB file on your local hard disk can also be opened from the [File] – [Open – Local] – [PDB] menu item.

== Operating molecules ==
Interactive mouse operations are possible for 3D images. By left-dragging the mouse on the 3D-display panel, molecules are rotated around the x-axis or y-axis. By left-dragging the mouse while holding the Shift key on the keyboard, molecules are translated along the z-axis. All mouse operations are as follows (as for the Macintosh environment, the Command key + left-drag substitutes for the right-drag).

{| border="1"
 ! Mouse operations !! Actions
 |-
 | Left-drag || The image is rotated around the x (for a vertical motion) and y (for a horizontal motion) axes.
 |-
 | Right-drag || The image is translated on the x-y plane.
 |-
 | [Shift] + left-drag || The image is translated along the z-axis.
 |-
 | [Shift] + right-drag || The image is rotated around the z-axis.
 |-
 | [Ctrl] + left-drag || The z-clipping plane is shifted when [Option]-[Slab] is checked.
 |-
 | Left-click || An atom of the molecule displayed on the screen is picked.
 |}

In the upper-right panel in the application window (see Figure 3), the file names that have been loaded to the application are listed, where sequential integers are automatically assigned to the individual file. Each integer is a file ID that can be used to specify the file in the command line interface. In addition, three checkboxes are attached to each file. If you change the status of a ‘Disp’ checkbox, the corresponding molecule is switched to be displayed or not to be displayed. If you change the status of a ‘Mouse’ checkbox, the corresponding molecule is switched to be a target of the mouse operations or not. For example, set the both ‘Disp’ checkboxes on, and the both ‘Mouse’ checkboxes off. In this case, either molecule does not move against mouse operations. 

Subsequently set the ‘Mouse’ checkbox of file 1 on. In this case, mouse operations work for the molecule 1. Thus, each file is assigned either selected or not selected, and transform operations, such as rotation or translation, act only on selected files. On the other hand, every atom in a molecule is also assigned either selected or not selected, independently of whether the molecule itself is selected or not. Operations that modify display models or colors work for selected atoms. To see this, choose the [Display] – [Spacefill] menu item. Then the both molecules are displayed with the space fill model because all atoms are initially selected. In the same way, if you choose the [Colors] – [Monochrome] menu item, the both molecules are colored white. A ‘Sel’ checkbox selects or disselects all atoms in each file. 

Let us next try a more detailed operation. Type ‘select *@2’ in the command line area and press Enter key. This command means to select all atoms contained in the file 2 (the usage of the [[Command_List#select|select command]] is summarized in the reference manual). Subsequently, choose the [Display] – [Cartoon] menu item. As a result, only the molecule 2 is displayed in the cartoon model. Furthermore select the [Colors] – [Structure] menu item, and each residue of the molecule 2 is colored according to its secondary structure type (see Figure 3). 

In order to reproduce the same view as that in Figure 3, first execute ‘reset’ command. It restores the position of the viewpoint and the transform of every file to the initial state. Note that the command line interface tries to complement a command word when the Tab key is pressed. If you enter ‘res’ to the command line and subsequently press the Tab key, the command ‘reset’ is automatically entered. Next set the both ‘Mouse’ checkboxes on, and execute ‘translate z 100’ command. This command means to translate the molecules along the z-axis by 100 angstroms.

[[File:Tutorial_fig3.jpg|thumb|Figure 3: An example of molecular images.|center|500px]]

== Displaying polygons ==
In addition to molecules, arbitrary shapes described by polygons can be read in and displayed together, where the polygon file is an XML file, whose document type is described in the section 6. Here, we use ’http://ef-site.hgc.jp/eF-site/jV/1yec.surface.gz’ as an example. This polygon file represents a molecular surface of the molecule 2 (1yec) and the surface is colored according to the electrostatic potential and the hydrophobicity. It is assumed that the current image is the same as that in Figure 3. Then, open the open-remote dialog by choosing the [File] – [Open – Remote] – [Polygon] menu item, enter the above URL to the text field at the top of the dialog, and click the 'OK' button. As a result, the polygon is loaded, displayed and assigned file ID 3. 

Note that the polygon is displayed at the different position from the molecule 2 since the molecule 2 is translated. However, because the polygon and the molecule 2 are described by the same coordinates in their files, their images can be exactly superposed by executing ‘fit 3 2’ from the command line, where the ‘fit’ command performs the copy of the transform matrix. Finally, the image in Figure 4 appears.

[[File:Tutorial_fig4.jpg|thumb|Figure4: An example of polygon images.|center|500px]]

You can control the transparency rate of polygons. Try ’set transparency 0.5’ from the command line, where 0.5 stands for 50% transparency. To restore the image, execute ‘reset transparency’ or ‘set transparency 0’. In the same sense as each atom of a molecule, each vertex of a polygon is assigned either selected or not selected. All vertices are selected in the initial state. Execute a command ’displayvertex off’ and all vertices become invisible. Next execute ’selectvertex within(10.0, 1&amp;*H@2)’, where this means to select vertices that exist within 10 angstroms from each atom that belongs to the first residue of the ‘H’ chain of the molecule 2. Subsequently execute ’displayvertex on’. As a result, only the selected vertices appear. The usage of the [[Command List#selectvertex|selectvertex command]] is summarized in the reference manual.

== Working with PDBMLplus ==
Functional site information on a molecule stored in PDBMLplus is available in jV3. Before trying this, let us close the molecule 2 and the polygon 3 to make the situation simple. Select the [File] – [Close] – [2. 1yec.pdb] and [File] – [Close] – [3. 1yec.surface.gz] menu items sequentially. Then execute a ‘reset’ command and the transform of the molecule 1 and the position of the viewpoint are initialized. 

Next, confirm that the ‘Mouse’ checkbox of the file 1 is checked, and try a ‘show pdbj’ command. The functional site information of the molecule ‘12as’ is read from the PDBMLplus and ‘type’ and ‘subtype’ keywords for each functional site are listed. These keywords can be used to select a set of atoms. For example, if a keyword ‘CATRES’ exists (probably it does), the command ‘select pdbj:CATRES’ selects the corresponding atoms. 

In addition, gene ontology information can be obtained from the PDBMLplus. The gene ontology information for the molecule 12as is displayed by the command ’show godata’. Similar operations can be applied to other external databases on the Internet provided that the external database supports the interface that jV3 requires. See the '[[Functional site information for molecules]]' section for details.

== Animation ==
The animation of molecules can be performed in jV3. The animation file takes the PDB format, where the MODEL line divides each frame. Let us open an animation file ’http://ef-site.hgc.jp/eF-site/jV/anim.pdb.gz’ as an example from the open-remote dialog shown by selecting the [File] – [Open – Remote] – [Animation] menu item. When an animation file is loaded to the application, the first frame is automatically displayed in the wire frame model. You can start the animation by using the animation-control dialog that is shown by choosing the [Options] – [Animation] menu item. The dialog provides operations such as start and stop of the animation, selection of the animation mode, and adjustment of the speed. Some [[GUI#Animation_control_dialog|sample figures]] of the dialog are shown in the GUI section.

== Saving your work ==
While in your work, you can create a script file that contains a set of commands that reproduces the current work by using the [File] – [Save] – [Script] menu item. The script file can be loaded by the [File] – [Open – Local] – [Script] menu item. On the other hand, the [File] – [Save] – [PDB] menu item enables to save a molecule to a PDB format file with the coordinates of the atoms being transformed according to the current image. Here, only one molecule must be selected and only selected atoms in the molecule are saved. The other two menu items in the [File] – [Save] menu, [PNG] and [JPEG], save the current screen image to an image file in the PNG and JPEG format, respectively. The created image file has the same size as that of the 3D-display panel in the application.

== Terminating the application ==
The application is terminated when the [File] – [Exit] menu item is chosen or the application window is closed by the way your operation system provides. You can also quit the application by executing ‘exit’ or ‘quit’ command.</text>
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    <id>445</id>
    <parentid>444</parentid>
    <timestamp>2010-12-15T03:14:11Z</timestamp>
    <contributor>
      <username>IMSsato</username>
      <id>4</id>
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    <comment>/* Starting up */</comment>
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    <format>text/x-wiki</format>
    <text bytes="11992" xml:space="preserve">{| style="float:right"
 |__TOC__
 |}
== Starting up ==
It is assumed that Java Runtime Environment has been appropriately installed. You can start up jV by downloading the binary distribution, however, an easier way is to follow this link [[http://ef-site.hgc.jp/eF-site/servlet/stable/jV.jnlp start up with stable JOGL]], which launch jV via Java Web Start technology.
Figure 1 shows the start-up screen. The window has a 3-panel structure, and the upper-left panel with the black background is a 3D image display area. The status of files that have been loaded to the application is shown in the upper-right panel and the lower panel is a command-input and a message-output area.
[[File:Tutorial_fig1.jpg|thumb|Figure 1: Start-up screen|center|500px]]

== Displaying molecules ==
If you are working in the environment that is getting on the Internet and know the PDB ID of the molecule that you want to display, the simplest way is as follows. A dialog shown in Figure 2 is opened by selecting the [File] – [Open – Remote] – [PDB ID] menu item. Enter a PDB ID '12as', for example, to the text field and click the 'OK' button, then the PDBML file is read through the Internet and the molecule is displayed. A molecule is displayed in a wire frame model with colored by atom type in the initial state.

[[File:Fig2.jpg|thumb|Figure 2: Dialog to open the molecule specified by PDB ID|center|200px]]

Let us next attempt to load an arbitrary file on the Internet. Here we use 'http://ef-site.hgc.jp/eF-site/jV/1yec.pdb' as an example. The file is a conventional PDB file whose PDB ID is 1yec. In this case we choose the [File] – [Open – Remote] – [PDB] menu item. Then the open-remote dialog appears. Enter the above URL to the text field at the top of the dialog and click the 'OK' button and the molecule is read in and displayed. In jV3, each molecule is displayed according to the space coordination described in its file. Therefore, when loading and displaying more than one molecule together, they can be viewed with an appropriate separation in some cases; however, they may be displayed far separately or may be overlapped depending on the combination. In any case, when adding a new file, the position of the viewpoint is automatically controlled for the whole to be displayed.

The coordinate system is the right hand system with the x-y plane being on the screen (the x-axis is a horizontal line with positive values to the right and the y-axis is a vertical line with positive values up). Although, the above examples are about operations for remote files, a PDB file on your local hard disk can also be opened from the [File] – [Open – Local] – [PDB] menu item.

== Operating molecules ==
Interactive mouse operations are possible for 3D images. By left-dragging the mouse on the 3D-display panel, molecules are rotated around the x-axis or y-axis. By left-dragging the mouse while holding the Shift key on the keyboard, molecules are translated along the z-axis. All mouse operations are as follows (as for the Macintosh environment, the Command key + left-drag substitutes for the right-drag).

{| border="1"
 ! Mouse operations !! Actions
 |-
 | Left-drag || The image is rotated around the x (for a vertical motion) and y (for a horizontal motion) axes.
 |-
 | Right-drag || The image is translated on the x-y plane.
 |-
 | [Shift] + left-drag || The image is translated along the z-axis.
 |-
 | [Shift] + right-drag || The image is rotated around the z-axis.
 |-
 | [Ctrl] + left-drag || The z-clipping plane is shifted when [Option]-[Slab] is checked.
 |-
 | Left-click || An atom of the molecule displayed on the screen is picked.
 |}

In the upper-right panel in the application window (see Figure 3), the file names that have been loaded to the application are listed, where sequential integers are automatically assigned to the individual file. Each integer is a file ID that can be used to specify the file in the command line interface. In addition, three checkboxes are attached to each file. If you change the status of a ‘Disp’ checkbox, the corresponding molecule is switched to be displayed or not to be displayed. If you change the status of a ‘Mouse’ checkbox, the corresponding molecule is switched to be a target of the mouse operations or not. For example, set the both ‘Disp’ checkboxes on, and the both ‘Mouse’ checkboxes off. In this case, either molecule does not move against mouse operations. 

Subsequently set the ‘Mouse’ checkbox of file 1 on. In this case, mouse operations work for the molecule 1. Thus, each file is assigned either selected or not selected, and transform operations, such as rotation or translation, act only on selected files. On the other hand, every atom in a molecule is also assigned either selected or not selected, independently of whether the molecule itself is selected or not. Operations that modify display models or colors work for selected atoms. To see this, choose the [Display] – [Spacefill] menu item. Then the both molecules are displayed with the space fill model because all atoms are initially selected. In the same way, if you choose the [Colors] – [Monochrome] menu item, the both molecules are colored white. A ‘Sel’ checkbox selects or disselects all atoms in each file. 

Let us next try a more detailed operation. Type ‘select *@2’ in the command line area and press Enter key. This command means to select all atoms contained in the file 2 (the usage of the [[Command_List#select|select command]] is summarized in the reference manual). Subsequently, choose the [Display] – [Cartoon] menu item. As a result, only the molecule 2 is displayed in the cartoon model. Furthermore select the [Colors] – [Structure] menu item, and each residue of the molecule 2 is colored according to its secondary structure type (see Figure 3). 

In order to reproduce the same view as that in Figure 3, first execute ‘reset’ command. It restores the position of the viewpoint and the transform of every file to the initial state. Note that the command line interface tries to complement a command word when the Tab key is pressed. If you enter ‘res’ to the command line and subsequently press the Tab key, the command ‘reset’ is automatically entered. Next set the both ‘Mouse’ checkboxes on, and execute ‘translate z 100’ command. This command means to translate the molecules along the z-axis by 100 angstroms.

[[File:Tutorial_fig3.jpg|thumb|Figure 3: An example of molecular images.|center|500px]]

== Displaying polygons ==
In addition to molecules, arbitrary shapes described by polygons can be read in and displayed together, where the polygon file is an XML file, whose document type is described in the section 6. Here, we use ’http://ef-site.hgc.jp/eF-site/jV/1yec.surface.gz’ as an example. This polygon file represents a molecular surface of the molecule 2 (1yec) and the surface is colored according to the electrostatic potential and the hydrophobicity. It is assumed that the current image is the same as that in Figure 3. Then, open the open-remote dialog by choosing the [File] – [Open – Remote] – [Polygon] menu item, enter the above URL to the text field at the top of the dialog, and click the 'OK' button. As a result, the polygon is loaded, displayed and assigned file ID 3. 

Note that the polygon is displayed at the different position from the molecule 2 since the molecule 2 is translated. However, because the polygon and the molecule 2 are described by the same coordinates in their files, their images can be exactly superposed by executing ‘fit 3 2’ from the command line, where the ‘fit’ command performs the copy of the transform matrix. Finally, the image in Figure 4 appears.

[[File:Tutorial_fig4.jpg|thumb|Figure4: An example of polygon images.|center|500px]]

You can control the transparency rate of polygons. Try ’set transparency 0.5’ from the command line, where 0.5 stands for 50% transparency. To restore the image, execute ‘reset transparency’ or ‘set transparency 0’. In the same sense as each atom of a molecule, each vertex of a polygon is assigned either selected or not selected. All vertices are selected in the initial state. Execute a command ’displayvertex off’ and all vertices become invisible. Next execute ’selectvertex within(10.0, 1&amp;*H@2)’, where this means to select vertices that exist within 10 angstroms from each atom that belongs to the first residue of the ‘H’ chain of the molecule 2. Subsequently execute ’displayvertex on’. As a result, only the selected vertices appear. The usage of the [[Command List#selectvertex|selectvertex command]] is summarized in the reference manual.

== Working with PDBMLplus ==
Functional site information on a molecule stored in PDBMLplus is available in jV3. Before trying this, let us close the molecule 2 and the polygon 3 to make the situation simple. Select the [File] – [Close] – [2. 1yec.pdb] and [File] – [Close] – [3. 1yec.surface.gz] menu items sequentially. Then execute a ‘reset’ command and the transform of the molecule 1 and the position of the viewpoint are initialized. 

Next, confirm that the ‘Mouse’ checkbox of the file 1 is checked, and try a ‘show pdbj’ command. The functional site information of the molecule ‘12as’ is read from the PDBMLplus and ‘type’ and ‘subtype’ keywords for each functional site are listed. These keywords can be used to select a set of atoms. For example, if a keyword ‘CATRES’ exists (probably it does), the command ‘select pdbj:CATRES’ selects the corresponding atoms. 

In addition, gene ontology information can be obtained from the PDBMLplus. The gene ontology information for the molecule 12as is displayed by the command ’show godata’. Similar operations can be applied to other external databases on the Internet provided that the external database supports the interface that jV3 requires. See the '[[Functional site information for molecules]]' section for details.

== Animation ==
The animation of molecules can be performed in jV3. The animation file takes the PDB format, where the MODEL line divides each frame. Let us open an animation file ’http://ef-site.hgc.jp/eF-site/jV/anim.pdb.gz’ as an example from the open-remote dialog shown by selecting the [File] – [Open – Remote] – [Animation] menu item. When an animation file is loaded to the application, the first frame is automatically displayed in the wire frame model. You can start the animation by using the animation-control dialog that is shown by choosing the [Options] – [Animation] menu item. The dialog provides operations such as start and stop of the animation, selection of the animation mode, and adjustment of the speed. Some [[GUI#Animation_control_dialog|sample figures]] of the dialog are shown in the GUI section.

== Saving your work ==
While in your work, you can create a script file that contains a set of commands that reproduces the current work by using the [File] – [Save] – [Script] menu item. The script file can be loaded by the [File] – [Open – Local] – [Script] menu item. On the other hand, the [File] – [Save] – [PDB] menu item enables to save a molecule to a PDB format file with the coordinates of the atoms being transformed according to the current image. Here, only one molecule must be selected and only selected atoms in the molecule are saved. The other two menu items in the [File] – [Save] menu, [PNG] and [JPEG], save the current screen image to an image file in the PNG and JPEG format, respectively. The created image file has the same size as that of the 3D-display panel in the application.

== Terminating the application ==
The application is terminated when the [File] – [Exit] menu item is chosen or the application window is closed by the way your operation system provides. You can also quit the application by executing ‘exit’ or ‘quit’ command.</text>
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    <id>446</id>
    <parentid>445</parentid>
    <timestamp>2010-12-15T04:09:27Z</timestamp>
    <contributor>
      <username>IMSsato</username>
      <id>4</id>
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    <comment>/* Operating molecules */</comment>
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 |__TOC__
 |}
== Starting up ==
It is assumed that Java Runtime Environment has been appropriately installed. You can start up jV by downloading the binary distribution, however, an easier way is to follow this link [[http://ef-site.hgc.jp/eF-site/servlet/stable/jV.jnlp start up with stable JOGL]], which launch jV via Java Web Start technology.
Figure 1 shows the start-up screen. The window has a 3-panel structure, and the upper-left panel with the black background is a 3D image display area. The status of files that have been loaded to the application is shown in the upper-right panel and the lower panel is a command-input and a message-output area.
[[File:Tutorial_fig1.jpg|thumb|Figure 1: Start-up screen|center|500px]]

== Displaying molecules ==
If you are working in the environment that is getting on the Internet and know the PDB ID of the molecule that you want to display, the simplest way is as follows. A dialog shown in Figure 2 is opened by selecting the [File] – [Open – Remote] – [PDB ID] menu item. Enter a PDB ID '12as', for example, to the text field and click the 'OK' button, then the PDBML file is read through the Internet and the molecule is displayed. A molecule is displayed in a wire frame model with colored by atom type in the initial state.

[[File:Fig2.jpg|thumb|Figure 2: Dialog to open the molecule specified by PDB ID|center|200px]]

Let us next attempt to load an arbitrary file on the Internet. Here we use 'http://ef-site.hgc.jp/eF-site/jV/1yec.pdb' as an example. The file is a conventional PDB file whose PDB ID is 1yec. In this case we choose the [File] – [Open – Remote] – [PDB] menu item. Then the open-remote dialog appears. Enter the above URL to the text field at the top of the dialog and click the 'OK' button and the molecule is read in and displayed. In jV3, each molecule is displayed according to the space coordination described in its file. Therefore, when loading and displaying more than one molecule together, they can be viewed with an appropriate separation in some cases; however, they may be displayed far separately or may be overlapped depending on the combination. In any case, when adding a new file, the position of the viewpoint is automatically controlled for the whole to be displayed.

The coordinate system is the right hand system with the x-y plane being on the screen (the x-axis is a horizontal line with positive values to the right and the y-axis is a vertical line with positive values up). Although, the above examples are about operations for remote files, a PDB file on your local hard disk can also be opened from the [File] – [Open – Local] – [PDB] menu item.

== Operating molecules ==
Interactive mouse operations are possible for 3D images. By left-dragging the mouse on the 3D-display panel, molecules are rotated around the x-axis or y-axis. By left-dragging the mouse while holding the Shift key on the keyboard, molecules are translated along the z-axis. All mouse operations are as follows (as for the Macintosh environment, the Command key + left-drag substitutes for the right-drag).

{| border="1"
 ! Mouse operations !! Actions
 |-
 | Left-drag || The image is rotated around the x (for a vertical motion) and y (for a horizontal motion) axes.
 |-
 | Right-drag || The image is translated on the x-y plane.
 |-
 | [Shift] + left-drag || The image is translated along the z-axis.
 |-
 | [Shift] + right-drag || The image is rotated around the z-axis.
 |-
 | [Alt or Ctrl] + left-drag || The z-clipping plane is shifted when [Option]-[Slab] is checked.
 |-
 | Left-click || An atom of the molecule displayed on the screen is picked.
 |}

In the upper-right panel in the application window (see Figure 3), the file names that have been loaded to the application are listed, where sequential integers are automatically assigned to the individual file. Each integer is a file ID that can be used to specify the file in the command line interface. In addition, three checkboxes are attached to each file. If you change the status of a ‘Disp’ checkbox, the corresponding molecule is switched to be displayed or not to be displayed. If you change the status of a ‘Mouse’ checkbox, the corresponding molecule is switched to be a target of the mouse operations or not. For example, set the both ‘Disp’ checkboxes on, and the both ‘Mouse’ checkboxes off. In this case, either molecule does not move against mouse operations. 

Subsequently set the ‘Mouse’ checkbox of file 1 on. In this case, mouse operations work for the molecule 1. Thus, each file is assigned either selected or not selected, and transform operations, such as rotation or translation, act only on selected files. On the other hand, every atom in a molecule is also assigned either selected or not selected, independently of whether the molecule itself is selected or not. Operations that modify display models or colors work for selected atoms. To see this, choose the [Display] – [Spacefill] menu item. Then the both molecules are displayed with the space fill model because all atoms are initially selected. In the same way, if you choose the [Colors] – [Monochrome] menu item, the both molecules are colored white. A ‘Sel’ checkbox selects or disselects all atoms in each file. 

Let us next try a more detailed operation. Type ‘select *@2’ in the command line area and press Enter key. This command means to select all atoms contained in the file 2 (the usage of the [[Command_List#select|select command]] is summarized in the reference manual). Subsequently, choose the [Display] – [Cartoon] menu item. As a result, only the molecule 2 is displayed in the cartoon model. Furthermore select the [Colors] – [Structure] menu item, and each residue of the molecule 2 is colored according to its secondary structure type (see Figure 3). 

In order to reproduce the same view as that in Figure 3, first execute ‘reset’ command. It restores the position of the viewpoint and the transform of every file to the initial state. Note that the command line interface tries to complement a command word when the Tab key is pressed. If you enter ‘res’ to the command line and subsequently press the Tab key, the command ‘reset’ is automatically entered. Next set the both ‘Mouse’ checkboxes on, and execute ‘translate z 100’ command. This command means to translate the molecules along the z-axis by 100 angstroms.

[[File:Tutorial_fig3.jpg|thumb|Figure 3: An example of molecular images.|center|500px]]

== Displaying polygons ==
In addition to molecules, arbitrary shapes described by polygons can be read in and displayed together, where the polygon file is an XML file, whose document type is described in the section 6. Here, we use ’http://ef-site.hgc.jp/eF-site/jV/1yec.surface.gz’ as an example. This polygon file represents a molecular surface of the molecule 2 (1yec) and the surface is colored according to the electrostatic potential and the hydrophobicity. It is assumed that the current image is the same as that in Figure 3. Then, open the open-remote dialog by choosing the [File] – [Open – Remote] – [Polygon] menu item, enter the above URL to the text field at the top of the dialog, and click the 'OK' button. As a result, the polygon is loaded, displayed and assigned file ID 3. 

Note that the polygon is displayed at the different position from the molecule 2 since the molecule 2 is translated. However, because the polygon and the molecule 2 are described by the same coordinates in their files, their images can be exactly superposed by executing ‘fit 3 2’ from the command line, where the ‘fit’ command performs the copy of the transform matrix. Finally, the image in Figure 4 appears.

[[File:Tutorial_fig4.jpg|thumb|Figure4: An example of polygon images.|center|500px]]

You can control the transparency rate of polygons. Try ’set transparency 0.5’ from the command line, where 0.5 stands for 50% transparency. To restore the image, execute ‘reset transparency’ or ‘set transparency 0’. In the same sense as each atom of a molecule, each vertex of a polygon is assigned either selected or not selected. All vertices are selected in the initial state. Execute a command ’displayvertex off’ and all vertices become invisible. Next execute ’selectvertex within(10.0, 1&amp;*H@2)’, where this means to select vertices that exist within 10 angstroms from each atom that belongs to the first residue of the ‘H’ chain of the molecule 2. Subsequently execute ’displayvertex on’. As a result, only the selected vertices appear. The usage of the [[Command List#selectvertex|selectvertex command]] is summarized in the reference manual.

== Working with PDBMLplus ==
Functional site information on a molecule stored in PDBMLplus is available in jV3. Before trying this, let us close the molecule 2 and the polygon 3 to make the situation simple. Select the [File] – [Close] – [2. 1yec.pdb] and [File] – [Close] – [3. 1yec.surface.gz] menu items sequentially. Then execute a ‘reset’ command and the transform of the molecule 1 and the position of the viewpoint are initialized. 

Next, confirm that the ‘Mouse’ checkbox of the file 1 is checked, and try a ‘show pdbj’ command. The functional site information of the molecule ‘12as’ is read from the PDBMLplus and ‘type’ and ‘subtype’ keywords for each functional site are listed. These keywords can be used to select a set of atoms. For example, if a keyword ‘CATRES’ exists (probably it does), the command ‘select pdbj:CATRES’ selects the corresponding atoms. 

In addition, gene ontology information can be obtained from the PDBMLplus. The gene ontology information for the molecule 12as is displayed by the command ’show godata’. Similar operations can be applied to other external databases on the Internet provided that the external database supports the interface that jV3 requires. See the '[[Functional site information for molecules]]' section for details.

== Animation ==
The animation of molecules can be performed in jV3. The animation file takes the PDB format, where the MODEL line divides each frame. Let us open an animation file ’http://ef-site.hgc.jp/eF-site/jV/anim.pdb.gz’ as an example from the open-remote dialog shown by selecting the [File] – [Open – Remote] – [Animation] menu item. When an animation file is loaded to the application, the first frame is automatically displayed in the wire frame model. You can start the animation by using the animation-control dialog that is shown by choosing the [Options] – [Animation] menu item. The dialog provides operations such as start and stop of the animation, selection of the animation mode, and adjustment of the speed. Some [[GUI#Animation_control_dialog|sample figures]] of the dialog are shown in the GUI section.

== Saving your work ==
While in your work, you can create a script file that contains a set of commands that reproduces the current work by using the [File] – [Save] – [Script] menu item. The script file can be loaded by the [File] – [Open – Local] – [Script] menu item. On the other hand, the [File] – [Save] – [PDB] menu item enables to save a molecule to a PDB format file with the coordinates of the atoms being transformed according to the current image. Here, only one molecule must be selected and only selected atoms in the molecule are saved. The other two menu items in the [File] – [Save] menu, [PNG] and [JPEG], save the current screen image to an image file in the PNG and JPEG format, respectively. The created image file has the same size as that of the 3D-display panel in the application.

== Terminating the application ==
The application is terminated when the [File] – [Exit] menu item is chosen or the application window is closed by the way your operation system provides. You can also quit the application by executing ‘exit’ or ‘quit’ command.</text>
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== Menu bar ==
The organization of the menu bar and the function of its components are shown below.

;1) File menu
{| class="wikitable" border="1"
 |-
 | style="background-color:gainsboro" colspan="2" | Component
 | style="background-color:gainsboro" | Function
 |-
 | rowspan="5" | Open - Local
 | PDBML
 | A local PDBML file is opened.
 |-
 | PDB
 | A local PDB file is opened.
 |-
 | Polygon
 | A local polygon file is opened.
 |-
 | Script 
 | A local script file is opened.
 |-
 | Animation
 | A local animation file is opened.
 |-
 | rowspan="7" | Open-Remote
 | PDBML
 | A remote PDBML file is opened.
 |-
 | PDB
 | A remote PDB file is opened.
 |-
 | Polygon
 | A remote polygon file is opened.
 |- 
 | Script
 | A remote script file is opened.
 |-
 | Animation
 | A remote animation file is opened.
 |-
 | PDB ID
 | A PDBML file at the PDBML FTP site is opened.
 |-
 | eF-site ID
 | A set of molecular and polygon files stored in eF-site database are opened.
 |-
 | colspan="2" | Information
 | Information about the selected files are shown.
 |-
 | colspan="2" | Close
 | The specified file is closed.
 |-
 | rowspan="4" | Save
 | PDB
 | A PDB format file that contains the current atom coordinates is created.
 |-
 | Script
 | A script by which the present condition is reproduced is created.
 |-
 | PNG
 | The current image is saved as PNG.
 |-
 | JPEG
 | The current image is saved as JPEG.
 |-
 | colspan="2" | Exit
 | The application is terminated.
 |}

;2) Display menu
{| class="wikitable" border="1"
 |-
 | style="background-color:gainsboro" | Component
 | style="background-color:gainsboro" | Function
 |-
 | Wireframe
 | The selected atoms are displayed in a wire frame model.
 |-
 | Backbone
 | The selected atoms are displayed in a backbone model.
 |-
 | Sticks
 | The selected atoms are displayed in a stick model.
 |-
 | Spacefill
 | The selected atoms are displayed in a space-fill model.
 |-
 | Ball&amp;Stick
 | The selected atoms are displayed in a ball &amp; stick model.
 |-
 | Ribbons
 | The selected atoms are displayed in a ribbon model.
 |-
 | Cartoon
 | The selected atoms are displayed in a cartoon model.
 |}

;3) Colors menu
{| class="wikitable" border="1"
 |-
 | style="background-color:gainsboro" | Component
 | style="background-color:gainsboro" | Function
 |-
 | Monochrome
 | The selected atoms are colored in white.
 |-
 | CPK
 | The selected atoms are colored by CPK color scheme.
 |-
 | Shapely
 | The selected atoms are colored by the color scheme in which each amino acid and nucleic acid is assigned a unique color according to the amino acid and nucleic acid properties.
 |-
 | Group
 | The atoms of every chain are drawn as a smooth spectrum from red (N-terminal of the molecule) to blue (C-terminal).
 |-
 | Chain
 | The selected atoms are colored by the color scheme in which each chain is assigned a unique color.
 |-
 | Temperature
 | The selected atoms are drawn as a smooth spectrum from red (high value) to blue (low value) according to the value of the temperature factor.
 |-
 | Structure
 | The secondary structures are colored by the color scheme in which each secondary structure is assigned a unique color.
 |-
 | Charge
 | The selected atoms are drawn as a smooth spectrum from blue (positive) to red (negative) according to the charge.
 |-
 | Amino
 | The selected atoms are colored by the color scheme in which each amino acid is assigned a unique color.
 |}

;4) Options menu
{| class="wikitable" border="1"
 |-
 | style="background-color:gainsboro" | Component
 | style="background-color:gainsboro" | Function
 |-
 | Hetero || Atoms	Users can choose whether the heterogeneous atoms described by ‘HETATM’ in PDB files are selected or not.
 |-
 | Hydrogens || Users can choose whether the hydrogen atoms are selected or not.
 |-
 | Slab || Users can choose whether the z-clipping plane is located on the default position or is shifted.
 |-
 | Stereo || Users can choose whether the stereo display is enabled or not.
 |-
 | Load To Center || Users can choose whether a new image is added to the center of screen or not when a new file is opened.
 |-
 | Pick Off || The mouse-pick is disabled. 
 |-
 | Pick Ident || The atom and residue names, their serial numbers, chain identifier and file ID of the object picked by mouse-click are represented.
 |-
 | Pick Coordinates || The atom and residue names, their serial numbers, chain identifier, file ID and coordinate of the object picked by mouse-click are represented.
 |-
 | Pick Distance || The distance between the first and second clicked atoms is calculated and shown.
 |-
 | Pick Center || The center of rotation and window are transferred to the clicked position.
 |-
 | Pick Select || Only clicked files are operated.
 |- 
 | Animation || The animation control dialog is opened.
 |}

;5) Help menu
{| class="wikitable" border="1"
 |-
 | style="background-color:gainsboro" | Component
 | style="background-color:gainsboro" | Function
 |-
 | About jV || Information about this application is shown.
 |}

== Open-Remode dialog ==
;1) URL with parameters
Selecting [PDBML], [PDB], [Polygon], [Script] or [Animation] menu item in the [File] – [Open – Remote] menu opens the open-remote dialog that can handle a URL with parameters. For example, Figure 5 shows a dialog opened by the [File] – [Open – Remote] – [PDBML] menu item.

[[File:Fig5.jpg|thumb|Figure5: The open-remote dialog|center|400px]]

When ‘Add’ button is clicked, a new parameter line is appended in the table at the center of the dialog. Figure 6 shows an example of a URL with one parameter. By clicking the ‘Add’ button the necessary number of times, you can attach multiple parameters. When ‘Remove’ button is clicked, a highlighted line in the parameter table is removed. When ‘Clear’ button is clicked, all parameters are removed.

[[File:Fig6.jpg|thumb|Figure6: Example of a URL with a parameter|center|400px]]

;2)'type' column and mouse pick
The ‘type’ column in the parameter table is selected from the follows.

{| class="wikitable" border="1"
 |-
 | style="background-color:gainsboro" | type
 | style="background-color:gainsboro" | values
 | style="background-color:gainsboro" | mouse pick
 |-
 | text || arbitrary value || does not work
 |-
 | atom ID || atom ID || work
 |-
 | atom || set of chain ID, residue ID and atom ID || work
 |-
 | residue || set of chain ID and residue ID || work
 |-
 | orig_coords || atom coordinates written in the molecule file || work
 |-
 | curr_coords || atom coordinates currently displayed || work
 |}

For the case of a type to which mouse pick works, selecting an atom in the screen by mouse pick sets the corresponding value to the ‘value’ column in a highlighted line in the parameter table. The value of the ‘delimiter’ field is used to delimit atom’s x, y, and z coordinate.

;3) Saving and loading the configuration
By clicking the ‘save’ button, a file chooser dialog is appeared and the current configuration can be saved to a file. In the same way, a configuration can be loaded by clicking the ‘load’ button. The contents of a configuration file are in XML format as follows.

 &lt;?xml version="1.0"?&gt;
 &amp;nbsp;
 &amp;nbsp;
 &lt;remote_file url="http://example.com"&gt;
  &lt;params attach="true" coordinates_delimiter=","&gt;
    &lt;param name="param1" value="value1" type="text"/&gt;
  &lt;/params&gt;
 &lt;/remote_file&gt;

;4) Copy of the transform
When a file ID that currently exists is entered to the ‘fit to’ field, the transform of the newly opened file is set identical to that of the specified file.

;5) Execution
When the ‘OK’ button is clicked, a new file is loaded and the dialog is closed. When you use ‘Submit’ button, on the other hand, the dialog remains visible even after a new file is loaded.

== Animation control dialog ==
The animation control dialog is visible only if [Options] - [Animation] menu is checked. When there is no animation file loaded, the animation control dialog is as Figure 7. If some animation files are opened, the animation control dialog is altered according to the number of the files. Figure 8 indicates the dialog in the presence of two files.

[[File:Tutorial_fig7.jpg|thumb|Figure7: The animation control dialog in the absence of files.|center|400px]]

[[File:Tutorial_fig8.jpg|thumb|Figure8: The animation control dialog in the presence of two files.|center|400px]]

Users can select which files are controlled by their checkbox. The frame position and playback and stop of the animation can be controlled individually to each file. The playback-speed and the selection of ‘loop’ and ‘swing’ modes are common for all files.</text>
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== Menu bar ==
The organization of the menu bar and the function of its components are shown below.

;1) File menu
{| class="wikitable" border="1"
 |-
 | style="background-color:gainsboro" colspan="2" | Component
 | style="background-color:gainsboro" | Function
 |-
 | rowspan="5" | Open - Local
 | PDBML
 | A local PDBML file is opened.
 |-
 | PDB
 | A local PDB file is opened.
 |-
 | Polygon
 | A local polygon file is opened.
 |-
 | Script 
 | A local script file is opened.
 |-
 | Animation
 | A local animation file is opened.
 |-
 | rowspan="7" | Open-Remote
 | PDB ID
 | A PDBML file at the PDBML FTP site is opened.
 |-
 | eF-site ID
 | A set of molecular and polygon files stored in eF-site database are opened.
 |-
 | PDBML
 | A remote PDBML file is opened.
 |-
 | PDB
 | A remote PDB file is opened.
 |-
 | Polygon
 | A remote polygon file is opened.
 |- 
 | Script
 | A remote script file is opened.
 |-
 | Animation
 | A remote animation file is opened.
 |-
 | colspan="2" | Information
 | Information about the selected files are shown.
 |-
 | colspan="2" | Close
 | The specified file is closed.
 |-
 | rowspan="4" | Save
 | PDB
 | A PDB format file that contains the current atom coordinates is created.
 |-
 | Script
 | A script by which the present condition is reproduced is created.
 |-
 | PNG
 | The current image is saved as PNG.
 |-
 | JPEG
 | The current image is saved as JPEG.
 |-
 | colspan="2" | Exit
 | The application is terminated.
 |}

;2) Display menu
{| class="wikitable" border="1"
 |-
 | style="background-color:gainsboro" | Component
 | style="background-color:gainsboro" | Function
 |-
 | Wireframe
 | The selected atoms are displayed in a wire frame model.
 |-
 | Backbone
 | The selected atoms are displayed in a backbone model.
 |-
 | Sticks
 | The selected atoms are displayed in a stick model.
 |-
 | Spacefill
 | The selected atoms are displayed in a space-fill model.
 |-
 | Ball&amp;Stick
 | The selected atoms are displayed in a ball &amp; stick model.
 |-
 | Ribbons
 | The selected atoms are displayed in a ribbon model.
 |-
 | Cartoon
 | The selected atoms are displayed in a cartoon model.
 |}

;3) Colors menu
{| class="wikitable" border="1"
 |-
 | style="background-color:gainsboro" | Component
 | style="background-color:gainsboro" | Function
 |-
 | Monochrome
 | The selected atoms are colored in white.
 |-
 | CPK
 | The selected atoms are colored by CPK color scheme.
 |-
 | Shapely
 | The selected atoms are colored by the color scheme in which each amino acid and nucleic acid is assigned a unique color according to the amino acid and nucleic acid properties.
 |-
 | Group
 | The atoms of every chain are drawn as a smooth spectrum from red (N-terminal of the molecule) to blue (C-terminal).
 |-
 | Chain
 | The selected atoms are colored by the color scheme in which each chain is assigned a unique color.
 |-
 | Temperature
 | The selected atoms are drawn as a smooth spectrum from red (high value) to blue (low value) according to the value of the temperature factor.
 |-
 | Structure
 | The secondary structures are colored by the color scheme in which each secondary structure is assigned a unique color.
 |-
 | Charge
 | The selected atoms are drawn as a smooth spectrum from blue (positive) to red (negative) according to the charge.
 |-
 | Amino
 | The selected atoms are colored by the color scheme in which each amino acid is assigned a unique color.
 |}

;4) Options menu
{| class="wikitable" border="1"
 |-
 | style="background-color:gainsboro" | Component
 | style="background-color:gainsboro" | Function
 |-
 | Hetero || Atoms	Users can choose whether the heterogeneous atoms described by ‘HETATM’ in PDB files are selected or not.
 |-
 | Hydrogens || Users can choose whether the hydrogen atoms are selected or not.
 |-
 | Slab || Users can choose whether the z-clipping plane is located on the default position or is shifted.
 |-
 | Stereo || Users can choose whether the stereo display is enabled or not.
 |-
 | Load To Center || Users can choose whether a new image is added to the center of screen or not when a new file is opened.
 |-
 | Pick Off || The mouse-pick is disabled. 
 |-
 | Pick Ident || The atom and residue names, their serial numbers, chain identifier and file ID of the object picked by mouse-click are represented.
 |-
 | Pick Coordinates || The atom and residue names, their serial numbers, chain identifier, file ID and coordinate of the object picked by mouse-click are represented.
 |-
 | Pick Distance || The distance between the first and second clicked atoms is calculated and shown.
 |-
 | Pick Center || The center of rotation and window are transferred to the clicked position.
 |-
 | Pick Select || Only clicked files are operated.
 |- 
 | Animation || The animation control dialog is opened.
 |}

;5) Help menu
{| class="wikitable" border="1"
 |-
 | style="background-color:gainsboro" | Component
 | style="background-color:gainsboro" | Function
 |-
 | About jV || Information about this application is shown.
 |-
 | Open Manual || A manual page is opened with a web browser.
 |}

== Open-Remode dialog ==
;1) URL with parameters
Selecting [PDBML], [PDB], [Polygon], [Script] or [Animation] menu item in the [File] – [Open – Remote] menu opens the open-remote dialog that can handle a URL with parameters. For example, Figure 5 shows a dialog opened by the [File] – [Open – Remote] – [PDBML] menu item.

[[File:Fig5.jpg|thumb|Figure5: The open-remote dialog|center|400px]]

When ‘Add’ button is clicked, a new parameter line is appended in the table at the center of the dialog. Figure 6 shows an example of a URL with one parameter. By clicking the ‘Add’ button the necessary number of times, you can attach multiple parameters. When ‘Remove’ button is clicked, a highlighted line in the parameter table is removed. When ‘Clear’ button is clicked, all parameters are removed.

[[File:Fig6.jpg|thumb|Figure6: Example of a URL with a parameter|center|400px]]

;2)'type' column and mouse pick
The ‘type’ column in the parameter table is selected from the follows.

{| class="wikitable" border="1"
 |-
 | style="background-color:gainsboro" | type
 | style="background-color:gainsboro" | values
 | style="background-color:gainsboro" | mouse pick
 |-
 | text || arbitrary value || does not work
 |-
 | atom ID || atom ID || work
 |-
 | atom || set of chain ID, residue ID and atom ID || work
 |-
 | residue || set of chain ID and residue ID || work
 |-
 | orig_coords || atom coordinates written in the molecule file || work
 |-
 | curr_coords || atom coordinates currently displayed || work
 |}

For the case of a type to which mouse pick works, selecting an atom in the screen by mouse pick sets the corresponding value to the ‘value’ column in a highlighted line in the parameter table. The value of the ‘delimiter’ field is used to delimit atom’s x, y, and z coordinate.

;3) Saving and loading the configuration
By clicking the ‘save’ button, a file chooser dialog appears and the current configuration can be saved to a file. In the same way, a configuration can be loaded by clicking the ‘load’ button. The contents of a configuration file are in XML format as follows.

 &lt;?xml version="1.0"?&gt;
 &amp;nbsp;
 &amp;nbsp;
 &lt;remote_file url="http://example.com"&gt;
  &lt;params attach="true" coordinates_delimiter=","&gt;
    &lt;param name="param1" value="value1" type="text"/&gt;
  &lt;/params&gt;
 &lt;/remote_file&gt;

;4) Copy of the transform
When a file ID that currently exists is entered to the ‘fit to’ field, the transform of the newly opened file is set identical to that of the specified file.

;5) Execution
When the ‘OK’ button is clicked, a new file is loaded and the dialog is closed. When you use ‘Submit’ button, on the other hand, the dialog remains visible even after a new file is loaded.

== Animation control dialog ==
The animation control dialog is visible only if [Options] - [Animation] menu is checked. When there is no animation file loaded, the animation control dialog is as Figure 7. If some animation files are opened, the animation control dialog is altered according to the number of the files. Figure 8 indicates the dialog in the presence of two files.

[[File:Tutorial_fig7.jpg|thumb|Figure7: The animation control dialog in the absence of files.|center|400px]]

[[File:Tutorial_fig8.jpg|thumb|Figure8: The animation control dialog in the presence of two files.|center|400px]]

Users can select which files are controlled by their checkbox. The frame position and playback and stop of the animation can be controlled individually to each file. The playback-speed and the selection of ‘loop’ and ‘swing’ modes are common for all files.</text>
    <sha1>0049f0036c37ae8396bd406203ab06d89a6718de</sha1>
  </revision>
</page>
<page arvcontinue="20100805022053|404">
  <title>Functional site information for molecules</title>
  <ns>0</ns>
  <id>36</id>
  <revision>
    <id>438</id>
    <parentid>240</parentid>
    <timestamp>2010-12-15T02:24:46Z</timestamp>
    <contributor>
      <username>IMSsato</username>
      <id>4</id>
    </contributor>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="5551" xml:space="preserve">A simple XML file is defined in jV3 in order to describe functional sites of a molecule. If an external database server that returns this type of XML file is prepared, you can let jV3 read the file through the network and obtain the functional site information. An example of the XML file is as follows.

 &lt;?xml version=”1.0” ?&gt;
 &amp;nbsp;
 &lt;site_list&gt;
  &lt;site id=”CATRES1” db=”CATRES” category=”catalytic”
        description=”a catalytic site defined by CATRES, Medline 98100076”&gt;
    &lt;region chain_id=”A” beg_seq_id=”100” end_seq_id=”100”/&gt;
    &lt;region chain_id=”A” beg_seq_id=”46” end_seq_id=”46”/&gt;
    &lt;region chain_id=”A” beg_seq_id=”116” end_seq_id=”116”/&gt;
  &lt;/site&gt;
  &lt;site id=”ASN” db=”pdb_hetatom” category=”binding”
        description=”ASPARAGINE binding site”&gt;
    &lt;region chain_id=”A” beg_seq_id=”48” end_seq_id=”48”/&gt;
    &lt;region chain_id=”A” beg_seq_id=”72” end_seq_id=”74”/&gt;
  &lt;/site&gt;
  &lt;site id=”0006529” db=”godata” category=”biological_process”
        description=”asparagine biosynthesis”&gt;
    &lt;region chain_id=”A”/&gt;
  &lt;/site&gt;
  &lt;site id=”0016874” db=”godata” category=”molecular_function”
        description=”ligase activity”&gt;
    &lt;region chain_id=”A”/&gt;
  &lt;/site&gt;
 &lt;/site_list&gt;

The XML schema file that defines the document type of the above XML file is published at http://ef-site.hgc.jp/eF-site/schema/sitelist10.xsd. When a text file ‘properties.txt’ exists in the same directory as the application jar file, jV3 reads the file as a configuration file for the application. The current configuration file, which is attached to the binary distribution, contains a set of URL necessary to connect to the PDBMLplus and eF-site system as follows.

 # PDBML files are retrieved from the following site.
 pdbml_noatom=ftp://ftp.pdbj.org/XML/all-noatom/
 pdbml_extatom=ftp://ftp.pdbj.org/XML/all-extatom/
 pdbml_plus=ftp://ftp.pdbj.org/XML/pdbmlplus/pdbml_xp_gz/
 &amp;nbsp;
 # eF-site data are retrieved from the following site.
 efsite=http://ef-site.hgc.jp/eF-site/

If a database server that returns the functional site file is prepared, its URL should be appended to the configuration file. Because one functional site file is assumed to exist for one PDB ID, the URL written in the configuration file depends on the PDB ID. Therefore, the URL is represented with the use of substitute characters {0}, {1}, {2} and {3} that are substituted by each column of the PDB ID sequentially. An example is as follows.

 # works with my database.
 mydb=http://myhost.jp/mydb/jv3/{0}{1}{2}{3}_jv.xml

Here, the property name, ‘mydb’ in the above example, is arbitrary. Note that a PDB ID {0}{1}{2}{3} is substituted as lowercases and available protocols are http:, ftp: and file:. For simplicity, it is assumed that only one molecule file that corresponds to the above example XML file is opened in the application. Then functional site information can be displayed by the ‘show’ command as follows.

 jV3&gt; show site mydb
 File 1:
  db           category
  -------------------------------
  CATRES       catalytic
  pdb_hetatom  binding
  godata       biological_process
  godata       molcular_function
 jV3&gt; show site mydb:CATRES
 File 1:
  id=CATRES1  category=catalytic  region=A:100-100,A:46-46,A:116-116
      description=a catalytic site defined by CATRES, Medline 98100076
 jV3&gt; show site mydb:pdb_hetatom:binding
 File 1:
  id=ASN  category=binding  region=A:48-48,A:72-74 
      description=ASPARAGINE binding site
 jV3&gt; show site mydb:godata
 File 1:
  id=0006529  category=biological_process  region=A
      description=asparagine biosynthesis
  id=0016874  category=molecular_function  region=A
      description=ligase activity
 jV3&gt; show site mydb:godata:molecular_function
 File 1:
  id=0016874  category=molecular_function  region=A
      description=ligase activity
 jV3&gt;

With a similar syntax, the ‘select’ command can be used to select the relevant set of atoms. To demonstrate the operations described in this section, let us add a following line to the configuration file ‘properties.txt’.

 ex=http://ef-site.hgc.jp/jv3site/servlet/Site?pdb={0}{1}{2}{3}

The above URL provides functional site information whose contents are equivalent to those of PDBMLplus for all PDB. To reload the configuration file, quit the application (if it runs) and restart it. Then open the molecule ‘1yec’ as an example. To do this, you can use [File] – [Open – Remote] – [PDB ID] menu item as in the section 4.2, or equivalently execute ‘load ftp 1yec’ in the command line. Subsequently, execute ‘show site ex’ and the following keywords will be listed (the contents may change in the future).

 jV3&gt; show site ex
 File 1:
  db           category
  ---------------------
  prosite      prosite
  pdb_hetatom  binding

Detail site information can be shown as follows.

 jV3&gt; show site ex:prosite
 File 1:
  id=PS00290  db=prosite  category=prosite  region=L:192-198
    description=Immunoglobulins and major histocompatibility complex proteins signature. [FY]-{L}-C-x-[VA]-{LC}-H

Atoms in the region ‘L:192-198’ can be selected with a similar syntax.

 jV3&gt; select ex:prosite
 56 Atoms Selected.

In the same way, the following atom selections are possible.

 jV3&gt; select ex:pdb_hetatom
 298 Atoms Selected.
 jV3&gt; select ex:
 354 Atoms Selected.

Here the last command selects both regions specified by ‘prosite’ and ‘pdb_hetatom’ keywords, respectively.</text>
    <sha1>1a4098199ecc5e5ce61cc9576274e6bee537a21c</sha1>
  </revision>
  <revision>
    <id>439</id>
    <parentid>438</parentid>
    <timestamp>2010-12-15T02:30:19Z</timestamp>
    <contributor>
      <username>IMSsato</username>
      <id>4</id>
    </contributor>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="5605" xml:space="preserve">A simple XML file is defined in jV3 in order to describe functional sites of a molecule. If an external database server that returns this type of XML file is prepared, you can let jV3 read the file through the network and obtain the functional site information. An example of the XML file is as follows.

 &lt;?xml version=”1.0” ?&gt;
 &amp;nbsp;
 &lt;site_list&gt;
  &lt;site id=”CATRES1” db=”CATRES” category=”catalytic”
        description=”a catalytic site defined by CATRES, Medline 98100076”&gt;
    &lt;region chain_id=”A” beg_seq_id=”100” end_seq_id=”100”/&gt;
    &lt;region chain_id=”A” beg_seq_id=”46” end_seq_id=”46”/&gt;
    &lt;region chain_id=”A” beg_seq_id=”116” end_seq_id=”116”/&gt;
  &lt;/site&gt;
  &lt;site id=”ASN” db=”pdb_hetatom” category=”binding”
        description=”ASPARAGINE binding site”&gt;
    &lt;region chain_id=”A” beg_seq_id=”48” end_seq_id=”48”/&gt;
    &lt;region chain_id=”A” beg_seq_id=”72” end_seq_id=”74”/&gt;
  &lt;/site&gt;
  &lt;site id=”0006529” db=”godata” category=”biological_process”
        description=”asparagine biosynthesis”&gt;
    &lt;region chain_id=”A”/&gt;
  &lt;/site&gt;
  &lt;site id=”0016874” db=”godata” category=”molecular_function”
        description=”ligase activity”&gt;
    &lt;region chain_id=”A”/&gt;
  &lt;/site&gt;
 &lt;/site_list&gt;

The XML schema file that defines the document type of the above XML file is published at http://ef-site.hgc.jp/eF-site/schema/sitelist10.xsd. When a text file ‘properties.txt’ exists in the same directory as the application jar file, jV3 reads the file as a configuration file for the application. The current configuration file, which is attached to the binary distribution, contains a set of URL necessary to connect to the PDBMLplus and eF-site system as follows.

 # PDBML files are retrieved from the following site.
 pdbml_noatom=ftp://ftp.pdbj.org/XML/all-noatom/
 pdbml_extatom=ftp://ftp.pdbj.org/XML/all-extatom/
 pdbml_plus=ftp://ftp.pdbj.org/XML/pdbmlplus/pdbml_xp_gz/
 &amp;nbsp;
 # eF-site data are retrieved from the following site.
 efsite=http://ef-site.hgc.jp/eF-site/

If a database server that returns the functional site file is prepared, its URL should be appended to the configuration file. Because one functional site file is assumed to exist for one PDB ID, the URL written in the configuration file depends on the PDB ID. Therefore, the URL is represented with the use of substitute characters {0}, {1}, {2} and {3} that are substituted by each column of the PDB ID sequentially. An example is as follows.

 # works with my database.
 mydb=http://myhost.jp/mydb/jv3/{0}{1}{2}{3}_jv.xml

Here, the property name, ‘mydb’ in the above example, is arbitrary. Note that a PDB ID {0}{1}{2}{3} is substituted as lowercases and available protocols are http:, ftp: and file:. For simplicity, it is assumed that only one molecule file that corresponds to the above example XML file is opened in the application. Then functional site information can be displayed by the ‘show’ command as follows.

 jV3&gt; show site mydb
 File 1:
  db           category
  -------------------------------
  CATRES       catalytic
  pdb_hetatom  binding
  godata       biological_process
  godata       molcular_function
 jV3&gt; show site mydb:CATRES
 File 1:
  id=CATRES1  category=catalytic  region=A:100-100,A:46-46,A:116-116
      description=a catalytic site defined by CATRES, Medline 98100076
 jV3&gt; show site mydb:pdb_hetatom:binding
 File 1:
  id=ASN  category=binding  region=A:48-48,A:72-74 
      description=ASPARAGINE binding site
 jV3&gt; show site mydb:godata
 File 1:
  id=0006529  category=biological_process  region=A
      description=asparagine biosynthesis
  id=0016874  category=molecular_function  region=A
      description=ligase activity
 jV3&gt; show site mydb:godata:molecular_function
 File 1:
  id=0016874  category=molecular_function  region=A
      description=ligase activity
 jV3&gt;

With a similar syntax, the ‘select’ command can be used to select the relevant set of atoms. To demonstrate the operations described in this section, let us add a following line to the configuration file ‘properties.txt’.

 ex=http://ef-site.hgc.jp/jv3site/servlet/Site?pdb={0}{1}{2}{3}

The above URL provides functional site information whose contents are equivalent to those of PDBMLplus for all PDB. To reload the configuration file, quit the application (if it runs) and restart it. Then open the molecule ‘1yec’ as an example. To do this, you can use [File] – [Open – Remote] – [PDB ID] menu item as in the '[[Tutorials#Displaying_molecules|Displaying molecules]]' section, or equivalently execute ‘load ftp 1yec’ in the command line. Subsequently, execute ‘show site ex’ and the following keywords will be listed (the contents may change in the future).

 jV3&gt; show site ex
 File 1:
  db           category
  ---------------------
  prosite      prosite
  pdb_hetatom  binding

Detail site information can be shown as follows.

 jV3&gt; show site ex:prosite
 File 1:
  id=PS00290  db=prosite  category=prosite  region=L:192-198
    description=Immunoglobulins and major histocompatibility complex proteins signature. [FY]-{L}-C-x-[VA]-{LC}-H

Atoms in the region ‘L:192-198’ can be selected with a similar syntax.

 jV3&gt; select ex:prosite
 56 Atoms Selected.

In the same way, the following atom selections are possible.

 jV3&gt; select ex:pdb_hetatom
 298 Atoms Selected.
 jV3&gt; select ex:
 354 Atoms Selected.

Here the last command selects both regions specified by ‘prosite’ and ‘pdb_hetatom’ keywords, respectively.</text>
    <sha1>c1e08b2c2c15ba34f3c8c30b0fece154d1d3e910</sha1>
  </revision>
</page>
<page arvcontinue="20100805022053|404">
  <title>Introduction</title>
  <ns>0</ns>
  <id>44</id>
  <revision>
    <id>447</id>
    <parentid>338</parentid>
    <timestamp>2010-12-15T04:16:27Z</timestamp>
    <contributor>
      <username>IMSsato</username>
      <id>4</id>
    </contributor>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="1910" xml:space="preserve">jV is an interactive 3D viewer program to visualize protein and nucleic acid molecules. The program reads in a PDBML file that is an XML format for PDB. Usual PDB format files are also accepted. More than one molecule files can be opened and displayed at the same time and their display models and transforms can be operated separately. In addition to molecule files, a polygon file written in XML can be read and displayed. More than one polygon files can be opened at the same time and superposed on molecule images. The [http://ef-site.hgc.jp/eF-site/schema/polygon12.xsd XML schema] of the polygon file is available. jV can perform an animation of molecules. The animation file is a PDB format file in which each frame is separated by a MODEL line.

jV runs on Java Runtime Environment ([http://java.sun.com/javase/ JRE]) and can be used both as a standalone program and an applet. The 3D rendering is performed with the use of [http://kenai.com/projects/jogl JOGL] API. The version requirements are as follows.

* JRE (includes Java Plug-in) 1.4.2 or later
* JOGL JSR-231 1.0.0 or later

Here, [http://java.sun.com/products/plugin/ Java Plug-in] is required in order to use the program as an applet.

The program allows an interactive mouse control and command execution. The commnad syntax follows that of [http://www.rasmol.org/ Rasmol] with some modifications. In order to handle the transform of each molecule and polygon separately, every files are set to be either selected or not selected. The transform operation commands, such as rotate or translate, act only on selected files. On the other hand, every atoms in a molecule are also set to be either selected or not selected independently of whether the molecule itself is selected or not selected. Only selected atoms are the target of display model operations, such as wireframe or spacefill commands, and coloring operations.

[[Release note]]</text>
    <sha1>df266c430fda46180d3a2860dc91cb889f838aed</sha1>
  </revision>
</page>
<page arvcontinue="20100805022053|404">
  <title>Use jV applet with applet launcher</title>
  <ns>0</ns>
  <id>16</id>
  <revision>
    <id>448</id>
    <parentid>328</parentid>
    <timestamp>2010-12-15T04:25:58Z</timestamp>
    <contributor>
      <username>IMSsato</username>
      <id>4</id>
    </contributor>
    <comment>/* Minimum Example */</comment>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="1864" xml:space="preserve">A brief introduction to use jV in applet.

== Minimum Example ==
One way to use jV applet is to use with applet-launcher. jV after v3.6 is fully compatible with applet-launcher.

 &lt;applet
   hspace="0" vspace="0" align="middle"
   name="jVwindow" height="600" width="600"
   archive="applet-launcher.jar,
   http://download.java.net/media/jogl/builds/archive/jsr-231-webstart-current/jogl.jar,
   http://download.java.net/media/gluegen/webstart/gluegen-rt.jar,'''jv3_6.jar'''"
   code="org.jdesktop.applet.util.JNLPAppletLauncher"&gt;
 &amp;lt;!-- param for applet-launcher --&gt;
   &lt;param name="subapplet.classname" value="'''org.pdbj.viewer.gui.ViewerApplet'''"&gt;
   &lt;param name="subapplet.displayname" value="jV applet"&gt;
   &lt;param name="noddraw.check" value="true"/&gt;
   &lt;param name="noddraw.check.silent" value="true"/&gt;
   &lt;param name="progressbar" value="true"/&gt;
   &lt;param name="jnlpNumExtensions" value="1"/&gt;
   &lt;param name="jnlpExtension1"
    value="http://download.java.net/media/jogl/builds/archive/jsr-231-webstart-current/jogl.jnlp"/&gt;
 '''&amp;lt;!-- param for jV --&gt;'''
   '''&lt;param value="" name="pdbURL"&gt;'''
    '''&amp;lt;!-- replace the following with an appropriate URL --&gt;'''
   '''&lt;param name="pdbmlURL" value="http://eprots.protein.osaka-u.ac.jp/Rep_PDBML/1ashA1.xml.gz"&gt;'''
   '''&lt;param value="" name="polygonURL"&gt;'''
   '''&lt;param value="set picking ident;background black;wireframe off;cartoon;color group" name="commands"&gt;'''
 &lt;/applet&gt;

Upper part is almost same as the usual usage of applet launcher. See the [https://applet-launcher.dev.java.net/ applet-launcher page] for details. The latter part is for jV parameters.

Only the &lt;B&gt;bold face&lt;/B&gt; part is specific for jV.

To use this template, you need to get applet-launcher.jar from http://download.java.net/media/applet-launcher/applet-launcher.jar, and put it in the same server that jv.jar is placed.</text>
    <sha1>0f10d5da0d74187494587de4762cf8f346aa272c</sha1>
  </revision>
</page>
<page arvcontinue="20100805022053|404">
  <title>How to use</title>
  <ns>0</ns>
  <id>11</id>
  <revision>
    <id>449</id>
    <parentid>382</parentid>
    <timestamp>2010-12-15T05:50:08Z</timestamp>
    <contributor>
      <username>IMSsato</username>
      <id>4</id>
    </contributor>
    <comment>/* Some examples */</comment>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="1160" xml:space="preserve">The following table shows how to do the minimum things with jV; the mouse controls.
For the detail, see the reference manual and User's guide.&lt;br /&gt;
{| class="wikitable" border="1" style="margin:0 auto" 
 ! Action !! Window, Linux !! Mac OS X 
 |-
 ! style="text-align:left" | rotate around X,Y axes
 | left drag || drag
 |-
 ! style="text-align:left" | rotate around Z axis
 | Shift + right drag || Shift + command + drag
 |-
 ! style="text-align:left" | translate along X,Y axes
 | right drag || command + drag
 |-
 ! style="text-align:left" | translate along Z axis (zoom in/out)
 | Shift + left drag || Shift + drag
 |-
 ! style="text-align:left" | translate slab plane along Z axis
 | (Alt or Ctrl) + left drag || Alt + drag
 |}


== Reference manual ==
# [[Introduction]]
# [[Command List]]
# [[Atom Expression]]
# [[Vertex Expression]]
# [[Color Expression]]
# [[Use as Applet]]


== User's Guide ==
# [[Tutorials]]
# [[GUI]]
# [[Document type of the polygon file]]
# [[Functional site information for molecules]]


== Some examples ==
# [[Basic examples]]
# [[Animation]]
# [[Use jV with next-generation Java Plug-in]]
# [[Use jV with applet launcher]]</text>
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  </revision>
</page>
<page arvcontinue="20100805022053|404">
  <title>Use jV applet with JNLP file</title>
  <ns>0</ns>
  <id>68</id>
  <revision>
    <id>450</id>
    <timestamp>2010-12-15T05:50:23Z</timestamp>
    <contributor>
      <username>IMSsato</username>
      <id>4</id>
    </contributor>
    <comment>Created page with 'A brief introduction to use jV as applet with next-generation Java Plug-in. Note that Mac users cannnot utilize the next-generation Java Plug-in at the moment.  == Example == The…'</comment>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="1683" xml:space="preserve">A brief introduction to use jV as applet with next-generation Java Plug-in.
Note that Mac users cannnot utilize the next-generation Java Plug-in at the moment.

== Example ==
The following code snippet shows how to embed jV applet in a web page.

 &lt;applet
     name="jVwindow" height="600" width="600"
     code="org.pdbj.viewer.gui.ViewerApplet"&gt;
   &lt;param name="jnlp_href" value="jV-applet.jnlp"/&gt;
   &amp;lt;!-- replace the following with an appropriate URL --&gt;
   &lt;param name="pdbmlURL" value="http://eprots.protein.osaka-u.ac.jp/Rep_PDBML/1ashA1.xml.gz"&gt;
   &lt;param name="commands" value="cartoon;color group" name="commands"&gt;
 &lt;/applet&gt;

The example assumes that a file named jV-applet.jnlp is placed at the same location as the HTML file that contains above applet tag. The contents of jV-applet.jnlp is as follows.

 &lt;?xml version="1.0" encoding="UTF-8"?&gt;
 &lt;jnlp href="jV-applet.jnlp"&gt;
   &lt;information&gt;
     &lt;title&gt;jV&lt;/title&gt;
     &lt;vendor&gt;Protein Data Bank Japan&lt;/vendor&gt;
     &lt;homepage href="http://ef-site.hgc.jp/jV/"/&gt;
     &lt;description&gt;Program to display molecular graphics of proteins and nucleic acids&lt;/description&gt;
     &lt;description kind="short"&gt;&lt;/description&gt;
     &lt;offline-allowed/&gt;
   &lt;/information&gt;
   &lt;resources&gt;
     &lt;j2se href="http://java.sun.com/products/autodl/j2se" version="1.4+"/&gt;
     &lt;property name="sun.java2d.noddraw" value="true"/&gt;
     &lt;jar href="jv3_8_2.jar"/&gt;
     &lt;extension name="jogl" href="http://download.java.net/media/jogl/builds/archive/jsr-231-webstart-current/jogl.jnlp" /&gt;
   &lt;/resources&gt;
   &lt;applet-desc
       name="jV"
       main-class="org.pdbj.viewer.gui.ViewerApplet"
       width="500"
       height="500"&gt;
   &lt;/applet-desc&gt;
 &lt;/jnlp&gt;</text>
    <sha1>02a7a62c5076e2a6bdd056e0a03cfeedc409edf8</sha1>
  </revision>
  <revision>
    <id>451</id>
    <parentid>450</parentid>
    <timestamp>2010-12-15T06:07:49Z</timestamp>
    <contributor>
      <username>IMSsato</username>
      <id>4</id>
    </contributor>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="1784" xml:space="preserve">A brief introduction to use jV as applet with next-generation Java Plug-in.
Note that Mac users cannnot utilize the next-generation Java Plug-in at the moment.

== Example ==
The following code snippet shows how to embed jV applet in a web page.

 &lt;applet name="jVwindow" height="600" width="600"&gt;
   &lt;param name="jnlp_href" value="jV-applet.jnlp"/&gt;
   &amp;lt;!-- replace the following with an appropriate URL --&gt;
   &lt;param name="pdbmlURL" value="http://eprots.protein.osaka-u.ac.jp/Rep_PDBML/1ashA1.xml.gz"&gt;
   &lt;param name="commands" value="cartoon;color group" name="commands"&gt;
 &lt;/applet&gt;

The example assumes that a file named jV-applet.jnlp is placed at the same location as the HTML file that contains above applet tag. The contents of jV-applet.jnlp is as follows.

 &lt;?xml version="1.0" encoding="UTF-8"?&gt;
 &lt;jnlp href="jV-applet.jnlp"&gt;
   &lt;information&gt;
     &lt;title&gt;jV&lt;/title&gt;
     &lt;vendor&gt;Protein Data Bank Japan&lt;/vendor&gt;
     &lt;homepage href="http://ef-site.hgc.jp/jV/"/&gt;
     &lt;description&gt;Program to display molecular graphics of proteins and nucleic acids&lt;/description&gt;
     &lt;description kind="short"&gt;&lt;/description&gt;
     &lt;offline-allowed/&gt;
   &lt;/information&gt;
   &lt;resources&gt;
     &lt;j2se href="http://java.sun.com/products/autodl/j2se" version="1.4+"/&gt;
     &lt;property name="sun.java2d.noddraw" value="true"/&gt;
     &lt;jar href="jv3_8_2.jar"/&gt;
     &lt;extension name="jogl" href="http://download.java.net/media/jogl/builds/archive/jsr-231-webstart-current/jogl.jnlp" /&gt;
   &lt;/resources&gt;
   &lt;applet-desc
       name="jV"
       main-class="org.pdbj.viewer.gui.ViewerApplet"
       width="500"
       height="500"&gt;
   &lt;/applet-desc&gt;
 &lt;/jnlp&gt;

Here, applet-desc tag has name, width and height attributes. These are required, however, their values are overridden by those of applet tag in HTML.</text>
    <sha1>7c127914558e571b884fff2933452787e3e6b930</sha1>
  </revision>
</page>
<page arvcontinue="20110106074224|454">
  <title>Installation of jV</title>
  <ns>0</ns>
  <id>38</id>
  <revision>
    <id>454</id>
    <parentid>327</parentid>
    <timestamp>2011-01-06T07:42:24Z</timestamp>
    <contributor>
      <username>IMSsato</username>
      <id>4</id>
    </contributor>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="614" xml:space="preserve">__NOTOC__
== System requirements ==
jV3 runs on the Java Runtime Environment (JRE) with JOGL API. The version requirements are as follows.
* [http://java.sun.com/j2se/ JRE] (includes Java Plug-in) 1.4.2 or later
* [https://jogl.dev.java.net/ JOGL] API JSR-231 1.0.0 or later 
These softwares are available on typical operation systems such as Windows (2000/XP/Vista), Mac OS X 10.3 or later, and Red Hat Linux 7.3 or later.

== Installing JOGL API ==
From the version 3.8.3, binary distribution of jV contains the JOGL library
and pre-installation of JOGL is not necessary.
Only JRE should be installed in advance.</text>
    <sha1>35d77323992e039539a3f2fcd89f22968cc34959</sha1>
  </revision>
  <revision>
    <id>457</id>
    <parentid>454</parentid>
    <timestamp>2011-01-07T03:44:34Z</timestamp>
    <contributor>
      <username>IMSsato</username>
      <id>4</id>
    </contributor>
    <comment>/* Installing JOGL API */</comment>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="776" xml:space="preserve">__NOTOC__
== System requirements ==
jV3 runs on the Java Runtime Environment (JRE) with JOGL API. The version requirements are as follows.
* [http://java.sun.com/j2se/ JRE] (includes Java Plug-in) 1.4.2 or later
* [https://jogl.dev.java.net/ JOGL] API JSR-231 1.0.0 or later 
These softwares are available on typical operation systems such as Windows (2000/XP/Vista), Mac OS X 10.3 or later, and Red Hat Linux 7.3 or later.

== Installation ==
From the version 3.8.3, binary distribution of jV contains the JOGL library
and pre-installation of JOGL is not necessary.
Just JRE is required on your computer in advance.
With JRE properly installed, you can download the binary distribution of jV 
and immediately use jV by running a start-up script contained in the distribution.</text>
    <sha1>cca4b7a2b6b8fbef0b7ef38c5111b2ce02da2686</sha1>
  </revision>
  <revision>
    <id>481</id>
    <parentid>457</parentid>
    <timestamp>2011-12-22T05:01:21Z</timestamp>
    <contributor>
      <username>IMSsato</username>
      <id>4</id>
    </contributor>
    <minor/>
    <comment>moved [[Installation of jV3]] to [[Installation of jV]]</comment>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="776" xml:space="preserve">__NOTOC__
== System requirements ==
jV3 runs on the Java Runtime Environment (JRE) with JOGL API. The version requirements are as follows.
* [http://java.sun.com/j2se/ JRE] (includes Java Plug-in) 1.4.2 or later
* [https://jogl.dev.java.net/ JOGL] API JSR-231 1.0.0 or later 
These softwares are available on typical operation systems such as Windows (2000/XP/Vista), Mac OS X 10.3 or later, and Red Hat Linux 7.3 or later.

== Installation ==
From the version 3.8.3, binary distribution of jV contains the JOGL library
and pre-installation of JOGL is not necessary.
Just JRE is required on your computer in advance.
With JRE properly installed, you can download the binary distribution of jV 
and immediately use jV by running a start-up script contained in the distribution.</text>
    <sha1>cca4b7a2b6b8fbef0b7ef38c5111b2ce02da2686</sha1>
  </revision>
  <revision>
    <id>484</id>
    <parentid>481</parentid>
    <timestamp>2011-12-22T05:07:32Z</timestamp>
    <contributor>
      <username>IMSsato</username>
      <id>4</id>
    </contributor>
    <comment>/* System requirements */</comment>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="765" xml:space="preserve">__NOTOC__
== System requirements ==
jV runs on the Java Runtime Environment (JRE) with JOGL API. The version requirements are as follows.
* [http://java.sun.com/j2se/ JRE] (includes Java Plug-in) 1.6 or later
* [http://jogamp.org/jogl/www/ JOGL] API 2.0-rc4 or later 
These softwares are available on typical operation systems such as Windows (XP/Vista/7), Mac OS X 10.6 or later, and Red Hat Linux 7.3 or later.

== Installation ==
From the version 3.8.3, binary distribution of jV contains the JOGL library
and pre-installation of JOGL is not necessary.
Just JRE is required on your computer in advance.
With JRE properly installed, you can download the binary distribution of jV 
and immediately use jV by running a start-up script contained in the distribution.</text>
    <sha1>8c9e0b11d1c0bbc9814eeb3af8c101ed597307a2</sha1>
  </revision>
</page>
<page arvcontinue="20110106074224|454">
  <title>Tutorials</title>
  <ns>0</ns>
  <id>25</id>
  <revision>
    <id>455</id>
    <parentid>446</parentid>
    <timestamp>2011-01-07T03:28:28Z</timestamp>
    <contributor>
      <username>IMSsato</username>
      <id>4</id>
    </contributor>
    <comment>/* Starting up */</comment>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="12030" xml:space="preserve">{| style="float:right"
 |__TOC__
 |}
== Starting up ==
It is assumed that Java Runtime Environment has been appropriately installed. You can start up jV by downloading the binary distribution and running a start-up script contained in the distribution. Another way to use jV is to follow [http://ef-site.hgc.jp/eF-site/servlet/stable/jV.jnlp this link], which launch jV via Java Web Start technology.
Figure 1 shows the start-up screen. The window has a 3-panel structure, and the upper-left panel with the black background is a 3D image display area. The status of files that have been loaded to the application is shown in the upper-right panel and the lower panel is a command-input and a message-output area.
[[File:Tutorial_fig1.jpg|thumb|Figure 1: Start-up screen|center|500px]]

== Displaying molecules ==
If you are working in the environment that is getting on the Internet and know the PDB ID of the molecule that you want to display, the simplest way is as follows. A dialog shown in Figure 2 is opened by selecting the [File] – [Open – Remote] – [PDB ID] menu item. Enter a PDB ID '12as', for example, to the text field and click the 'OK' button, then the PDBML file is read through the Internet and the molecule is displayed. A molecule is displayed in a wire frame model with colored by atom type in the initial state.

[[File:Fig2.jpg|thumb|Figure 2: Dialog to open the molecule specified by PDB ID|center|200px]]

Let us next attempt to load an arbitrary file on the Internet. Here we use 'http://ef-site.hgc.jp/eF-site/jV/1yec.pdb' as an example. The file is a conventional PDB file whose PDB ID is 1yec. In this case we choose the [File] – [Open – Remote] – [PDB] menu item. Then the open-remote dialog appears. Enter the above URL to the text field at the top of the dialog and click the 'OK' button and the molecule is read in and displayed. In jV3, each molecule is displayed according to the space coordination described in its file. Therefore, when loading and displaying more than one molecule together, they can be viewed with an appropriate separation in some cases; however, they may be displayed far separately or may be overlapped depending on the combination. In any case, when adding a new file, the position of the viewpoint is automatically controlled for the whole to be displayed.

The coordinate system is the right hand system with the x-y plane being on the screen (the x-axis is a horizontal line with positive values to the right and the y-axis is a vertical line with positive values up). Although, the above examples are about operations for remote files, a PDB file on your local hard disk can also be opened from the [File] – [Open – Local] – [PDB] menu item.

== Operating molecules ==
Interactive mouse operations are possible for 3D images. By left-dragging the mouse on the 3D-display panel, molecules are rotated around the x-axis or y-axis. By left-dragging the mouse while holding the Shift key on the keyboard, molecules are translated along the z-axis. All mouse operations are as follows (as for the Macintosh environment, the Command key + left-drag substitutes for the right-drag).

{| border="1"
 ! Mouse operations !! Actions
 |-
 | Left-drag || The image is rotated around the x (for a vertical motion) and y (for a horizontal motion) axes.
 |-
 | Right-drag || The image is translated on the x-y plane.
 |-
 | [Shift] + left-drag || The image is translated along the z-axis.
 |-
 | [Shift] + right-drag || The image is rotated around the z-axis.
 |-
 | [Alt or Ctrl] + left-drag || The z-clipping plane is shifted when [Option]-[Slab] is checked.
 |-
 | Left-click || An atom of the molecule displayed on the screen is picked.
 |}

In the upper-right panel in the application window (see Figure 3), the file names that have been loaded to the application are listed, where sequential integers are automatically assigned to the individual file. Each integer is a file ID that can be used to specify the file in the command line interface. In addition, three checkboxes are attached to each file. If you change the status of a ‘Disp’ checkbox, the corresponding molecule is switched to be displayed or not to be displayed. If you change the status of a ‘Mouse’ checkbox, the corresponding molecule is switched to be a target of the mouse operations or not. For example, set the both ‘Disp’ checkboxes on, and the both ‘Mouse’ checkboxes off. In this case, either molecule does not move against mouse operations. 

Subsequently set the ‘Mouse’ checkbox of file 1 on. In this case, mouse operations work for the molecule 1. Thus, each file is assigned either selected or not selected, and transform operations, such as rotation or translation, act only on selected files. On the other hand, every atom in a molecule is also assigned either selected or not selected, independently of whether the molecule itself is selected or not. Operations that modify display models or colors work for selected atoms. To see this, choose the [Display] – [Spacefill] menu item. Then the both molecules are displayed with the space fill model because all atoms are initially selected. In the same way, if you choose the [Colors] – [Monochrome] menu item, the both molecules are colored white. A ‘Sel’ checkbox selects or disselects all atoms in each file. 

Let us next try a more detailed operation. Type ‘select *@2’ in the command line area and press Enter key. This command means to select all atoms contained in the file 2 (the usage of the [[Command_List#select|select command]] is summarized in the reference manual). Subsequently, choose the [Display] – [Cartoon] menu item. As a result, only the molecule 2 is displayed in the cartoon model. Furthermore select the [Colors] – [Structure] menu item, and each residue of the molecule 2 is colored according to its secondary structure type (see Figure 3). 

In order to reproduce the same view as that in Figure 3, first execute ‘reset’ command. It restores the position of the viewpoint and the transform of every file to the initial state. Note that the command line interface tries to complement a command word when the Tab key is pressed. If you enter ‘res’ to the command line and subsequently press the Tab key, the command ‘reset’ is automatically entered. Next set the both ‘Mouse’ checkboxes on, and execute ‘translate z 100’ command. This command means to translate the molecules along the z-axis by 100 angstroms.

[[File:Tutorial_fig3.jpg|thumb|Figure 3: An example of molecular images.|center|500px]]

== Displaying polygons ==
In addition to molecules, arbitrary shapes described by polygons can be read in and displayed together, where the polygon file is an XML file, whose document type is described in the section 6. Here, we use ’http://ef-site.hgc.jp/eF-site/jV/1yec.surface.gz’ as an example. This polygon file represents a molecular surface of the molecule 2 (1yec) and the surface is colored according to the electrostatic potential and the hydrophobicity. It is assumed that the current image is the same as that in Figure 3. Then, open the open-remote dialog by choosing the [File] – [Open – Remote] – [Polygon] menu item, enter the above URL to the text field at the top of the dialog, and click the 'OK' button. As a result, the polygon is loaded, displayed and assigned file ID 3. 

Note that the polygon is displayed at the different position from the molecule 2 since the molecule 2 is translated. However, because the polygon and the molecule 2 are described by the same coordinates in their files, their images can be exactly superposed by executing ‘fit 3 2’ from the command line, where the ‘fit’ command performs the copy of the transform matrix. Finally, the image in Figure 4 appears.

[[File:Tutorial_fig4.jpg|thumb|Figure4: An example of polygon images.|center|500px]]

You can control the transparency rate of polygons. Try ’set transparency 0.5’ from the command line, where 0.5 stands for 50% transparency. To restore the image, execute ‘reset transparency’ or ‘set transparency 0’. In the same sense as each atom of a molecule, each vertex of a polygon is assigned either selected or not selected. All vertices are selected in the initial state. Execute a command ’displayvertex off’ and all vertices become invisible. Next execute ’selectvertex within(10.0, 1&amp;*H@2)’, where this means to select vertices that exist within 10 angstroms from each atom that belongs to the first residue of the ‘H’ chain of the molecule 2. Subsequently execute ’displayvertex on’. As a result, only the selected vertices appear. The usage of the [[Command List#selectvertex|selectvertex command]] is summarized in the reference manual.

== Working with PDBMLplus ==
Functional site information on a molecule stored in PDBMLplus is available in jV3. Before trying this, let us close the molecule 2 and the polygon 3 to make the situation simple. Select the [File] – [Close] – [2. 1yec.pdb] and [File] – [Close] – [3. 1yec.surface.gz] menu items sequentially. Then execute a ‘reset’ command and the transform of the molecule 1 and the position of the viewpoint are initialized. 

Next, confirm that the ‘Mouse’ checkbox of the file 1 is checked, and try a ‘show pdbj’ command. The functional site information of the molecule ‘12as’ is read from the PDBMLplus and ‘type’ and ‘subtype’ keywords for each functional site are listed. These keywords can be used to select a set of atoms. For example, if a keyword ‘CATRES’ exists (probably it does), the command ‘select pdbj:CATRES’ selects the corresponding atoms. 

In addition, gene ontology information can be obtained from the PDBMLplus. The gene ontology information for the molecule 12as is displayed by the command ’show godata’. Similar operations can be applied to other external databases on the Internet provided that the external database supports the interface that jV3 requires. See the '[[Functional site information for molecules]]' section for details.

== Animation ==
The animation of molecules can be performed in jV3. The animation file takes the PDB format, where the MODEL line divides each frame. Let us open an animation file ’http://ef-site.hgc.jp/eF-site/jV/anim.pdb.gz’ as an example from the open-remote dialog shown by selecting the [File] – [Open – Remote] – [Animation] menu item. When an animation file is loaded to the application, the first frame is automatically displayed in the wire frame model. You can start the animation by using the animation-control dialog that is shown by choosing the [Options] – [Animation] menu item. The dialog provides operations such as start and stop of the animation, selection of the animation mode, and adjustment of the speed. Some [[GUI#Animation_control_dialog|sample figures]] of the dialog are shown in the GUI section.

== Saving your work ==
While in your work, you can create a script file that contains a set of commands that reproduces the current work by using the [File] – [Save] – [Script] menu item. The script file can be loaded by the [File] – [Open – Local] – [Script] menu item. On the other hand, the [File] – [Save] – [PDB] menu item enables to save a molecule to a PDB format file with the coordinates of the atoms being transformed according to the current image. Here, only one molecule must be selected and only selected atoms in the molecule are saved. The other two menu items in the [File] – [Save] menu, [PNG] and [JPEG], save the current screen image to an image file in the PNG and JPEG format, respectively. The created image file has the same size as that of the 3D-display panel in the application.

== Terminating the application ==
The application is terminated when the [File] – [Exit] menu item is chosen or the application window is closed by the way your operation system provides. You can also quit the application by executing ‘exit’ or ‘quit’ command.</text>
    <sha1>4edc64ca8c2d09a07e30b40c42a9e07d16c797bc</sha1>
  </revision>
  <revision>
    <id>456</id>
    <parentid>455</parentid>
    <timestamp>2011-01-07T03:39:50Z</timestamp>
    <contributor>
      <username>IMSsato</username>
      <id>4</id>
    </contributor>
    <comment>/* Starting up */</comment>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="12025" xml:space="preserve">{| style="float:right"
 |__TOC__
 |}
== Starting up ==
It is assumed that Java Runtime Environment has been properly installed. You can start up jV by downloading the binary distribution and running a start-up script contained in the distribution. Another way to use jV is to follow [http://ef-site.hgc.jp/eF-site/servlet/stable/jV.jnlp this link], which launch jV via Java Web Start technology.
Figure 1 shows the start-up screen. The window has a 3-panel structure, and the upper-left panel with the black background is a 3D image display area. The status of files that have been loaded to the application is shown in the upper-right panel and the lower panel is a command-input and a message-output area.
[[File:Tutorial_fig1.jpg|thumb|Figure 1: Start-up screen|center|500px]]

== Displaying molecules ==
If you are working in the environment that is getting on the Internet and know the PDB ID of the molecule that you want to display, the simplest way is as follows. A dialog shown in Figure 2 is opened by selecting the [File] – [Open – Remote] – [PDB ID] menu item. Enter a PDB ID '12as', for example, to the text field and click the 'OK' button, then the PDBML file is read through the Internet and the molecule is displayed. A molecule is displayed in a wire frame model with colored by atom type in the initial state.

[[File:Fig2.jpg|thumb|Figure 2: Dialog to open the molecule specified by PDB ID|center|200px]]

Let us next attempt to load an arbitrary file on the Internet. Here we use 'http://ef-site.hgc.jp/eF-site/jV/1yec.pdb' as an example. The file is a conventional PDB file whose PDB ID is 1yec. In this case we choose the [File] – [Open – Remote] – [PDB] menu item. Then the open-remote dialog appears. Enter the above URL to the text field at the top of the dialog and click the 'OK' button and the molecule is read in and displayed. In jV3, each molecule is displayed according to the space coordination described in its file. Therefore, when loading and displaying more than one molecule together, they can be viewed with an appropriate separation in some cases; however, they may be displayed far separately or may be overlapped depending on the combination. In any case, when adding a new file, the position of the viewpoint is automatically controlled for the whole to be displayed.

The coordinate system is the right hand system with the x-y plane being on the screen (the x-axis is a horizontal line with positive values to the right and the y-axis is a vertical line with positive values up). Although, the above examples are about operations for remote files, a PDB file on your local hard disk can also be opened from the [File] – [Open – Local] – [PDB] menu item.

== Operating molecules ==
Interactive mouse operations are possible for 3D images. By left-dragging the mouse on the 3D-display panel, molecules are rotated around the x-axis or y-axis. By left-dragging the mouse while holding the Shift key on the keyboard, molecules are translated along the z-axis. All mouse operations are as follows (as for the Macintosh environment, the Command key + left-drag substitutes for the right-drag).

{| border="1"
 ! Mouse operations !! Actions
 |-
 | Left-drag || The image is rotated around the x (for a vertical motion) and y (for a horizontal motion) axes.
 |-
 | Right-drag || The image is translated on the x-y plane.
 |-
 | [Shift] + left-drag || The image is translated along the z-axis.
 |-
 | [Shift] + right-drag || The image is rotated around the z-axis.
 |-
 | [Alt or Ctrl] + left-drag || The z-clipping plane is shifted when [Option]-[Slab] is checked.
 |-
 | Left-click || An atom of the molecule displayed on the screen is picked.
 |}

In the upper-right panel in the application window (see Figure 3), the file names that have been loaded to the application are listed, where sequential integers are automatically assigned to the individual file. Each integer is a file ID that can be used to specify the file in the command line interface. In addition, three checkboxes are attached to each file. If you change the status of a ‘Disp’ checkbox, the corresponding molecule is switched to be displayed or not to be displayed. If you change the status of a ‘Mouse’ checkbox, the corresponding molecule is switched to be a target of the mouse operations or not. For example, set the both ‘Disp’ checkboxes on, and the both ‘Mouse’ checkboxes off. In this case, either molecule does not move against mouse operations. 

Subsequently set the ‘Mouse’ checkbox of file 1 on. In this case, mouse operations work for the molecule 1. Thus, each file is assigned either selected or not selected, and transform operations, such as rotation or translation, act only on selected files. On the other hand, every atom in a molecule is also assigned either selected or not selected, independently of whether the molecule itself is selected or not. Operations that modify display models or colors work for selected atoms. To see this, choose the [Display] – [Spacefill] menu item. Then the both molecules are displayed with the space fill model because all atoms are initially selected. In the same way, if you choose the [Colors] – [Monochrome] menu item, the both molecules are colored white. A ‘Sel’ checkbox selects or disselects all atoms in each file. 

Let us next try a more detailed operation. Type ‘select *@2’ in the command line area and press Enter key. This command means to select all atoms contained in the file 2 (the usage of the [[Command_List#select|select command]] is summarized in the reference manual). Subsequently, choose the [Display] – [Cartoon] menu item. As a result, only the molecule 2 is displayed in the cartoon model. Furthermore select the [Colors] – [Structure] menu item, and each residue of the molecule 2 is colored according to its secondary structure type (see Figure 3). 

In order to reproduce the same view as that in Figure 3, first execute ‘reset’ command. It restores the position of the viewpoint and the transform of every file to the initial state. Note that the command line interface tries to complement a command word when the Tab key is pressed. If you enter ‘res’ to the command line and subsequently press the Tab key, the command ‘reset’ is automatically entered. Next set the both ‘Mouse’ checkboxes on, and execute ‘translate z 100’ command. This command means to translate the molecules along the z-axis by 100 angstroms.

[[File:Tutorial_fig3.jpg|thumb|Figure 3: An example of molecular images.|center|500px]]

== Displaying polygons ==
In addition to molecules, arbitrary shapes described by polygons can be read in and displayed together, where the polygon file is an XML file, whose document type is described in the section 6. Here, we use ’http://ef-site.hgc.jp/eF-site/jV/1yec.surface.gz’ as an example. This polygon file represents a molecular surface of the molecule 2 (1yec) and the surface is colored according to the electrostatic potential and the hydrophobicity. It is assumed that the current image is the same as that in Figure 3. Then, open the open-remote dialog by choosing the [File] – [Open – Remote] – [Polygon] menu item, enter the above URL to the text field at the top of the dialog, and click the 'OK' button. As a result, the polygon is loaded, displayed and assigned file ID 3. 

Note that the polygon is displayed at the different position from the molecule 2 since the molecule 2 is translated. However, because the polygon and the molecule 2 are described by the same coordinates in their files, their images can be exactly superposed by executing ‘fit 3 2’ from the command line, where the ‘fit’ command performs the copy of the transform matrix. Finally, the image in Figure 4 appears.

[[File:Tutorial_fig4.jpg|thumb|Figure4: An example of polygon images.|center|500px]]

You can control the transparency rate of polygons. Try ’set transparency 0.5’ from the command line, where 0.5 stands for 50% transparency. To restore the image, execute ‘reset transparency’ or ‘set transparency 0’. In the same sense as each atom of a molecule, each vertex of a polygon is assigned either selected or not selected. All vertices are selected in the initial state. Execute a command ’displayvertex off’ and all vertices become invisible. Next execute ’selectvertex within(10.0, 1&amp;*H@2)’, where this means to select vertices that exist within 10 angstroms from each atom that belongs to the first residue of the ‘H’ chain of the molecule 2. Subsequently execute ’displayvertex on’. As a result, only the selected vertices appear. The usage of the [[Command List#selectvertex|selectvertex command]] is summarized in the reference manual.

== Working with PDBMLplus ==
Functional site information on a molecule stored in PDBMLplus is available in jV3. Before trying this, let us close the molecule 2 and the polygon 3 to make the situation simple. Select the [File] – [Close] – [2. 1yec.pdb] and [File] – [Close] – [3. 1yec.surface.gz] menu items sequentially. Then execute a ‘reset’ command and the transform of the molecule 1 and the position of the viewpoint are initialized. 

Next, confirm that the ‘Mouse’ checkbox of the file 1 is checked, and try a ‘show pdbj’ command. The functional site information of the molecule ‘12as’ is read from the PDBMLplus and ‘type’ and ‘subtype’ keywords for each functional site are listed. These keywords can be used to select a set of atoms. For example, if a keyword ‘CATRES’ exists (probably it does), the command ‘select pdbj:CATRES’ selects the corresponding atoms. 

In addition, gene ontology information can be obtained from the PDBMLplus. The gene ontology information for the molecule 12as is displayed by the command ’show godata’. Similar operations can be applied to other external databases on the Internet provided that the external database supports the interface that jV3 requires. See the '[[Functional site information for molecules]]' section for details.

== Animation ==
The animation of molecules can be performed in jV3. The animation file takes the PDB format, where the MODEL line divides each frame. Let us open an animation file ’http://ef-site.hgc.jp/eF-site/jV/anim.pdb.gz’ as an example from the open-remote dialog shown by selecting the [File] – [Open – Remote] – [Animation] menu item. When an animation file is loaded to the application, the first frame is automatically displayed in the wire frame model. You can start the animation by using the animation-control dialog that is shown by choosing the [Options] – [Animation] menu item. The dialog provides operations such as start and stop of the animation, selection of the animation mode, and adjustment of the speed. Some [[GUI#Animation_control_dialog|sample figures]] of the dialog are shown in the GUI section.

== Saving your work ==
While in your work, you can create a script file that contains a set of commands that reproduces the current work by using the [File] – [Save] – [Script] menu item. The script file can be loaded by the [File] – [Open – Local] – [Script] menu item. On the other hand, the [File] – [Save] – [PDB] menu item enables to save a molecule to a PDB format file with the coordinates of the atoms being transformed according to the current image. Here, only one molecule must be selected and only selected atoms in the molecule are saved. The other two menu items in the [File] – [Save] menu, [PNG] and [JPEG], save the current screen image to an image file in the PNG and JPEG format, respectively. The created image file has the same size as that of the 3D-display panel in the application.

== Terminating the application ==
The application is terminated when the [File] – [Exit] menu item is chosen or the application window is closed by the way your operation system provides. You can also quit the application by executing ‘exit’ or ‘quit’ command.</text>
    <sha1>8e83ea9b4a0330749889007a270af9f7a82de1bf</sha1>
  </revision>
</page>
<page arvcontinue="20110106074224|454">
  <title>Release note</title>
  <ns>0</ns>
  <id>17</id>
  <revision>
    <id>458</id>
    <parentid>418</parentid>
    <timestamp>2011-01-07T05:12:32Z</timestamp>
    <contributor>
      <username>IMSsato</username>
      <id>4</id>
    </contributor>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="3971" xml:space="preserve">Changes and improvements have been made as follows.

* version 3.1
** The following commands have been added; 'animrange', 'set adjustview', 'show godata', and 'show xps3'.
** The xPSSS expression has been added in order to select a group of atoms.
** Several public methods have been added to the applet so as to append molecule or polygon files after the applet started.
** The applet can send information about mouse-picked atoms to JavaScript.
* version 3.1.1
** Some problems in GUI menu [Options]-[Hetero Atoms] and [Hydrogens] have been fixed.
** Some problems in 'trace' command have been fixed.
* version 3.1.2
** eF-site ID has been changed to a new format.
* version 3.1.3
** Some problems in xps3 atom selection have been fixed.
* version 3.1.4
** Some problems in finalization process of openGL rendering have been fixed.
* version 3.1.5
** The output of 'show xps3' command has been modified.
** Some problems in 'save png/jpeg' command have been fixed.
* version 3.1.6
** Some problems in loading an empty polygon file have been fixed.
* version 3.1.7
** Some problems in initialization process of the applet have been fixed.
* version 3.2
** 'show site' command has been added.
* version 3.3 beta 1
** Availabe JOGL version is restricted to JSR-231 beta 5 only.
* version 3.3
** Both the previous JOGL (version 1.1.1) and JSR-231 are available.
** The following commands have been added; 'set viewpoint', 'show viewpoint', 'set imagesize', and 'show imagesize'.
* version 3.3.1
** Some problems in reading a pdbMLplus file have been fixed.
* version 3.4
** PDB format version 3 can be processed.
* version 3.5
** Discrimination of DNA and RNA linking nucleotides is based on [http://remediation.wwpdb.org/ccd.html Chemical Component Dictionary] for PDB format version 3.
** The default representation of the cartoon model has been changed. Commands 'set cartoon_loop_tube', 'set cartoon_round' and 'set ribbonback' have been added.
** The default parameters of lighting have been changed. Commands 'set ambient', 'set diffuse1', 'set diffuse1_direction', 'set diffuse2' and 'set diffuse1_direction' have been added.
** Commands 'set pdbml_noatom_url', 'set pdbml_extatom_url', 'set pdbml_plus_url', 'set efsite_url', 'set ext_site_url', 'show pdbml_url', 'show efsite_url' and 'show ext_site_url' have been added.
** The command-line option '-stdin' has been added to receive commands from stdin stream.
* version 3.6
** Users can specify the JavaScript function name used in Applet-to-JavaScript Communication.
** Applet parameter 'file_load_message' has been added.
* version 3.6.1
** Predefined set of residues has been modified.
** Old JOGL API is not supported.
* version 3.6.2
** Latest version of PDBML can be processed.
** Some problems in mouse control on Mac have been fixed.
* version 3.6.3
** Molecule file parsing has been modified to detect chain breaks properly by reading the 'label_asym_id' column in PDBML and the TER line in PDB flat file, respectively.
* version 3.6.4
** Some problems in GUI menu on Mac have been fixed.
* version 3.6.5
** The jV applet can invoke a JavaScript function when it started.
* version 3.7
** Commands 'pdbj_describe' and 'pdbj_execute' have been added.
** Keyword 'xps3' have been replaced by 'pdbj'.
* version 3.7.1
** Default PDBML URLs have been changed.
* version 3.7.2
** Some problems in creating png/jpeg image files have been fixed.
* version 3.8
** Command 'displayatom' has been added.
** The signed jV applet can save PNG/JPEG image files.
* version 3.8.1
** In commands 'cartoon', 'ribbons' and 'trace', a backbone will be drawn instead when a chain does not have enough atoms to draw those models.
** Recognition of amino acids is based on [http://remediation.wwpdb.org/ccd.html Chemical Component Dictionary].
* version 3.8.2
** Command 'ball_and_stick' has been added.
* version 3.8.3
** Binary distribution contains the JOGL library and pre-installation of JOGL is not necessary to use jV.</text>
    <sha1>f25c0ec5649a66189382ce7543d08c88667fdac4</sha1>
  </revision>
  <revision>
    <id>470</id>
    <parentid>458</parentid>
    <timestamp>2011-07-11T07:17:21Z</timestamp>
    <contributor>
      <username>IMSsato</username>
      <id>4</id>
    </contributor>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="4132" xml:space="preserve">Changes and improvements have been made as follows.

* version 3.1
** The following commands have been added; 'animrange', 'set adjustview', 'show godata', and 'show xps3'.
** The xPSSS expression has been added in order to select a group of atoms.
** Several public methods have been added to the applet so as to append molecule or polygon files after the applet started.
** The applet can send information about mouse-picked atoms to JavaScript.
* version 3.1.1
** Some problems in GUI menu [Options]-[Hetero Atoms] and [Hydrogens] have been fixed.
** Some problems in 'trace' command have been fixed.
* version 3.1.2
** eF-site ID has been changed to a new format.
* version 3.1.3
** Some problems in xps3 atom selection have been fixed.
* version 3.1.4
** Some problems in finalization process of openGL rendering have been fixed.
* version 3.1.5
** The output of 'show xps3' command has been modified.
** Some problems in 'save png/jpeg' command have been fixed.
* version 3.1.6
** Some problems in loading an empty polygon file have been fixed.
* version 3.1.7
** Some problems in initialization process of the applet have been fixed.
* version 3.2
** 'show site' command has been added.
* version 3.3 beta 1
** Availabe JOGL version is restricted to JSR-231 beta 5 only.
* version 3.3
** Both the previous JOGL (version 1.1.1) and JSR-231 are available.
** The following commands have been added; 'set viewpoint', 'show viewpoint', 'set imagesize', and 'show imagesize'.
* version 3.3.1
** Some problems in reading a pdbMLplus file have been fixed.
* version 3.4
** PDB format version 3 can be processed.
* version 3.5
** Discrimination of DNA and RNA linking nucleotides is based on [http://remediation.wwpdb.org/ccd.html Chemical Component Dictionary] for PDB format version 3.
** The default representation of the cartoon model has been changed. Commands 'set cartoon_loop_tube', 'set cartoon_round' and 'set ribbonback' have been added.
** The default parameters of lighting have been changed. Commands 'set ambient', 'set diffuse1', 'set diffuse1_direction', 'set diffuse2' and 'set diffuse1_direction' have been added.
** Commands 'set pdbml_noatom_url', 'set pdbml_extatom_url', 'set pdbml_plus_url', 'set efsite_url', 'set ext_site_url', 'show pdbml_url', 'show efsite_url' and 'show ext_site_url' have been added.
** The command-line option '-stdin' has been added to receive commands from stdin stream.
* version 3.6
** Users can specify the JavaScript function name used in Applet-to-JavaScript Communication.
** Applet parameter 'file_load_message' has been added.
* version 3.6.1
** Predefined set of residues has been modified.
** Old JOGL API is not supported.
* version 3.6.2
** Latest version of PDBML can be processed.
** Some problems in mouse control on Mac have been fixed.
* version 3.6.3
** Molecule file parsing has been modified to detect chain breaks properly by reading the 'label_asym_id' column in PDBML and the TER line in PDB flat file, respectively.
* version 3.6.4
** Some problems in GUI menu on Mac have been fixed.
* version 3.6.5
** The jV applet can invoke a JavaScript function when it started.
* version 3.7
** Commands 'pdbj_describe' and 'pdbj_execute' have been added.
** Keyword 'xps3' have been replaced by 'pdbj'.
* version 3.7.1
** Default PDBML URLs have been changed.
* version 3.7.2
** Some problems in creating png/jpeg image files have been fixed.
* version 3.8
** Command 'displayatom' has been added.
** The signed jV applet can save PNG/JPEG image files.
* version 3.8.1
** In commands 'cartoon', 'ribbons' and 'trace', a backbone will be drawn instead when a chain does not have enough atoms to draw those models.
** Recognition of amino acids is based on [http://remediation.wwpdb.org/ccd.html Chemical Component Dictionary].
* version 3.8.2
** Command 'ball_and_stick' has been added.
* version 3.8.3
** Binary distribution contains the JOGL library and pre-installation of JOGL is not necessary to use jV.
* version 4.0
** The program supports PDB format version 4.0.
** Atom expression has been extended to handle case-sensitive chain ID and label_asym_id in PDBML.</text>
    <sha1>84bd51b4b774642b201ac28dbfb5a810f7f7b8dd</sha1>
  </revision>
  <revision>
    <id>497</id>
    <parentid>470</parentid>
    <timestamp>2011-12-22T06:11:06Z</timestamp>
    <contributor>
      <username>IMSsato</username>
      <id>4</id>
    </contributor>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="4447" xml:space="preserve">Changes and improvements have been made as follows.

* version 3.1
** The following commands have been added; 'animrange', 'set adjustview', 'show godata', and 'show xps3'.
** The xPSSS expression has been added in order to select a group of atoms.
** Several public methods have been added to the applet so as to append molecule or polygon files after the applet started.
** The applet can send information about mouse-picked atoms to JavaScript.
* version 3.1.1
** Some problems in GUI menu [Options]-[Hetero Atoms] and [Hydrogens] have been fixed.
** Some problems in 'trace' command have been fixed.
* version 3.1.2
** eF-site ID has been changed to a new format.
* version 3.1.3
** Some problems in xps3 atom selection have been fixed.
* version 3.1.4
** Some problems in finalization process of openGL rendering have been fixed.
* version 3.1.5
** The output of 'show xps3' command has been modified.
** Some problems in 'save png/jpeg' command have been fixed.
* version 3.1.6
** Some problems in loading an empty polygon file have been fixed.
* version 3.1.7
** Some problems in initialization process of the applet have been fixed.
* version 3.2
** 'show site' command has been added.
* version 3.3 beta 1
** Availabe JOGL version is restricted to JSR-231 beta 5 only.
* version 3.3
** Both the previous JOGL (version 1.1.1) and JSR-231 are available.
** The following commands have been added; 'set viewpoint', 'show viewpoint', 'set imagesize', and 'show imagesize'.
* version 3.3.1
** Some problems in reading a pdbMLplus file have been fixed.
* version 3.4
** PDB format version 3 can be processed.
* version 3.5
** Discrimination of DNA and RNA linking nucleotides is based on [http://remediation.wwpdb.org/ccd.html Chemical Component Dictionary] for PDB format version 3.
** The default representation of the cartoon model has been changed. Commands 'set cartoon_loop_tube', 'set cartoon_round' and 'set ribbonback' have been added.
** The default parameters of lighting have been changed. Commands 'set ambient', 'set diffuse1', 'set diffuse1_direction', 'set diffuse2' and 'set diffuse1_direction' have been added.
** Commands 'set pdbml_noatom_url', 'set pdbml_extatom_url', 'set pdbml_plus_url', 'set efsite_url', 'set ext_site_url', 'show pdbml_url', 'show efsite_url' and 'show ext_site_url' have been added.
** The command-line option '-stdin' has been added to receive commands from stdin stream.
* version 3.6
** Users can specify the JavaScript function name used in Applet-to-JavaScript Communication.
** Applet parameter 'file_load_message' has been added.
* version 3.6.1
** Predefined set of residues has been modified.
** Old JOGL API is not supported.
* version 3.6.2
** Latest version of PDBML can be processed.
** Some problems in mouse control on Mac have been fixed.
* version 3.6.3
** Molecule file parsing has been modified to detect chain breaks properly by reading the 'label_asym_id' column in PDBML and the TER line in PDB flat file, respectively.
* version 3.6.4
** Some problems in GUI menu on Mac have been fixed.
* version 3.6.5
** The jV applet can invoke a JavaScript function when it started.
* version 3.7
** Commands 'pdbj_describe' and 'pdbj_execute' have been added.
** Keyword 'xps3' have been replaced by 'pdbj'.
* version 3.7.1
** Default PDBML URLs have been changed.
* version 3.7.2
** Some problems in creating png/jpeg image files have been fixed.
* version 3.8
** Command 'displayatom' has been added.
** The signed jV applet can save PNG/JPEG image files.
* version 3.8.1
** In commands 'cartoon', 'ribbons' and 'trace', a backbone will be drawn instead when a chain does not have enough atoms to draw those models.
** Recognition of amino acids is based on [http://remediation.wwpdb.org/ccd.html Chemical Component Dictionary].
* version 3.8.2
** Command 'ball_and_stick' has been added.
* version 3.8.3
** Binary distribution contains the JOGL library and pre-installation of JOGL is not necessary to use jV.
* version 4.0
** The program supports PDB format version 4.0.
** Atom expression has been extended to handle case-sensitive chain ID and label_asym_id in PDBML.
* version 4.1
** The program runs with new JOGL library (2.0-rc4 or later) which enables jV applets to run on Mac.
** From this release, the program requires JRE 1.6 or later.
** Command 'add_backbone' has been added.
** The program uses MODRES data and chem_comp/type data (PDBML only) to determine residue types.</text>
    <sha1>3734e9f79771f0e8645c0961b80d50cf86472e8a</sha1>
  </revision>
</page>
<page arvcontinue="20110106074224|454">
  <title>Main Page</title>
  <ns>0</ns>
  <id>1</id>
  <revision>
    <id>459</id>
    <parentid>453</parentid>
    <timestamp>2011-01-17T06:36:08Z</timestamp>
    <contributor>
      <username>IMSsato</username>
      <id>4</id>
    </contributor>
    <comment>/* Other resources */</comment>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="6410" xml:space="preserve">&lt;big&gt;'''Welcome to jV wiki.'''&lt;/big&gt;

jV version 3 (formerly known as PDBjViewer) is a program to display molecular graphics of protein and nucleic acids. 
jV supports the following features:
* jV can read and display PDBML files, the canonical XML format for the Protein Data Bank.
* Of course, jV can read and display the traditional PDB format files, too.
* RasMol-like usability.
* jV can process more than one molecules.
* jV can display polygons specified by XML. ([http://ef-site.hgc.jp/eF-site/schema/polygon12.xsd XML Schema for polygons] is available.)
* Multiple polygons can be processed simultaneously, and be superimposed onto molecular images.
* Animation can be realized.
* jV runs on the Java Runtime Environment ([http://java.sun.com/javase/index.jsp JRE]) so that it can work as a stand-alone application as well as an applet.
* The graphics of jV is based on OpenGL ([http://kenai.com/projects/jogl JOGL]), thereby producing fairly beautiful pictures.


The program 'jV' has been developed by [http://www.hgc.jp/~kinosita/TOP.html Kengo Kinoshita] ([http://www.is.tohoku.ac.jp/index-e.html Graduate School of Information Sciences], [http://www.tohoku.ac.jp/english/ Tohoku University]) and [http://www.protein.osaka-u.ac.jp/rcsfp/pi/ Haruki Nakamura] ([http://www.protein.osaka-u.ac.jp/index_e.php Institute for Protein Research], [http://www.osaka-u.ac.jp/eng/index.html Osaka Univeristy]), with the support from [http://www-bird.jst.go.jp/index_e.html JST-BIRD].


&lt;gallery&gt;
File:Spacefill.jpg
File:Cartoon.jpg
File:Surface.jpg
File:edmap.jpg
&lt;/gallery&gt;


== Start up ==
You can start up jV (3.8.3) with Java Web Start technology immediately from here.
* [http://ef-site.hgc.jp/eF-site/servlet/stable/jV.jnlp stable JOGL version] (recommended)
* [http://ef-site.hgc.jp/eF-site/servlet/current/jV.jnlp recent JOGL version]

== Basic Usage ==
You can execute basic operations such as rotation and translation with mouse action. Major actions are described in the following table:
{| style="margin:auto;border:1px solid gray"
! rowspan="2" style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap;font-weight:bold" |Action
! colspan="2" style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap;font-weight:bold" |Mouse Operation
|-
! style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap;font-weight:bold" |Windows, Linux
! style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap;font-weight:bold" |Mac OS X
|-
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |rotate around X (horizontal) axis&lt;br /&gt;rotate around Y (vertical) axis
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |left drag
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |drag
|-
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |translate along X axis (holizontally)&lt;br /&gt;translate along Y axis (vertically)
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |right drag
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |Command + drag
|-
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |translate along Z axis (zoom in/out)
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |Shift + left drag
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |Shift + drag
|}

Operations such as changing display models and colors and saving the image, can be executed with a menu. The location of the menu is at the top of the application window in Windows and at the top of screen in Mac as the stand-alone application. As an applet usage, a popup menu appears by clicking the right mouse button on the display screen, or clicking with a "Command" button in case of Mac.

{| style="margin:auto;border:0"
|-
| [[File:Jv_menu_win.png|The location of menu in jV stand-alone version in Windows.|250px]]
| [[File:Jv_menu_mac.png|The location of menu in jV stand-alone version in Mac.|250px]]
| [[File:popupmenu_en.png|The location of menu in applet version.|250px]]
|-
| style="text-align:center" |Stand-alone (Windows)
| style="text-align:center" |Stand-alone (Mac)
| style="text-align:center" |Applet
|}

Basic menu operations are following (see also [[GUI]] for details):

{| style="margin:auto;border:1px solid gray;border-collapse:collapse"
! style="padding:0 0.5em;border:1px solid gray" | Operations
! style="padding:0 0.5em;border:1px solid gray" | Menu location
|-
| style="padding:0 0.5em;border:1px solid gray" | Save a static image
| style="padding:0 0.5em;border:1px solid gray" | [File]-[Save]-[PNG/JPEG]
|-
| style="padding:0 0.5em;border:1px solid gray" | Change the expression format
| style="padding:0 0.5em;border:1px solid gray" | [File]-[Display]-[Wireframe/Backbone/Sticks/Spacefill/Ball&amp;amp;Stick/Ribbons/Cartoon]
|-
| style="padding:0 0.5em;border:1px solid gray" | Change the color
| style="padding:0 0.5em;border:1px solid gray" | [File]-[Colors]-[Monochrome/CPK/Shapely/Group/Chain/Temperature/Structure/Charge/Amino]
|}

To execute more complicated operation such as diplaying some piece of the molecule or changing some part of molecule in another style, use command line operation.

See also [[#Other resources]] for details:


== Download ==
You can also download the program and start it up locally.
In this case, installing JOGL is required in advance (see [[Installation_of_jV3 | Installation]] page).
The following links take you to the download pages. (latest version is 3.8.3@2011/1/6)
* [http://ef-site.hgc.jp/eF-site/servlet/DownloadViewerBinary binary (3.8.3)] 
* [http://ef-site.hgc.jp/eF-site/servlet/Registration source code (3.8.3)] (registration will be required)

== Other resources ==
* [http://ef-site.hgc.jp/eF-site/jV/jV_manual.html Manual] (html in English)
* [[How_to_use]] (in this site in English)
* [http://www.pdbj.org/jv/manual/index_ja.html Manual] (html in Japanese)
* [http://www.pdbj.org/jv/manual/jV_manual.pdf Manual] (pdf in English, for ver. 3.3)
* [http://ef-site.hgc.jp/eF-site/jV/jV3_User'sGuide.pdf User's guide] (for ver. 3.8.3 in English)</text>
    <sha1>1bcb27b22f8baf9b95941d69f12d2be958933be5</sha1>
  </revision>
  <revision>
    <id>467</id>
    <parentid>459</parentid>
    <timestamp>2011-07-11T06:55:23Z</timestamp>
    <contributor>
      <username>IMSsato</username>
      <id>4</id>
    </contributor>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="6393" xml:space="preserve">&lt;big&gt;'''Welcome to jV wiki.'''&lt;/big&gt;

jV (formerly known as PDBjViewer) is a program to display molecular graphics of protein and nucleic acids. 
jV supports the following features:
* jV can read and display PDBML files, the canonical XML format for the Protein Data Bank.
* Of course, jV can read and display the traditional PDB format files, too.
* RasMol-like usability.
* jV can process more than one molecules.
* jV can display polygons specified by XML. ([http://ef-site.hgc.jp/eF-site/schema/polygon12.xsd XML Schema for polygons] is available.)
* Multiple polygons can be processed simultaneously, and be superimposed onto molecular images.
* Animation can be realized.
* jV runs on the Java Runtime Environment ([http://java.sun.com/javase/index.jsp JRE]) so that it can work as a stand-alone application as well as an applet.
* The graphics of jV is based on OpenGL ([http://kenai.com/projects/jogl JOGL]), thereby producing fairly beautiful pictures.


The program 'jV' has been developed by [http://www.hgc.jp/~kinosita/TOP.html Kengo Kinoshita] ([http://www.is.tohoku.ac.jp/index-e.html Graduate School of Information Sciences], [http://www.tohoku.ac.jp/english/ Tohoku University]) and [http://www.protein.osaka-u.ac.jp/rcsfp/pi/ Haruki Nakamura] ([http://www.protein.osaka-u.ac.jp/index_e.php Institute for Protein Research], [http://www.osaka-u.ac.jp/eng/index.html Osaka Univeristy]), with the support from [http://www-bird.jst.go.jp/index_e.html JST-BIRD].


&lt;gallery&gt;
File:Spacefill.jpg
File:Cartoon.jpg
File:Surface.jpg
File:edmap.jpg
&lt;/gallery&gt;


== Start up ==
You can start up jV (4.0) with Java Web Start technology immediately from here.
* [http://ef-site.hgc.jp/eF-site/servlet/stable/jV.jnlp stable JOGL version] (recommended)
* [http://ef-site.hgc.jp/eF-site/servlet/current/jV.jnlp recent JOGL version]

== Basic Usage ==
You can execute basic operations such as rotation and translation with mouse action. Major actions are described in the following table:
{| style="margin:auto;border:1px solid gray"
! rowspan="2" style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap;font-weight:bold" |Action
! colspan="2" style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap;font-weight:bold" |Mouse Operation
|-
! style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap;font-weight:bold" |Windows, Linux
! style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap;font-weight:bold" |Mac OS X
|-
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |rotate around X (horizontal) axis&lt;br /&gt;rotate around Y (vertical) axis
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |left drag
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |drag
|-
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |translate along X axis (holizontally)&lt;br /&gt;translate along Y axis (vertically)
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |right drag
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |Command + drag
|-
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |translate along Z axis (zoom in/out)
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |Shift + left drag
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |Shift + drag
|}

Operations such as changing display models and colors and saving the image, can be executed with a menu. The location of the menu is at the top of the application window in Windows and at the top of screen in Mac as the stand-alone application. As an applet usage, a popup menu appears by clicking the right mouse button on the display screen, or clicking with a "Command" button in case of Mac.

{| style="margin:auto;border:0"
|-
| [[File:Jv_menu_win.png|The location of menu in jV stand-alone version in Windows.|250px]]
| [[File:Jv_menu_mac.png|The location of menu in jV stand-alone version in Mac.|250px]]
| [[File:popupmenu_en.png|The location of menu in applet version.|250px]]
|-
| style="text-align:center" |Stand-alone (Windows)
| style="text-align:center" |Stand-alone (Mac)
| style="text-align:center" |Applet
|}

Basic menu operations are following (see also [[GUI]] for details):

{| style="margin:auto;border:1px solid gray;border-collapse:collapse"
! style="padding:0 0.5em;border:1px solid gray" | Operations
! style="padding:0 0.5em;border:1px solid gray" | Menu location
|-
| style="padding:0 0.5em;border:1px solid gray" | Save a static image
| style="padding:0 0.5em;border:1px solid gray" | [File]-[Save]-[PNG/JPEG]
|-
| style="padding:0 0.5em;border:1px solid gray" | Change the expression format
| style="padding:0 0.5em;border:1px solid gray" | [File]-[Display]-[Wireframe/Backbone/Sticks/Spacefill/Ball&amp;amp;Stick/Ribbons/Cartoon]
|-
| style="padding:0 0.5em;border:1px solid gray" | Change the color
| style="padding:0 0.5em;border:1px solid gray" | [File]-[Colors]-[Monochrome/CPK/Shapely/Group/Chain/Temperature/Structure/Charge/Amino]
|}

To execute more complicated operation such as diplaying some piece of the molecule or changing some part of molecule in another style, use command line operation.

See also [[#Other resources]] for details:


== Download ==
You can also download the program and start it up locally.
In this case, installing JOGL is required in advance (see [[Installation_of_jV3 | Installation]] page).
The following links take you to the download pages. (latest version is 4.0@2011/7/11)
* [http://ef-site.hgc.jp/eF-site/servlet/DownloadViewerBinary binary (4.0)] 
* [http://ef-site.hgc.jp/eF-site/servlet/Registration source code (4.0)] (registration will be required)

== Other resources ==
* [http://ef-site.hgc.jp/eF-site/jV/jV_manual.html Manual] (html in English)
* [[How_to_use]] (in this site in English)
* [http://www.pdbj.org/jv/manual/index_ja.html Manual] (html in Japanese)
* [http://www.pdbj.org/jv/manual/jV_manual.pdf Manual] (pdf in English, for ver. 3.3)
* [http://ef-site.hgc.jp/eF-site/jV/jV3_User'sGuide.pdf User's guide] (for ver. 3.8.3 in English)</text>
    <sha1>45ad16000e50151437cefa7abbb5530a2feb4a02</sha1>
  </revision>
  <revision>
    <id>471</id>
    <parentid>467</parentid>
    <timestamp>2011-07-12T07:17:43Z</timestamp>
    <contributor>
      <username>Cudo29</username>
      <id>5</id>
    </contributor>
    <comment>The description about support was updated.</comment>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="6435" xml:space="preserve">&lt;big&gt;'''Welcome to jV wiki.'''&lt;/big&gt;

jV (formerly known as PDBjViewer) is a program to display molecular graphics of protein and nucleic acids. 
jV supports the following features:
* jV can read and display PDBML files, the canonical XML format for the Protein Data Bank.
* Of course, jV can read and display the traditional PDB format files, too.
* RasMol-like usability.
* jV can process more than one molecules.
* jV can display polygons specified by XML. ([http://ef-site.hgc.jp/eF-site/schema/polygon12.xsd XML Schema for polygons] is available.)
* Multiple polygons can be processed simultaneously, and be superimposed onto molecular images.
* Animation can be realized.
* jV runs on the Java Runtime Environment ([http://java.sun.com/javase/index.jsp JRE]) so that it can work as a stand-alone application as well as an applet.
* The graphics of jV is based on OpenGL ([http://kenai.com/projects/jogl JOGL]), thereby producing fairly beautiful pictures.


The program 'jV' has been developed by [http://www.hgc.jp/~kinosita/TOP.html Kengo Kinoshita] ([http://www.is.tohoku.ac.jp/index-e.html Graduate School of Information Sciences], [http://www.tohoku.ac.jp/english/ Tohoku University]) and [http://www.protein.osaka-u.ac.jp/rcsfp/pi/ Haruki Nakamura] ([http://www.protein.osaka-u.ac.jp/index_e.php Institute for Protein Research], [http://www.osaka-u.ac.jp/eng/index.html Osaka Univeristy]), with the support from [http://biosciencedbc.jp/ JST-NBDC] and [http://www.osaka-u.ac.jp/ Osaka University].
      

&lt;gallery&gt;
File:Spacefill.jpg
File:Cartoon.jpg
File:Surface.jpg
File:edmap.jpg
&lt;/gallery&gt;


== Start up ==
You can start up jV (4.0) with Java Web Start technology immediately from here.
* [http://ef-site.hgc.jp/eF-site/servlet/stable/jV.jnlp stable JOGL version] (recommended)
* [http://ef-site.hgc.jp/eF-site/servlet/current/jV.jnlp recent JOGL version]

== Basic Usage ==
You can execute basic operations such as rotation and translation with mouse action. Major actions are described in the following table:
{| style="margin:auto;border:1px solid gray"
! rowspan="2" style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap;font-weight:bold" |Action
! colspan="2" style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap;font-weight:bold" |Mouse Operation
|-
! style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap;font-weight:bold" |Windows, Linux
! style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap;font-weight:bold" |Mac OS X
|-
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |rotate around X (horizontal) axis&lt;br /&gt;rotate around Y (vertical) axis
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |left drag
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |drag
|-
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |translate along X axis (holizontally)&lt;br /&gt;translate along Y axis (vertically)
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |right drag
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |Command + drag
|-
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |translate along Z axis (zoom in/out)
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |Shift + left drag
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |Shift + drag
|}

Operations such as changing display models and colors and saving the image, can be executed with a menu. The location of the menu is at the top of the application window in Windows and at the top of screen in Mac as the stand-alone application. As an applet usage, a popup menu appears by clicking the right mouse button on the display screen, or clicking with a "Command" button in case of Mac.

{| style="margin:auto;border:0"
|-
| [[File:Jv_menu_win.png|The location of menu in jV stand-alone version in Windows.|250px]]
| [[File:Jv_menu_mac.png|The location of menu in jV stand-alone version in Mac.|250px]]
| [[File:popupmenu_en.png|The location of menu in applet version.|250px]]
|-
| style="text-align:center" |Stand-alone (Windows)
| style="text-align:center" |Stand-alone (Mac)
| style="text-align:center" |Applet
|}

Basic menu operations are following (see also [[GUI]] for details):

{| style="margin:auto;border:1px solid gray;border-collapse:collapse"
! style="padding:0 0.5em;border:1px solid gray" | Operations
! style="padding:0 0.5em;border:1px solid gray" | Menu location
|-
| style="padding:0 0.5em;border:1px solid gray" | Save a static image
| style="padding:0 0.5em;border:1px solid gray" | [File]-[Save]-[PNG/JPEG]
|-
| style="padding:0 0.5em;border:1px solid gray" | Change the expression format
| style="padding:0 0.5em;border:1px solid gray" | [File]-[Display]-[Wireframe/Backbone/Sticks/Spacefill/Ball&amp;amp;Stick/Ribbons/Cartoon]
|-
| style="padding:0 0.5em;border:1px solid gray" | Change the color
| style="padding:0 0.5em;border:1px solid gray" | [File]-[Colors]-[Monochrome/CPK/Shapely/Group/Chain/Temperature/Structure/Charge/Amino]
|}

To execute more complicated operation such as diplaying some piece of the molecule or changing some part of molecule in another style, use command line operation.

See also [[#Other resources]] for details:


== Download ==
You can also download the program and start it up locally.
In this case, installing JOGL is required in advance (see [[Installation_of_jV3 | Installation]] page).
The following links take you to the download pages. (latest version is 4.0@2011/7/11)
* [http://ef-site.hgc.jp/eF-site/servlet/DownloadViewerBinary binary (4.0)] 
* [http://ef-site.hgc.jp/eF-site/servlet/Registration source code (4.0)] (registration will be required)

== Other resources ==
* [http://ef-site.hgc.jp/eF-site/jV/jV_manual.html Manual] (html in English)
* [[How_to_use]] (in this site in English)
* [http://www.pdbj.org/jv/manual/index_ja.html Manual] (html in Japanese)
* [http://www.pdbj.org/jv/manual/jV_manual.pdf Manual] (pdf in English, for ver. 3.3)
* [http://ef-site.hgc.jp/eF-site/jV/jV3_User'sGuide.pdf User's guide] (for ver. 3.8.3 in English)</text>
    <sha1>83e696364d4324ee703eb78f294080e3ef20fad3</sha1>
  </revision>
  <revision>
    <id>479</id>
    <parentid>471</parentid>
    <timestamp>2011-12-21T07:01:47Z</timestamp>
    <contributor>
      <username>IMSsato</username>
      <id>4</id>
    </contributor>
    <comment>/* Start up */</comment>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="6600" xml:space="preserve">&lt;big&gt;'''Welcome to jV wiki.'''&lt;/big&gt;

jV (formerly known as PDBjViewer) is a program to display molecular graphics of protein and nucleic acids. 
jV supports the following features:
* jV can read and display PDBML files, the canonical XML format for the Protein Data Bank.
* Of course, jV can read and display the traditional PDB format files, too.
* RasMol-like usability.
* jV can process more than one molecules.
* jV can display polygons specified by XML. ([http://ef-site.hgc.jp/eF-site/schema/polygon12.xsd XML Schema for polygons] is available.)
* Multiple polygons can be processed simultaneously, and be superimposed onto molecular images.
* Animation can be realized.
* jV runs on the Java Runtime Environment ([http://java.sun.com/javase/index.jsp JRE]) so that it can work as a stand-alone application as well as an applet.
* The graphics of jV is based on OpenGL ([http://kenai.com/projects/jogl JOGL]), thereby producing fairly beautiful pictures.


The program 'jV' has been developed by [http://www.hgc.jp/~kinosita/TOP.html Kengo Kinoshita] ([http://www.is.tohoku.ac.jp/index-e.html Graduate School of Information Sciences], [http://www.tohoku.ac.jp/english/ Tohoku University]) and [http://www.protein.osaka-u.ac.jp/rcsfp/pi/ Haruki Nakamura] ([http://www.protein.osaka-u.ac.jp/index_e.php Institute for Protein Research], [http://www.osaka-u.ac.jp/eng/index.html Osaka Univeristy]), with the support from [http://biosciencedbc.jp/ JST-NBDC] and [http://www.osaka-u.ac.jp/ Osaka University].
      

&lt;gallery&gt;
File:Spacefill.jpg
File:Cartoon.jpg
File:Surface.jpg
File:edmap.jpg
&lt;/gallery&gt;


== Start up ==
You can start up jV (4.1) with Java Web Start technology immediately from here.
* [http://ef-site.hgc.jp/eF-site/servlet/stable/jV.jnlp stable JOGL version] (recommended)
* [http://ef-site.hgc.jp/eF-site/servlet/current/jV.jnlp recent JOGL version]
The current jV requires JRE 1.6 or later.
The previous version, jV version 4.0, can run with JRE 1.4 and 1.5.
* [http://ef-site.hgc.jp/jV/stable/jV_4_0.jnlp jV 4.0]

== Basic Usage ==
You can execute basic operations such as rotation and translation with mouse action. Major actions are described in the following table:
{| style="margin:auto;border:1px solid gray"
! rowspan="2" style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap;font-weight:bold" |Action
! colspan="2" style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap;font-weight:bold" |Mouse Operation
|-
! style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap;font-weight:bold" |Windows, Linux
! style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap;font-weight:bold" |Mac OS X
|-
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |rotate around X (horizontal) axis&lt;br /&gt;rotate around Y (vertical) axis
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |left drag
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |drag
|-
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |translate along X axis (holizontally)&lt;br /&gt;translate along Y axis (vertically)
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |right drag
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |Command + drag
|-
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |translate along Z axis (zoom in/out)
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |Shift + left drag
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |Shift + drag
|}

Operations such as changing display models and colors and saving the image, can be executed with a menu. The location of the menu is at the top of the application window in Windows and at the top of screen in Mac as the stand-alone application. As an applet usage, a popup menu appears by clicking the right mouse button on the display screen, or clicking with a "Command" button in case of Mac.

{| style="margin:auto;border:0"
|-
| [[File:Jv_menu_win.png|The location of menu in jV stand-alone version in Windows.|250px]]
| [[File:Jv_menu_mac.png|The location of menu in jV stand-alone version in Mac.|250px]]
| [[File:popupmenu_en.png|The location of menu in applet version.|250px]]
|-
| style="text-align:center" |Stand-alone (Windows)
| style="text-align:center" |Stand-alone (Mac)
| style="text-align:center" |Applet
|}

Basic menu operations are following (see also [[GUI]] for details):

{| style="margin:auto;border:1px solid gray;border-collapse:collapse"
! style="padding:0 0.5em;border:1px solid gray" | Operations
! style="padding:0 0.5em;border:1px solid gray" | Menu location
|-
| style="padding:0 0.5em;border:1px solid gray" | Save a static image
| style="padding:0 0.5em;border:1px solid gray" | [File]-[Save]-[PNG/JPEG]
|-
| style="padding:0 0.5em;border:1px solid gray" | Change the expression format
| style="padding:0 0.5em;border:1px solid gray" | [File]-[Display]-[Wireframe/Backbone/Sticks/Spacefill/Ball&amp;amp;Stick/Ribbons/Cartoon]
|-
| style="padding:0 0.5em;border:1px solid gray" | Change the color
| style="padding:0 0.5em;border:1px solid gray" | [File]-[Colors]-[Monochrome/CPK/Shapely/Group/Chain/Temperature/Structure/Charge/Amino]
|}

To execute more complicated operation such as diplaying some piece of the molecule or changing some part of molecule in another style, use command line operation.

See also [[#Other resources]] for details:


== Download ==
You can also download the program and start it up locally.
In this case, installing JOGL is required in advance (see [[Installation_of_jV3 | Installation]] page).
The following links take you to the download pages. (latest version is 4.0@2011/7/11)
* [http://ef-site.hgc.jp/eF-site/servlet/DownloadViewerBinary binary (4.0)] 
* [http://ef-site.hgc.jp/eF-site/servlet/Registration source code (4.0)] (registration will be required)

== Other resources ==
* [http://ef-site.hgc.jp/eF-site/jV/jV_manual.html Manual] (html in English)
* [[How_to_use]] (in this site in English)
* [http://www.pdbj.org/jv/manual/index_ja.html Manual] (html in Japanese)
* [http://www.pdbj.org/jv/manual/jV_manual.pdf Manual] (pdf in English, for ver. 3.3)
* [http://ef-site.hgc.jp/eF-site/jV/jV3_User'sGuide.pdf User's guide] (for ver. 3.8.3 in English)</text>
    <sha1>af275677e98c9896d5cd30e23d229b0dfc912d42</sha1>
  </revision>
  <revision>
    <id>480</id>
    <parentid>479</parentid>
    <timestamp>2011-12-21T07:02:26Z</timestamp>
    <contributor>
      <username>IMSsato</username>
      <id>4</id>
    </contributor>
    <comment>/* Download */</comment>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="6601" xml:space="preserve">&lt;big&gt;'''Welcome to jV wiki.'''&lt;/big&gt;

jV (formerly known as PDBjViewer) is a program to display molecular graphics of protein and nucleic acids. 
jV supports the following features:
* jV can read and display PDBML files, the canonical XML format for the Protein Data Bank.
* Of course, jV can read and display the traditional PDB format files, too.
* RasMol-like usability.
* jV can process more than one molecules.
* jV can display polygons specified by XML. ([http://ef-site.hgc.jp/eF-site/schema/polygon12.xsd XML Schema for polygons] is available.)
* Multiple polygons can be processed simultaneously, and be superimposed onto molecular images.
* Animation can be realized.
* jV runs on the Java Runtime Environment ([http://java.sun.com/javase/index.jsp JRE]) so that it can work as a stand-alone application as well as an applet.
* The graphics of jV is based on OpenGL ([http://kenai.com/projects/jogl JOGL]), thereby producing fairly beautiful pictures.


The program 'jV' has been developed by [http://www.hgc.jp/~kinosita/TOP.html Kengo Kinoshita] ([http://www.is.tohoku.ac.jp/index-e.html Graduate School of Information Sciences], [http://www.tohoku.ac.jp/english/ Tohoku University]) and [http://www.protein.osaka-u.ac.jp/rcsfp/pi/ Haruki Nakamura] ([http://www.protein.osaka-u.ac.jp/index_e.php Institute for Protein Research], [http://www.osaka-u.ac.jp/eng/index.html Osaka Univeristy]), with the support from [http://biosciencedbc.jp/ JST-NBDC] and [http://www.osaka-u.ac.jp/ Osaka University].
      

&lt;gallery&gt;
File:Spacefill.jpg
File:Cartoon.jpg
File:Surface.jpg
File:edmap.jpg
&lt;/gallery&gt;


== Start up ==
You can start up jV (4.1) with Java Web Start technology immediately from here.
* [http://ef-site.hgc.jp/eF-site/servlet/stable/jV.jnlp stable JOGL version] (recommended)
* [http://ef-site.hgc.jp/eF-site/servlet/current/jV.jnlp recent JOGL version]
The current jV requires JRE 1.6 or later.
The previous version, jV version 4.0, can run with JRE 1.4 and 1.5.
* [http://ef-site.hgc.jp/jV/stable/jV_4_0.jnlp jV 4.0]

== Basic Usage ==
You can execute basic operations such as rotation and translation with mouse action. Major actions are described in the following table:
{| style="margin:auto;border:1px solid gray"
! rowspan="2" style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap;font-weight:bold" |Action
! colspan="2" style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap;font-weight:bold" |Mouse Operation
|-
! style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap;font-weight:bold" |Windows, Linux
! style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap;font-weight:bold" |Mac OS X
|-
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |rotate around X (horizontal) axis&lt;br /&gt;rotate around Y (vertical) axis
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |left drag
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |drag
|-
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |translate along X axis (holizontally)&lt;br /&gt;translate along Y axis (vertically)
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |right drag
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |Command + drag
|-
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |translate along Z axis (zoom in/out)
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |Shift + left drag
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |Shift + drag
|}

Operations such as changing display models and colors and saving the image, can be executed with a menu. The location of the menu is at the top of the application window in Windows and at the top of screen in Mac as the stand-alone application. As an applet usage, a popup menu appears by clicking the right mouse button on the display screen, or clicking with a "Command" button in case of Mac.

{| style="margin:auto;border:0"
|-
| [[File:Jv_menu_win.png|The location of menu in jV stand-alone version in Windows.|250px]]
| [[File:Jv_menu_mac.png|The location of menu in jV stand-alone version in Mac.|250px]]
| [[File:popupmenu_en.png|The location of menu in applet version.|250px]]
|-
| style="text-align:center" |Stand-alone (Windows)
| style="text-align:center" |Stand-alone (Mac)
| style="text-align:center" |Applet
|}

Basic menu operations are following (see also [[GUI]] for details):

{| style="margin:auto;border:1px solid gray;border-collapse:collapse"
! style="padding:0 0.5em;border:1px solid gray" | Operations
! style="padding:0 0.5em;border:1px solid gray" | Menu location
|-
| style="padding:0 0.5em;border:1px solid gray" | Save a static image
| style="padding:0 0.5em;border:1px solid gray" | [File]-[Save]-[PNG/JPEG]
|-
| style="padding:0 0.5em;border:1px solid gray" | Change the expression format
| style="padding:0 0.5em;border:1px solid gray" | [File]-[Display]-[Wireframe/Backbone/Sticks/Spacefill/Ball&amp;amp;Stick/Ribbons/Cartoon]
|-
| style="padding:0 0.5em;border:1px solid gray" | Change the color
| style="padding:0 0.5em;border:1px solid gray" | [File]-[Colors]-[Monochrome/CPK/Shapely/Group/Chain/Temperature/Structure/Charge/Amino]
|}

To execute more complicated operation such as diplaying some piece of the molecule or changing some part of molecule in another style, use command line operation.

See also [[#Other resources]] for details:


== Download ==
You can also download the program and start it up locally.
In this case, installing JOGL is required in advance (see [[Installation_of_jV3 | Installation]] page).
The following links take you to the download pages. (latest version is 4.1@2011/12/21)
* [http://ef-site.hgc.jp/eF-site/servlet/DownloadViewerBinary binary (4.1)] 
* [http://ef-site.hgc.jp/eF-site/servlet/Registration source code (4.1)] (registration will be required)

== Other resources ==
* [http://ef-site.hgc.jp/eF-site/jV/jV_manual.html Manual] (html in English)
* [[How_to_use]] (in this site in English)
* [http://www.pdbj.org/jv/manual/index_ja.html Manual] (html in Japanese)
* [http://www.pdbj.org/jv/manual/jV_manual.pdf Manual] (pdf in English, for ver. 3.3)
* [http://ef-site.hgc.jp/eF-site/jV/jV3_User'sGuide.pdf User's guide] (for ver. 3.8.3 in English)</text>
    <sha1>2041b194790f10088897c4b64e4f3bf25910b22c</sha1>
  </revision>
  <revision>
    <id>495</id>
    <parentid>480</parentid>
    <timestamp>2011-12-22T06:08:12Z</timestamp>
    <contributor>
      <username>IMSsato</username>
      <id>4</id>
    </contributor>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="6598" xml:space="preserve">&lt;big&gt;'''Welcome to jV wiki.'''&lt;/big&gt;

jV (formerly known as PDBjViewer) is a program to display molecular graphics of protein and nucleic acids. 
jV supports the following features:
* jV can read and display PDBML files, the canonical XML format for the Protein Data Bank.
* Of course, jV can read and display the traditional PDB format files, too.
* RasMol-like usability.
* jV can process more than one molecules.
* jV can display polygons specified by XML. ([http://ef-site.hgc.jp/eF-site/schema/polygon12.xsd XML Schema for polygons] is available.)
* Multiple polygons can be processed simultaneously, and be superimposed onto molecular images.
* Animation can be realized.
* jV runs on the Java Runtime Environment ([http://java.sun.com/javase/index.jsp JRE]) so that it can work as a stand-alone application as well as an applet.
* The graphics of jV is based on OpenGL ([http://jogamp.org/jogl/www/ JOGL]), thereby producing fairly beautiful pictures.


The program 'jV' has been developed by [http://www.hgc.jp/~kinosita/TOP.html Kengo Kinoshita] ([http://www.is.tohoku.ac.jp/index-e.html Graduate School of Information Sciences], [http://www.tohoku.ac.jp/english/ Tohoku University]) and [http://www.protein.osaka-u.ac.jp/rcsfp/pi/ Haruki Nakamura] ([http://www.protein.osaka-u.ac.jp/index_e.php Institute for Protein Research], [http://www.osaka-u.ac.jp/eng/index.html Osaka Univeristy]), with the support from [http://biosciencedbc.jp/ JST-NBDC] and [http://www.osaka-u.ac.jp/ Osaka University].
      

&lt;gallery&gt;
File:Spacefill.jpg
File:Cartoon.jpg
File:Surface.jpg
File:edmap.jpg
&lt;/gallery&gt;


== Start up ==
You can start up jV (4.1) with Java Web Start technology immediately from here.
* [http://ef-site.hgc.jp/eF-site/servlet/stable/jV.jnlp stable JOGL version] (recommended)
* [http://ef-site.hgc.jp/eF-site/servlet/current/jV.jnlp recent JOGL version]
The current jV requires JRE 1.6 or later.
The previous version, jV version 4.0, can run with JRE 1.4 and 1.5.
* [http://ef-site.hgc.jp/jV/stable/jV_4_0.jnlp jV 4.0]

== Basic Usage ==
You can execute basic operations such as rotation and translation with mouse action. Major actions are described in the following table:
{| style="margin:auto;border:1px solid gray"
! rowspan="2" style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap;font-weight:bold" |Action
! colspan="2" style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap;font-weight:bold" |Mouse Operation
|-
! style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap;font-weight:bold" |Windows, Linux
! style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap;font-weight:bold" |Mac OS X
|-
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |rotate around X (horizontal) axis&lt;br /&gt;rotate around Y (vertical) axis
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |left drag
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |drag
|-
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |translate along X axis (holizontally)&lt;br /&gt;translate along Y axis (vertically)
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |right drag
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |Command + drag
|-
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |translate along Z axis (zoom in/out)
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |Shift + left drag
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |Shift + drag
|}

Operations such as changing display models and colors and saving the image, can be executed with a menu. The location of the menu is at the top of the application window in Windows and at the top of screen in Mac as the stand-alone application. As an applet usage, a popup menu appears by clicking the right mouse button on the display screen, or clicking with a "Command" button in case of Mac.

{| style="margin:auto;border:0"
|-
| [[File:Jv_menu_win.png|The location of menu in jV stand-alone version in Windows.|250px]]
| [[File:Jv_menu_mac.png|The location of menu in jV stand-alone version in Mac.|250px]]
| [[File:popupmenu_en.png|The location of menu in applet version.|250px]]
|-
| style="text-align:center" |Stand-alone (Windows)
| style="text-align:center" |Stand-alone (Mac)
| style="text-align:center" |Applet
|}

Basic menu operations are following (see also [[GUI]] for details):

{| style="margin:auto;border:1px solid gray;border-collapse:collapse"
! style="padding:0 0.5em;border:1px solid gray" | Operations
! style="padding:0 0.5em;border:1px solid gray" | Menu location
|-
| style="padding:0 0.5em;border:1px solid gray" | Save a static image
| style="padding:0 0.5em;border:1px solid gray" | [File]-[Save]-[PNG/JPEG]
|-
| style="padding:0 0.5em;border:1px solid gray" | Change the expression format
| style="padding:0 0.5em;border:1px solid gray" | [File]-[Display]-[Wireframe/Backbone/Sticks/Spacefill/Ball&amp;amp;Stick/Ribbons/Cartoon]
|-
| style="padding:0 0.5em;border:1px solid gray" | Change the color
| style="padding:0 0.5em;border:1px solid gray" | [File]-[Colors]-[Monochrome/CPK/Shapely/Group/Chain/Temperature/Structure/Charge/Amino]
|}

To execute more complicated operation such as diplaying some piece of the molecule or changing some part of molecule in another style, use command line operation.

See also [[#Other resources]] for details:


== Download ==
You can also download the program and start it up locally.
In this case, installing JOGL is required in advance (see [[Installation_of_jV3 | Installation]] page).
The following links take you to the download pages. (latest version is 4.1@2011/12/21)
* [http://ef-site.hgc.jp/eF-site/servlet/DownloadViewerBinary binary (4.1)] 
* [http://ef-site.hgc.jp/eF-site/servlet/Registration source code (4.1)] (registration will be required)

== Other resources ==
* [http://ef-site.hgc.jp/eF-site/jV/jV_manual.html Manual] (html in English)
* [[How_to_use]] (in this site in English)
* [http://www.pdbj.org/jv/manual/index_ja.html Manual] (html in Japanese)
* [http://www.pdbj.org/jv/manual/jV_manual.pdf Manual] (pdf in English, for ver. 3.3)
* [http://ef-site.hgc.jp/eF-site/jV/jV3_User'sGuide.pdf User's guide] (for ver. 3.8.3 in English)</text>
    <sha1>ffc5ebe08a359e6fdb5c2380ca284d8105b5f09a</sha1>
  </revision>
  <revision>
    <id>501</id>
    <parentid>495</parentid>
    <timestamp>2012-03-26T07:15:45Z</timestamp>
    <contributor>
      <username>IMSsato</username>
      <id>4</id>
    </contributor>
    <comment>/* Start up */</comment>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="6598" xml:space="preserve">&lt;big&gt;'''Welcome to jV wiki.'''&lt;/big&gt;

jV (formerly known as PDBjViewer) is a program to display molecular graphics of protein and nucleic acids. 
jV supports the following features:
* jV can read and display PDBML files, the canonical XML format for the Protein Data Bank.
* Of course, jV can read and display the traditional PDB format files, too.
* RasMol-like usability.
* jV can process more than one molecules.
* jV can display polygons specified by XML. ([http://ef-site.hgc.jp/eF-site/schema/polygon12.xsd XML Schema for polygons] is available.)
* Multiple polygons can be processed simultaneously, and be superimposed onto molecular images.
* Animation can be realized.
* jV runs on the Java Runtime Environment ([http://java.sun.com/javase/index.jsp JRE]) so that it can work as a stand-alone application as well as an applet.
* The graphics of jV is based on OpenGL ([http://jogamp.org/jogl/www/ JOGL]), thereby producing fairly beautiful pictures.


The program 'jV' has been developed by [http://www.hgc.jp/~kinosita/TOP.html Kengo Kinoshita] ([http://www.is.tohoku.ac.jp/index-e.html Graduate School of Information Sciences], [http://www.tohoku.ac.jp/english/ Tohoku University]) and [http://www.protein.osaka-u.ac.jp/rcsfp/pi/ Haruki Nakamura] ([http://www.protein.osaka-u.ac.jp/index_e.php Institute for Protein Research], [http://www.osaka-u.ac.jp/eng/index.html Osaka Univeristy]), with the support from [http://biosciencedbc.jp/ JST-NBDC] and [http://www.osaka-u.ac.jp/ Osaka University].
      

&lt;gallery&gt;
File:Spacefill.jpg
File:Cartoon.jpg
File:Surface.jpg
File:edmap.jpg
&lt;/gallery&gt;


== Start up ==
You can start up jV (4.2) with Java Web Start technology immediately from here.
* [http://ef-site.hgc.jp/eF-site/servlet/stable/jV.jnlp stable JOGL version] (recommended)
* [http://ef-site.hgc.jp/eF-site/servlet/current/jV.jnlp recent JOGL version]
The current jV requires JRE 1.6 or later.
The previous version, jV version 4.0, can run with JRE 1.4 and 1.5.
* [http://ef-site.hgc.jp/jV/stable/jV_4_0.jnlp jV 4.0]

== Basic Usage ==
You can execute basic operations such as rotation and translation with mouse action. Major actions are described in the following table:
{| style="margin:auto;border:1px solid gray"
! rowspan="2" style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap;font-weight:bold" |Action
! colspan="2" style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap;font-weight:bold" |Mouse Operation
|-
! style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap;font-weight:bold" |Windows, Linux
! style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap;font-weight:bold" |Mac OS X
|-
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |rotate around X (horizontal) axis&lt;br /&gt;rotate around Y (vertical) axis
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |left drag
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |drag
|-
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |translate along X axis (holizontally)&lt;br /&gt;translate along Y axis (vertically)
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |right drag
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |Command + drag
|-
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |translate along Z axis (zoom in/out)
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |Shift + left drag
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |Shift + drag
|}

Operations such as changing display models and colors and saving the image, can be executed with a menu. The location of the menu is at the top of the application window in Windows and at the top of screen in Mac as the stand-alone application. As an applet usage, a popup menu appears by clicking the right mouse button on the display screen, or clicking with a "Command" button in case of Mac.

{| style="margin:auto;border:0"
|-
| [[File:Jv_menu_win.png|The location of menu in jV stand-alone version in Windows.|250px]]
| [[File:Jv_menu_mac.png|The location of menu in jV stand-alone version in Mac.|250px]]
| [[File:popupmenu_en.png|The location of menu in applet version.|250px]]
|-
| style="text-align:center" |Stand-alone (Windows)
| style="text-align:center" |Stand-alone (Mac)
| style="text-align:center" |Applet
|}

Basic menu operations are following (see also [[GUI]] for details):

{| style="margin:auto;border:1px solid gray;border-collapse:collapse"
! style="padding:0 0.5em;border:1px solid gray" | Operations
! style="padding:0 0.5em;border:1px solid gray" | Menu location
|-
| style="padding:0 0.5em;border:1px solid gray" | Save a static image
| style="padding:0 0.5em;border:1px solid gray" | [File]-[Save]-[PNG/JPEG]
|-
| style="padding:0 0.5em;border:1px solid gray" | Change the expression format
| style="padding:0 0.5em;border:1px solid gray" | [File]-[Display]-[Wireframe/Backbone/Sticks/Spacefill/Ball&amp;amp;Stick/Ribbons/Cartoon]
|-
| style="padding:0 0.5em;border:1px solid gray" | Change the color
| style="padding:0 0.5em;border:1px solid gray" | [File]-[Colors]-[Monochrome/CPK/Shapely/Group/Chain/Temperature/Structure/Charge/Amino]
|}

To execute more complicated operation such as diplaying some piece of the molecule or changing some part of molecule in another style, use command line operation.

See also [[#Other resources]] for details:


== Download ==
You can also download the program and start it up locally.
In this case, installing JOGL is required in advance (see [[Installation_of_jV3 | Installation]] page).
The following links take you to the download pages. (latest version is 4.1@2011/12/21)
* [http://ef-site.hgc.jp/eF-site/servlet/DownloadViewerBinary binary (4.1)] 
* [http://ef-site.hgc.jp/eF-site/servlet/Registration source code (4.1)] (registration will be required)

== Other resources ==
* [http://ef-site.hgc.jp/eF-site/jV/jV_manual.html Manual] (html in English)
* [[How_to_use]] (in this site in English)
* [http://www.pdbj.org/jv/manual/index_ja.html Manual] (html in Japanese)
* [http://www.pdbj.org/jv/manual/jV_manual.pdf Manual] (pdf in English, for ver. 3.3)
* [http://ef-site.hgc.jp/eF-site/jV/jV3_User'sGuide.pdf User's guide] (for ver. 3.8.3 in English)</text>
    <sha1>858020d0df6e3807f593abf2863796068035bb87</sha1>
  </revision>
  <revision>
    <id>502</id>
    <parentid>501</parentid>
    <timestamp>2012-03-26T07:16:09Z</timestamp>
    <contributor>
      <username>IMSsato</username>
      <id>4</id>
    </contributor>
    <comment>/* Download */</comment>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="6597" xml:space="preserve">&lt;big&gt;'''Welcome to jV wiki.'''&lt;/big&gt;

jV (formerly known as PDBjViewer) is a program to display molecular graphics of protein and nucleic acids. 
jV supports the following features:
* jV can read and display PDBML files, the canonical XML format for the Protein Data Bank.
* Of course, jV can read and display the traditional PDB format files, too.
* RasMol-like usability.
* jV can process more than one molecules.
* jV can display polygons specified by XML. ([http://ef-site.hgc.jp/eF-site/schema/polygon12.xsd XML Schema for polygons] is available.)
* Multiple polygons can be processed simultaneously, and be superimposed onto molecular images.
* Animation can be realized.
* jV runs on the Java Runtime Environment ([http://java.sun.com/javase/index.jsp JRE]) so that it can work as a stand-alone application as well as an applet.
* The graphics of jV is based on OpenGL ([http://jogamp.org/jogl/www/ JOGL]), thereby producing fairly beautiful pictures.


The program 'jV' has been developed by [http://www.hgc.jp/~kinosita/TOP.html Kengo Kinoshita] ([http://www.is.tohoku.ac.jp/index-e.html Graduate School of Information Sciences], [http://www.tohoku.ac.jp/english/ Tohoku University]) and [http://www.protein.osaka-u.ac.jp/rcsfp/pi/ Haruki Nakamura] ([http://www.protein.osaka-u.ac.jp/index_e.php Institute for Protein Research], [http://www.osaka-u.ac.jp/eng/index.html Osaka Univeristy]), with the support from [http://biosciencedbc.jp/ JST-NBDC] and [http://www.osaka-u.ac.jp/ Osaka University].
      

&lt;gallery&gt;
File:Spacefill.jpg
File:Cartoon.jpg
File:Surface.jpg
File:edmap.jpg
&lt;/gallery&gt;


== Start up ==
You can start up jV (4.2) with Java Web Start technology immediately from here.
* [http://ef-site.hgc.jp/eF-site/servlet/stable/jV.jnlp stable JOGL version] (recommended)
* [http://ef-site.hgc.jp/eF-site/servlet/current/jV.jnlp recent JOGL version]
The current jV requires JRE 1.6 or later.
The previous version, jV version 4.0, can run with JRE 1.4 and 1.5.
* [http://ef-site.hgc.jp/jV/stable/jV_4_0.jnlp jV 4.0]

== Basic Usage ==
You can execute basic operations such as rotation and translation with mouse action. Major actions are described in the following table:
{| style="margin:auto;border:1px solid gray"
! rowspan="2" style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap;font-weight:bold" |Action
! colspan="2" style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap;font-weight:bold" |Mouse Operation
|-
! style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap;font-weight:bold" |Windows, Linux
! style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap;font-weight:bold" |Mac OS X
|-
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |rotate around X (horizontal) axis&lt;br /&gt;rotate around Y (vertical) axis
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |left drag
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |drag
|-
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |translate along X axis (holizontally)&lt;br /&gt;translate along Y axis (vertically)
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |right drag
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |Command + drag
|-
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |translate along Z axis (zoom in/out)
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |Shift + left drag
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |Shift + drag
|}

Operations such as changing display models and colors and saving the image, can be executed with a menu. The location of the menu is at the top of the application window in Windows and at the top of screen in Mac as the stand-alone application. As an applet usage, a popup menu appears by clicking the right mouse button on the display screen, or clicking with a "Command" button in case of Mac.

{| style="margin:auto;border:0"
|-
| [[File:Jv_menu_win.png|The location of menu in jV stand-alone version in Windows.|250px]]
| [[File:Jv_menu_mac.png|The location of menu in jV stand-alone version in Mac.|250px]]
| [[File:popupmenu_en.png|The location of menu in applet version.|250px]]
|-
| style="text-align:center" |Stand-alone (Windows)
| style="text-align:center" |Stand-alone (Mac)
| style="text-align:center" |Applet
|}

Basic menu operations are following (see also [[GUI]] for details):

{| style="margin:auto;border:1px solid gray;border-collapse:collapse"
! style="padding:0 0.5em;border:1px solid gray" | Operations
! style="padding:0 0.5em;border:1px solid gray" | Menu location
|-
| style="padding:0 0.5em;border:1px solid gray" | Save a static image
| style="padding:0 0.5em;border:1px solid gray" | [File]-[Save]-[PNG/JPEG]
|-
| style="padding:0 0.5em;border:1px solid gray" | Change the expression format
| style="padding:0 0.5em;border:1px solid gray" | [File]-[Display]-[Wireframe/Backbone/Sticks/Spacefill/Ball&amp;amp;Stick/Ribbons/Cartoon]
|-
| style="padding:0 0.5em;border:1px solid gray" | Change the color
| style="padding:0 0.5em;border:1px solid gray" | [File]-[Colors]-[Monochrome/CPK/Shapely/Group/Chain/Temperature/Structure/Charge/Amino]
|}

To execute more complicated operation such as diplaying some piece of the molecule or changing some part of molecule in another style, use command line operation.

See also [[#Other resources]] for details:


== Download ==
You can also download the program and start it up locally.
In this case, installing JOGL is required in advance (see [[Installation_of_jV3 | Installation]] page).
The following links take you to the download pages. (latest version is 4.2@2012/3/26)
* [http://ef-site.hgc.jp/eF-site/servlet/DownloadViewerBinary binary (4.2)] 
* [http://ef-site.hgc.jp/eF-site/servlet/Registration source code (4.2)] (registration will be required)

== Other resources ==
* [http://ef-site.hgc.jp/eF-site/jV/jV_manual.html Manual] (html in English)
* [[How_to_use]] (in this site in English)
* [http://www.pdbj.org/jv/manual/index_ja.html Manual] (html in Japanese)
* [http://www.pdbj.org/jv/manual/jV_manual.pdf Manual] (pdf in English, for ver. 3.3)
* [http://ef-site.hgc.jp/eF-site/jV/jV3_User'sGuide.pdf User's guide] (for ver. 3.8.3 in English)</text>
    <sha1>2480d2663c83d1124a9cc05c475e918932eff378</sha1>
  </revision>
  <revision>
    <id>503</id>
    <parentid>502</parentid>
    <timestamp>2012-03-26T07:19:07Z</timestamp>
    <contributor>
      <username>IMSsato</username>
      <id>4</id>
    </contributor>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="6583" xml:space="preserve">&lt;big&gt;'''Welcome to jV wiki.'''&lt;/big&gt;

jV (formerly known as PDBjViewer) is a program to display molecular graphics of protein and nucleic acids. 
jV supports the following features:
* jV can read and display PDBML files, the canonical XML format for the Protein Data Bank.
* Of course, jV can read and display the traditional PDB format files, too.
* RasMol-like usability.
* jV can process more than one molecules.
* jV can display polygons specified by XML. ([http://www.pdbj.org/jv/polygonSchema XML Schema for polygons] is available.)
* Multiple polygons can be processed simultaneously, and be superimposed onto molecular images.
* Animation can be realized.
* jV runs on the Java Runtime Environment ([http://java.sun.com/javase/index.jsp JRE]) so that it can work as a stand-alone application as well as an applet.
* The graphics of jV is based on OpenGL ([http://jogamp.org/jogl/www/ JOGL]), thereby producing fairly beautiful pictures.


The program 'jV' has been developed by [http://www.hgc.jp/~kinosita/TOP.html Kengo Kinoshita] ([http://www.is.tohoku.ac.jp/index-e.html Graduate School of Information Sciences], [http://www.tohoku.ac.jp/english/ Tohoku University]) and [http://www.protein.osaka-u.ac.jp/rcsfp/pi/ Haruki Nakamura] ([http://www.protein.osaka-u.ac.jp/index_e.php Institute for Protein Research], [http://www.osaka-u.ac.jp/eng/index.html Osaka Univeristy]), with the support from [http://biosciencedbc.jp/ JST-NBDC] and [http://www.osaka-u.ac.jp/ Osaka University].
      

&lt;gallery&gt;
File:Spacefill.jpg
File:Cartoon.jpg
File:Surface.jpg
File:edmap.jpg
&lt;/gallery&gt;


== Start up ==
You can start up jV (4.2) with Java Web Start technology immediately from here.
* [http://ef-site.hgc.jp/eF-site/servlet/stable/jV.jnlp stable JOGL version] (recommended)
* [http://ef-site.hgc.jp/eF-site/servlet/current/jV.jnlp recent JOGL version]
The current jV requires JRE 1.6 or later.
The previous version, jV version 4.0, can run with JRE 1.4 and 1.5.
* [http://ef-site.hgc.jp/jV/stable/jV_4_0.jnlp jV 4.0]

== Basic Usage ==
You can execute basic operations such as rotation and translation with mouse action. Major actions are described in the following table:
{| style="margin:auto;border:1px solid gray"
! rowspan="2" style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap;font-weight:bold" |Action
! colspan="2" style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap;font-weight:bold" |Mouse Operation
|-
! style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap;font-weight:bold" |Windows, Linux
! style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap;font-weight:bold" |Mac OS X
|-
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |rotate around X (horizontal) axis&lt;br /&gt;rotate around Y (vertical) axis
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |left drag
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |drag
|-
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |translate along X axis (holizontally)&lt;br /&gt;translate along Y axis (vertically)
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |right drag
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |Command + drag
|-
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |translate along Z axis (zoom in/out)
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |Shift + left drag
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |Shift + drag
|}

Operations such as changing display models and colors and saving the image, can be executed with a menu. The location of the menu is at the top of the application window in Windows and at the top of screen in Mac as the stand-alone application. As an applet usage, a popup menu appears by clicking the right mouse button on the display screen, or clicking with a "Command" button in case of Mac.

{| style="margin:auto;border:0"
|-
| [[File:Jv_menu_win.png|The location of menu in jV stand-alone version in Windows.|250px]]
| [[File:Jv_menu_mac.png|The location of menu in jV stand-alone version in Mac.|250px]]
| [[File:popupmenu_en.png|The location of menu in applet version.|250px]]
|-
| style="text-align:center" |Stand-alone (Windows)
| style="text-align:center" |Stand-alone (Mac)
| style="text-align:center" |Applet
|}

Basic menu operations are following (see also [[GUI]] for details):

{| style="margin:auto;border:1px solid gray;border-collapse:collapse"
! style="padding:0 0.5em;border:1px solid gray" | Operations
! style="padding:0 0.5em;border:1px solid gray" | Menu location
|-
| style="padding:0 0.5em;border:1px solid gray" | Save a static image
| style="padding:0 0.5em;border:1px solid gray" | [File]-[Save]-[PNG/JPEG]
|-
| style="padding:0 0.5em;border:1px solid gray" | Change the expression format
| style="padding:0 0.5em;border:1px solid gray" | [File]-[Display]-[Wireframe/Backbone/Sticks/Spacefill/Ball&amp;amp;Stick/Ribbons/Cartoon]
|-
| style="padding:0 0.5em;border:1px solid gray" | Change the color
| style="padding:0 0.5em;border:1px solid gray" | [File]-[Colors]-[Monochrome/CPK/Shapely/Group/Chain/Temperature/Structure/Charge/Amino]
|}

To execute more complicated operation such as diplaying some piece of the molecule or changing some part of molecule in another style, use command line operation.

See also [[#Other resources]] for details:


== Download ==
You can also download the program and start it up locally.
In this case, installing JOGL is required in advance (see [[Installation_of_jV3 | Installation]] page).
The following links take you to the download pages. (latest version is 4.2@2012/3/26)
* [http://ef-site.hgc.jp/eF-site/servlet/DownloadViewerBinary binary (4.2)] 
* [http://ef-site.hgc.jp/eF-site/servlet/Registration source code (4.2)] (registration will be required)

== Other resources ==
* [http://ef-site.hgc.jp/eF-site/jV/jV_manual.html Manual] (html in English)
* [[How_to_use]] (in this site in English)
* [http://www.pdbj.org/jv/manual/index_ja.html Manual] (html in Japanese)
* [http://www.pdbj.org/jv/manual/jV_manual.pdf Manual] (pdf in English, for ver. 3.3)
* [http://ef-site.hgc.jp/eF-site/jV/jV3_User'sGuide.pdf User's guide] (for ver. 3.8.3 in English)</text>
    <sha1>38908c1244f01d037306518702367cd6bdaf78dc</sha1>
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    <comment>Image of Java Preferences Window in Mac OS X 10.4.</comment>
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    <text bytes="50" xml:space="preserve">Image of Java Preferences Window in Mac OS X 10.4.</text>
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      <id>5</id>
    </contributor>
    <comment>The window to inquiring target to delete when java cache file removing on Mac OS X.</comment>
    <model>wikitext</model>
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    <text bytes="83" xml:space="preserve">The window to inquiring target to delete when java cache file removing on Mac OS X.</text>
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<page arvcontinue="20110106074224|454">
  <title>Trouble shooting</title>
  <ns>0</ns>
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    <id>462</id>
    <parentid>408</parentid>
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    <contributor>
      <username>Cudo29</username>
      <id>5</id>
    </contributor>
    <comment>/* clear cached files */ Updated involved in the Mac OS version dependency.</comment>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="5527" xml:space="preserve">{| style="left"
 |__TOC__
 |}

== Certificate error on applet ==

When you use JRE6 Update15 (1.6.0_15) or JRE6 Update16 (1.6.0_16) on Windows or Linux,
jV applet and applet-launcher fail to start up with the following error.

 Error:java.io.IOException:Cannot find certificates for JNLP AppletLauncher class

Please use JRE6 Update17 (1.6.0_17) or later.

== JOGL library conflict ==

If you cannot start jV via Java Web Start or view jV applets due to a failure of locating the JOGL library, try the followings.

===clear cached files===

On JRE of version 1.6.0_15 and 1.6.0_16, previously cached JOGL files cause a problem
even if newer files are placed on the server.
JRE of version 1.6.0_17 or later is recommended.
On Mac OS X Snow Leopard, however, the latest JRE is of version 1.6.0_15 at the moment.
The following steps show how to clear cached files.

;1) Open the Java Preferences window
:Double-click the [Java Preferences] icon, then the Java Preferences window appears. The place of [Java Preferences] depends on the version of Mac OS as following:
:{|style="border:1px solid gray;border-collapse:collapse"
!style="border:1px solid gray;padding:0 0.5em;background-color:lightyellow"|Max OS X version
!style="border:1px solid gray;padding:0 0.5em;background-color:lightyellow"|place
|-
|style="border:1px solid gray;padding:0 0.5em"|10.4
|style="border:1px solid gray;padding:0 0.5em"|[Applications]-[Utilities]-[Java]-[J2SE 5.0]
|-
|style="border:1px solid gray;padding:0 0.5em"|10.5 (before installing Java for Mac OS X 10.5 Update 4)
|style="border:1px solid gray;padding:0 0.5em"|[Applications]-[Utilities]-[Java]
|-
|style="border:1px solid gray;padding:0 0.5em"|10.5 (after installing Java for Mac OS X 10.5 Update 4 or later)
|style="border:1px solid gray;padding:0 0.5em"|[Applications]-[Utilities]
|-
|style="border:1px solid gray;padding:0 0.5em"|10.6
|style="border:1px solid gray;padding:0 0.5em"|[Applications]-[Utilities]
|}
:The contents of the [Java Preferences] differ for the version of Mac OS. In case 10.4, use the [General] tab, which is default displayed. In case 10.5 or later, click to display [Network] tab.
:{|style="border:1px solid gray;border-collapse:collapse"
!style="border:1px solid gray;padding:0 0.5em;background-color:lightyellow"|Max OS X 10.4
!style="border:1px solid gray;padding:0 0.5em;background-color:lightyellow"|Max OS X 10.5 or later
|-
|style="border:1px solid gray;padding:0.5ex 0.5em;text-align:center;vertical-align:top"|[[File:Javapref_tiger.png|400px]]
|style="border:1px solid gray;padding:0.5ex 0.5em;text-align:center;vertical-align:top"|[[File:Java_prefs1.png|400px]]&lt;br/&gt;&amp;darr;&lt;br/&gt;[[File:Java_prefs2.png|400px]]
|}

;2) Press 'Delete Files...' button
:The [Delete Temporary Files] window, which asks which items are to remove, will be opened.

:[[File:Javacache_del.png]]

;3) Leave all the checkboxs on and click 'OK' button.

===remove local JOGL library===

Locally-installed JOGL libraries of different version cause conflicts with Java Web Start technology.
JOGL library files are different between operating systems.

'''Mac OS X'''

Open the [Macintosh HD]-[Library]-[Java]-[Extensions] folder.
If some of the following files

* jogl.jar
* gluegen-rt.jar
* libjogl.jnilib
* libjogl_awt.jnilib
* libjogl_cg.jnilib
* libgluegen-rt.jnilib

exist in the folder, remove them.
Here, this operation requires root privilege.

'''Windows'''

Files that should be removed are as follows.

* &lt;JRE&gt;\lib\ext\jogl.jar
* &lt;JRE&gt;\lib\ext\gluegen-rt.jar
* &lt;JRE&gt;\bin\jogl.dll
* &lt;JRE&gt;\bin\jogl_cg.dll
* &lt;JRE&gt;\bin\jogl_awt.dll
* &lt;JRE&gt;\bin\gluegen-rt.dll

Here, &lt;JRE&gt; denotes the folder that JRE has been installed; typically &lt;JRE&gt;=C:\Program Files\Java\jre6.

'''Linux'''

Files that should be removed are as follows.

* &lt;JRE&gt;/lib/ext/jogl.jar
* &lt;JRE&gt;/lib/ext/gluegen-rt.jar
* &lt;JRE&gt;/lib/&lt;arch&gt;/libjogl.so
* &lt;JRE&gt;/lib/&lt;arch&gt;/libjogl_cg.so
* &lt;JRE&gt;/lib/&lt;arch&gt;/libjogl_awt.so
* &lt;JRE&gt;/lib/&lt;arch&gt;/libjogl_drihack.so
* &lt;JRE&gt;/lib/&lt;arch&gt;/libgluegen-rt.so

Here, &lt;JRE&gt; denotes the directory that JRE has been installed; typically &lt;JRE&gt;=/usr/java/jdk1.6.0_17/jre,
and &lt;arch&gt; the processor architecture such as &lt;arch&gt;=i386.

== jV applet with Internet Explorer ==

When visiting a web page that contains a jV applet with Internet Explorer, there sometimes occurs trouble in working with native JOGL libraries especially on Windows Vista. Please use Firefox web browser in that case.

== Class not found error on applet ==

When you use JRE6 Update21 (1.6.0_21) with the next-generation Java Plug-in enabled on Windows or Linux, 
the following error occurs for the combination of jV applet and applet-launcher.

 Error: Class not found: org.pdbj.viewer.gui.ViewerApplet

You can avoid this problem by disabling the next-generation Java Plug-in.
[http://www.java.com/en/download/help/new_plugin.xml Here] is how to do that for Windows users.
On Linux platform, users can manually replace the symbolic link to new plug-in &lt;tt&gt;libnpjp2.so&lt;/tt&gt;
with the symbolic link to classic plug-in &lt;tt&gt;libjavaplugin_oji.so&lt;/tt&gt;
(see [http://www.oracle.com/technetwork/java/javase/manual-plugin-install-linux-136395.html this page] for help).
If you are using firefox 3.6 or later, however, you need to downgrade JRE to 1.6.0_20
because firefox of those versions run applets only with the new Java Plug-in.
To get JRE 1.6.0_20, see [https://cds.sun.com/is-bin/INTERSHOP.enfinity/WFS/CDS-CDS_Developer-Site/en_US/-/USD/ViewProductDetail-Start?ProductRef=jre-6u20-oth-JPR@CDS-CDS_Developer this page].</text>
    <sha1>6d92f7c83c2d14e3fe9c1ea3608b60e24ecf111b</sha1>
  </revision>
  <revision>
    <id>464</id>
    <parentid>462</parentid>
    <timestamp>2011-04-14T08:21:19Z</timestamp>
    <contributor>
      <username>Cudo29</username>
      <id>5</id>
    </contributor>
    <comment>/* clear cached files */ File:Javacache_del.png was replaced to the English version.</comment>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="5530" xml:space="preserve">{| style="left"
 |__TOC__
 |}

== Certificate error on applet ==

When you use JRE6 Update15 (1.6.0_15) or JRE6 Update16 (1.6.0_16) on Windows or Linux,
jV applet and applet-launcher fail to start up with the following error.

 Error:java.io.IOException:Cannot find certificates for JNLP AppletLauncher class

Please use JRE6 Update17 (1.6.0_17) or later.

== JOGL library conflict ==

If you cannot start jV via Java Web Start or view jV applets due to a failure of locating the JOGL library, try the followings.

===clear cached files===

On JRE of version 1.6.0_15 and 1.6.0_16, previously cached JOGL files cause a problem
even if newer files are placed on the server.
JRE of version 1.6.0_17 or later is recommended.
On Mac OS X Snow Leopard, however, the latest JRE is of version 1.6.0_15 at the moment.
The following steps show how to clear cached files.

;1) Open the Java Preferences window
:Double-click the [Java Preferences] icon, then the Java Preferences window appears. The place of [Java Preferences] depends on the version of Mac OS as following:
:{|style="border:1px solid gray;border-collapse:collapse"
!style="border:1px solid gray;padding:0 0.5em;background-color:lightyellow"|Max OS X version
!style="border:1px solid gray;padding:0 0.5em;background-color:lightyellow"|place
|-
|style="border:1px solid gray;padding:0 0.5em"|10.4
|style="border:1px solid gray;padding:0 0.5em"|[Applications]-[Utilities]-[Java]-[J2SE 5.0]
|-
|style="border:1px solid gray;padding:0 0.5em"|10.5 (before installing Java for Mac OS X 10.5 Update 4)
|style="border:1px solid gray;padding:0 0.5em"|[Applications]-[Utilities]-[Java]
|-
|style="border:1px solid gray;padding:0 0.5em"|10.5 (after installing Java for Mac OS X 10.5 Update 4 or later)
|style="border:1px solid gray;padding:0 0.5em"|[Applications]-[Utilities]
|-
|style="border:1px solid gray;padding:0 0.5em"|10.6
|style="border:1px solid gray;padding:0 0.5em"|[Applications]-[Utilities]
|}
:The contents of the [Java Preferences] differ for the version of Mac OS. In case 10.4, use the [General] tab, which is default displayed. In case 10.5 or later, click to display [Network] tab.
:{|style="border:1px solid gray;border-collapse:collapse"
!style="border:1px solid gray;padding:0 0.5em;background-color:lightyellow"|Max OS X 10.4
!style="border:1px solid gray;padding:0 0.5em;background-color:lightyellow"|Max OS X 10.5 or later
|-
|style="border:1px solid gray;padding:0.5ex 0.5em;text-align:center;vertical-align:top"|[[File:Javapref_tiger.png|400px]]
|style="border:1px solid gray;padding:0.5ex 0.5em;text-align:center;vertical-align:top"|[[File:Java_prefs1.png|400px]]&lt;br/&gt;&amp;darr;&lt;br/&gt;[[File:Java_prefs2.png|400px]]
|}

;2) Press 'Delete Files...' button
:The [Delete Temporary Files] window, which asks which items are to remove, will be opened.

:[[File:Javacache_del_en.png]]

;3) Leave all the checkboxs on and click 'OK' button.

===remove local JOGL library===

Locally-installed JOGL libraries of different version cause conflicts with Java Web Start technology.
JOGL library files are different between operating systems.

'''Mac OS X'''

Open the [Macintosh HD]-[Library]-[Java]-[Extensions] folder.
If some of the following files

* jogl.jar
* gluegen-rt.jar
* libjogl.jnilib
* libjogl_awt.jnilib
* libjogl_cg.jnilib
* libgluegen-rt.jnilib

exist in the folder, remove them.
Here, this operation requires root privilege.

'''Windows'''

Files that should be removed are as follows.

* &lt;JRE&gt;\lib\ext\jogl.jar
* &lt;JRE&gt;\lib\ext\gluegen-rt.jar
* &lt;JRE&gt;\bin\jogl.dll
* &lt;JRE&gt;\bin\jogl_cg.dll
* &lt;JRE&gt;\bin\jogl_awt.dll
* &lt;JRE&gt;\bin\gluegen-rt.dll

Here, &lt;JRE&gt; denotes the folder that JRE has been installed; typically &lt;JRE&gt;=C:\Program Files\Java\jre6.

'''Linux'''

Files that should be removed are as follows.

* &lt;JRE&gt;/lib/ext/jogl.jar
* &lt;JRE&gt;/lib/ext/gluegen-rt.jar
* &lt;JRE&gt;/lib/&lt;arch&gt;/libjogl.so
* &lt;JRE&gt;/lib/&lt;arch&gt;/libjogl_cg.so
* &lt;JRE&gt;/lib/&lt;arch&gt;/libjogl_awt.so
* &lt;JRE&gt;/lib/&lt;arch&gt;/libjogl_drihack.so
* &lt;JRE&gt;/lib/&lt;arch&gt;/libgluegen-rt.so

Here, &lt;JRE&gt; denotes the directory that JRE has been installed; typically &lt;JRE&gt;=/usr/java/jdk1.6.0_17/jre,
and &lt;arch&gt; the processor architecture such as &lt;arch&gt;=i386.

== jV applet with Internet Explorer ==

When visiting a web page that contains a jV applet with Internet Explorer, there sometimes occurs trouble in working with native JOGL libraries especially on Windows Vista. Please use Firefox web browser in that case.

== Class not found error on applet ==

When you use JRE6 Update21 (1.6.0_21) with the next-generation Java Plug-in enabled on Windows or Linux, 
the following error occurs for the combination of jV applet and applet-launcher.

 Error: Class not found: org.pdbj.viewer.gui.ViewerApplet

You can avoid this problem by disabling the next-generation Java Plug-in.
[http://www.java.com/en/download/help/new_plugin.xml Here] is how to do that for Windows users.
On Linux platform, users can manually replace the symbolic link to new plug-in &lt;tt&gt;libnpjp2.so&lt;/tt&gt;
with the symbolic link to classic plug-in &lt;tt&gt;libjavaplugin_oji.so&lt;/tt&gt;
(see [http://www.oracle.com/technetwork/java/javase/manual-plugin-install-linux-136395.html this page] for help).
If you are using firefox 3.6 or later, however, you need to downgrade JRE to 1.6.0_20
because firefox of those versions run applets only with the new Java Plug-in.
To get JRE 1.6.0_20, see [https://cds.sun.com/is-bin/INTERSHOP.enfinity/WFS/CDS-CDS_Developer-Site/en_US/-/USD/ViewProductDetail-Start?ProductRef=jre-6u20-oth-JPR@CDS-CDS_Developer this page].</text>
    <sha1>7fbf6f579609454065710882d7636291a15527ae</sha1>
  </revision>
  <revision>
    <id>466</id>
    <parentid>464</parentid>
    <timestamp>2011-04-28T02:25:16Z</timestamp>
    <contributor>
      <username>Cudo29</username>
      <id>5</id>
    </contributor>
    <comment>/* clear cached files */ A procedure to restore the Java environment was added.</comment>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="5774" xml:space="preserve">{| style="left"
 |__TOC__
 |}

== Certificate error on applet ==

When you use JRE6 Update15 (1.6.0_15) or JRE6 Update16 (1.6.0_16) on Windows or Linux,
jV applet and applet-launcher fail to start up with the following error.

 Error:java.io.IOException:Cannot find certificates for JNLP AppletLauncher class

Please use JRE6 Update17 (1.6.0_17) or later.

== JOGL library conflict ==

If you cannot start jV via Java Web Start or view jV applets due to a failure of locating the JOGL library, try the followings.

===clear cached files===

On JRE of version 1.6.0_15 and 1.6.0_16, previously cached JOGL files cause a problem
even if newer files are placed on the server.
JRE of version 1.6.0_17 or later is recommended.
On Mac OS X Snow Leopard, however, the latest JRE is of version 1.6.0_15 at the moment.
The following steps show how to clear cached files.

;1) Open the Java Preferences window
:Double-click the [Java Preferences] icon, then the Java Preferences window appears. The place of [Java Preferences] depends on the version of Mac OS as following:
:{|style="border:1px solid gray;border-collapse:collapse"
!style="border:1px solid gray;padding:0 0.5em;background-color:lightyellow"|Max OS X version
!style="border:1px solid gray;padding:0 0.5em;background-color:lightyellow"|place
|-
|style="border:1px solid gray;padding:0 0.5em"|10.4
|style="border:1px solid gray;padding:0 0.5em"|[Applications]-[Utilities]-[Java]-[J2SE 5.0]
|-
|style="border:1px solid gray;padding:0 0.5em"|10.5 (before installing Java for Mac OS X 10.5 Update 4)
|style="border:1px solid gray;padding:0 0.5em"|[Applications]-[Utilities]-[Java]
|-
|style="border:1px solid gray;padding:0 0.5em"|10.5 (after installing Java for Mac OS X 10.5 Update 4 or later)
|style="border:1px solid gray;padding:0 0.5em"|[Applications]-[Utilities]
|-
|style="border:1px solid gray;padding:0 0.5em"|10.6
|style="border:1px solid gray;padding:0 0.5em"|[Applications]-[Utilities]
|}
:The contents of the [Java Preferences] differ for the version of Mac OS. In case 10.4, use the [General] tab, which is default displayed. In case 10.5 or later, click to display [Network] tab.
:{|style="border:1px solid gray;border-collapse:collapse"
!style="border:1px solid gray;padding:0 0.5em;background-color:lightyellow"|Max OS X 10.4
!style="border:1px solid gray;padding:0 0.5em;background-color:lightyellow"|Max OS X 10.5 or later
|-
|style="border:1px solid gray;padding:0.5ex 0.5em;text-align:center;vertical-align:top"|[[File:Javapref_tiger.png|400px]]
|style="border:1px solid gray;padding:0.5ex 0.5em;text-align:center;vertical-align:top"|[[File:Java_prefs1.png|400px]]&lt;br/&gt;&amp;darr;&lt;br/&gt;[[File:Java_prefs2.png|400px]]
|}

;2) Press 'Delete Files...' button
:The [Delete Temporary Files] window, which asks which items are to remove, will be opened.

:[[File:Javacache_del_en.png]]

;3) Leave all the checkboxs on and click 'OK' button.

;4) In some case, restoring the Java environment to the default may be also required. 
:To do it, click "Restore Defaults" button in the Java Preferences (the following figure is the case of Mac OS X 10.6).
:[[File:Javapref_general_10_6.png]]

===remove local JOGL library===

Locally-installed JOGL libraries of different version cause conflicts with Java Web Start technology.
JOGL library files are different between operating systems.

'''Mac OS X'''

Open the [Macintosh HD]-[Library]-[Java]-[Extensions] folder.
If some of the following files

* jogl.jar
* gluegen-rt.jar
* libjogl.jnilib
* libjogl_awt.jnilib
* libjogl_cg.jnilib
* libgluegen-rt.jnilib

exist in the folder, remove them.
Here, this operation requires root privilege.

'''Windows'''

Files that should be removed are as follows.

* &lt;JRE&gt;\lib\ext\jogl.jar
* &lt;JRE&gt;\lib\ext\gluegen-rt.jar
* &lt;JRE&gt;\bin\jogl.dll
* &lt;JRE&gt;\bin\jogl_cg.dll
* &lt;JRE&gt;\bin\jogl_awt.dll
* &lt;JRE&gt;\bin\gluegen-rt.dll

Here, &lt;JRE&gt; denotes the folder that JRE has been installed; typically &lt;JRE&gt;=C:\Program Files\Java\jre6.

'''Linux'''

Files that should be removed are as follows.

* &lt;JRE&gt;/lib/ext/jogl.jar
* &lt;JRE&gt;/lib/ext/gluegen-rt.jar
* &lt;JRE&gt;/lib/&lt;arch&gt;/libjogl.so
* &lt;JRE&gt;/lib/&lt;arch&gt;/libjogl_cg.so
* &lt;JRE&gt;/lib/&lt;arch&gt;/libjogl_awt.so
* &lt;JRE&gt;/lib/&lt;arch&gt;/libjogl_drihack.so
* &lt;JRE&gt;/lib/&lt;arch&gt;/libgluegen-rt.so

Here, &lt;JRE&gt; denotes the directory that JRE has been installed; typically &lt;JRE&gt;=/usr/java/jdk1.6.0_17/jre,
and &lt;arch&gt; the processor architecture such as &lt;arch&gt;=i386.

== jV applet with Internet Explorer ==

When visiting a web page that contains a jV applet with Internet Explorer, there sometimes occurs trouble in working with native JOGL libraries especially on Windows Vista. Please use Firefox web browser in that case.

== Class not found error on applet ==

When you use JRE6 Update21 (1.6.0_21) with the next-generation Java Plug-in enabled on Windows or Linux, 
the following error occurs for the combination of jV applet and applet-launcher.

 Error: Class not found: org.pdbj.viewer.gui.ViewerApplet

You can avoid this problem by disabling the next-generation Java Plug-in.
[http://www.java.com/en/download/help/new_plugin.xml Here] is how to do that for Windows users.
On Linux platform, users can manually replace the symbolic link to new plug-in &lt;tt&gt;libnpjp2.so&lt;/tt&gt;
with the symbolic link to classic plug-in &lt;tt&gt;libjavaplugin_oji.so&lt;/tt&gt;
(see [http://www.oracle.com/technetwork/java/javase/manual-plugin-install-linux-136395.html this page] for help).
If you are using firefox 3.6 or later, however, you need to downgrade JRE to 1.6.0_20
because firefox of those versions run applets only with the new Java Plug-in.
To get JRE 1.6.0_20, see [https://cds.sun.com/is-bin/INTERSHOP.enfinity/WFS/CDS-CDS_Developer-Site/en_US/-/USD/ViewProductDetail-Start?ProductRef=jre-6u20-oth-JPR@CDS-CDS_Developer this page].</text>
    <sha1>27dd0376c8bfc7375742270deaa9cc6eeec62fbd</sha1>
  </revision>
  <revision>
    <id>472</id>
    <parentid>466</parentid>
    <timestamp>2011-09-05T07:04:38Z</timestamp>
    <contributor>
      <username>Cudo29</username>
      <id>5</id>
    </contributor>
    <comment>/* The jV applet can't display on Mac + Firefox/Safari */  Added.</comment>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="6798" xml:space="preserve">{| style="left"
 |__TOC__
 |}

== Certificate error on applet ==

When you use JRE6 Update15 (1.6.0_15) or JRE6 Update16 (1.6.0_16) on Windows or Linux,
jV applet and applet-launcher fail to start up with the following error.

 Error:java.io.IOException:Cannot find certificates for JNLP AppletLauncher class

Please use JRE6 Update17 (1.6.0_17) or later.

== JOGL library conflict ==

If you cannot start jV via Java Web Start or view jV applets due to a failure of locating the JOGL library, try the followings.

===clear cached files===

On JRE of version 1.6.0_15 and 1.6.0_16, previously cached JOGL files cause a problem
even if newer files are placed on the server.
JRE of version 1.6.0_17 or later is recommended.
On Mac OS X Snow Leopard, however, the latest JRE is of version 1.6.0_15 at the moment.
The following steps show how to clear cached files.

;1) Open the Java Preferences window
:Double-click the [Java Preferences] icon, then the Java Preferences window appears. The place of [Java Preferences] depends on the version of Mac OS as following:
:{|style="border:1px solid gray;border-collapse:collapse"
!style="border:1px solid gray;padding:0 0.5em;background-color:lightyellow"|Max OS X version
!style="border:1px solid gray;padding:0 0.5em;background-color:lightyellow"|place
|-
|style="border:1px solid gray;padding:0 0.5em"|10.4
|style="border:1px solid gray;padding:0 0.5em"|[Applications]-[Utilities]-[Java]-[J2SE 5.0]
|-
|style="border:1px solid gray;padding:0 0.5em"|10.5 (before installing Java for Mac OS X 10.5 Update 4)
|style="border:1px solid gray;padding:0 0.5em"|[Applications]-[Utilities]-[Java]
|-
|style="border:1px solid gray;padding:0 0.5em"|10.5 (after installing Java for Mac OS X 10.5 Update 4 or later)
|style="border:1px solid gray;padding:0 0.5em"|[Applications]-[Utilities]
|-
|style="border:1px solid gray;padding:0 0.5em"|10.6
|style="border:1px solid gray;padding:0 0.5em"|[Applications]-[Utilities]
|}
:The contents of the [Java Preferences] differ for the version of Mac OS. In case 10.4, use the [General] tab, which is default displayed. In case 10.5 or later, click to display [Network] tab.
:{|style="border:1px solid gray;border-collapse:collapse"
!style="border:1px solid gray;padding:0 0.5em;background-color:lightyellow"|Max OS X 10.4
!style="border:1px solid gray;padding:0 0.5em;background-color:lightyellow"|Max OS X 10.5 or later
|-
|style="border:1px solid gray;padding:0.5ex 0.5em;text-align:center;vertical-align:top"|[[File:Javapref_tiger.png|400px]]
|style="border:1px solid gray;padding:0.5ex 0.5em;text-align:center;vertical-align:top"|[[File:Java_prefs1.png|400px]]&lt;br/&gt;&amp;darr;&lt;br/&gt;[[File:Java_prefs2.png|400px]]
|}

;2) Press 'Delete Files...' button
:The [Delete Temporary Files] window, which asks which items are to remove, will be opened.

:[[File:Javacache_del_en.png]]

;3) Leave all the checkboxs on and click 'OK' button.

;4) In some case, restoring the Java environment to the default may be also required. 
:To do it, click "Restore Defaults" button in the Java Preferences (the following figure is the case of Mac OS X 10.6).
:[[File:Javapref_general_10_6.png]]

===remove local JOGL library===

Locally-installed JOGL libraries of different version cause conflicts with Java Web Start technology.
JOGL library files are different between operating systems.

'''Mac OS X'''

Open the [Macintosh HD]-[Library]-[Java]-[Extensions] folder.
If some of the following files

* jogl.jar
* gluegen-rt.jar
* libjogl.jnilib
* libjogl_awt.jnilib
* libjogl_cg.jnilib
* libgluegen-rt.jnilib

exist in the folder, remove them.
Here, this operation requires root privilege.

'''Windows'''

Files that should be removed are as follows.

* &lt;JRE&gt;\lib\ext\jogl.jar
* &lt;JRE&gt;\lib\ext\gluegen-rt.jar
* &lt;JRE&gt;\bin\jogl.dll
* &lt;JRE&gt;\bin\jogl_cg.dll
* &lt;JRE&gt;\bin\jogl_awt.dll
* &lt;JRE&gt;\bin\gluegen-rt.dll

Here, &lt;JRE&gt; denotes the folder that JRE has been installed; typically &lt;JRE&gt;=C:\Program Files\Java\jre6.

'''Linux'''

Files that should be removed are as follows.

* &lt;JRE&gt;/lib/ext/jogl.jar
* &lt;JRE&gt;/lib/ext/gluegen-rt.jar
* &lt;JRE&gt;/lib/&lt;arch&gt;/libjogl.so
* &lt;JRE&gt;/lib/&lt;arch&gt;/libjogl_cg.so
* &lt;JRE&gt;/lib/&lt;arch&gt;/libjogl_awt.so
* &lt;JRE&gt;/lib/&lt;arch&gt;/libjogl_drihack.so
* &lt;JRE&gt;/lib/&lt;arch&gt;/libgluegen-rt.so

Here, &lt;JRE&gt; denotes the directory that JRE has been installed; typically &lt;JRE&gt;=/usr/java/jdk1.6.0_17/jre,
and &lt;arch&gt; the processor architecture such as &lt;arch&gt;=i386.

== jV applet with Internet Explorer ==

When visiting a web page that contains a jV applet with Internet Explorer, there sometimes occurs trouble in working with native JOGL libraries especially on Windows Vista. Please use Firefox web browser in that case.

== Class not found error on applet ==

When you use JRE6 Update21 (1.6.0_21) with the next-generation Java Plug-in enabled on Windows or Linux, 
the following error occurs for the combination of jV applet and applet-launcher.

 Error: Class not found: org.pdbj.viewer.gui.ViewerApplet

You can avoid this problem by disabling the next-generation Java Plug-in.
[http://www.java.com/en/download/help/new_plugin.xml Here] is how to do that for Windows users.
On Linux platform, users can manually replace the symbolic link to new plug-in &lt;tt&gt;libnpjp2.so&lt;/tt&gt;
with the symbolic link to classic plug-in &lt;tt&gt;libjavaplugin_oji.so&lt;/tt&gt;
(see [http://www.oracle.com/technetwork/java/javase/manual-plugin-install-linux-136395.html this page] for help).
If you are using firefox 3.6 or later, however, you need to downgrade JRE to 1.6.0_20
because firefox of those versions run applets only with the new Java Plug-in.
To get JRE 1.6.0_20, see [https://cds.sun.com/is-bin/INTERSHOP.enfinity/WFS/CDS-CDS_Developer-Site/en_US/-/USD/ViewProductDetail-Start?ProductRef=jre-6u20-oth-JPR@CDS-CDS_Developer this page].


== The jV applet can't display on Mac + Firefox/Safari ==
The Mac OS and browser described below can't display jV applets.
To display them, please downgrade the browser or use another browser such as Opera, Camino, Shiira.
We are sorry for the inconvenient.
;OS
:Mac OS X 10.5 update 4 or later
;Browser
* Firefox 6.0 or later
* Safari 5.1 or later
;Reason
:You can specify which Java Plug-in is to use at the Java Preferences. If you select 'In their own process' to use new Java Plug-in, and select 'Within the browser process' to use classic Java Plug-in. But none the less, Firefox 6.0 or later and Safari 5.1 or later forces to use new Java Plug-in. Currently the new Java Plug-in for Mac doesn't support hardware-accelerated technologies like JOGL and Java3D, so the jV applet under these environment can't be displayed.

* The Windows and Linux users don't affect this problem.
* The Firefox 5.0 or older can display jV applets even if on Mac OS.
* The Safari 5.0 or older can display jV applets even if on Mac OS.</text>
    <sha1>fedc3f2b03df2f0ce35cb15cae9e1369d55983b7</sha1>
  </revision>
  <revision>
    <id>473</id>
    <parentid>472</parentid>
    <timestamp>2011-09-05T07:06:45Z</timestamp>
    <contributor>
      <username>Cudo29</username>
      <id>5</id>
    </contributor>
    <comment>/* The jV applet can't display on Mac + Firefox/Safari */ A url was added.</comment>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="6983" xml:space="preserve">{| style="left"
 |__TOC__
 |}

== Certificate error on applet ==

When you use JRE6 Update15 (1.6.0_15) or JRE6 Update16 (1.6.0_16) on Windows or Linux,
jV applet and applet-launcher fail to start up with the following error.

 Error:java.io.IOException:Cannot find certificates for JNLP AppletLauncher class

Please use JRE6 Update17 (1.6.0_17) or later.

== JOGL library conflict ==

If you cannot start jV via Java Web Start or view jV applets due to a failure of locating the JOGL library, try the followings.

===clear cached files===

On JRE of version 1.6.0_15 and 1.6.0_16, previously cached JOGL files cause a problem
even if newer files are placed on the server.
JRE of version 1.6.0_17 or later is recommended.
On Mac OS X Snow Leopard, however, the latest JRE is of version 1.6.0_15 at the moment.
The following steps show how to clear cached files.

;1) Open the Java Preferences window
:Double-click the [Java Preferences] icon, then the Java Preferences window appears. The place of [Java Preferences] depends on the version of Mac OS as following:
:{|style="border:1px solid gray;border-collapse:collapse"
!style="border:1px solid gray;padding:0 0.5em;background-color:lightyellow"|Max OS X version
!style="border:1px solid gray;padding:0 0.5em;background-color:lightyellow"|place
|-
|style="border:1px solid gray;padding:0 0.5em"|10.4
|style="border:1px solid gray;padding:0 0.5em"|[Applications]-[Utilities]-[Java]-[J2SE 5.0]
|-
|style="border:1px solid gray;padding:0 0.5em"|10.5 (before installing Java for Mac OS X 10.5 Update 4)
|style="border:1px solid gray;padding:0 0.5em"|[Applications]-[Utilities]-[Java]
|-
|style="border:1px solid gray;padding:0 0.5em"|10.5 (after installing Java for Mac OS X 10.5 Update 4 or later)
|style="border:1px solid gray;padding:0 0.5em"|[Applications]-[Utilities]
|-
|style="border:1px solid gray;padding:0 0.5em"|10.6
|style="border:1px solid gray;padding:0 0.5em"|[Applications]-[Utilities]
|}
:The contents of the [Java Preferences] differ for the version of Mac OS. In case 10.4, use the [General] tab, which is default displayed. In case 10.5 or later, click to display [Network] tab.
:{|style="border:1px solid gray;border-collapse:collapse"
!style="border:1px solid gray;padding:0 0.5em;background-color:lightyellow"|Max OS X 10.4
!style="border:1px solid gray;padding:0 0.5em;background-color:lightyellow"|Max OS X 10.5 or later
|-
|style="border:1px solid gray;padding:0.5ex 0.5em;text-align:center;vertical-align:top"|[[File:Javapref_tiger.png|400px]]
|style="border:1px solid gray;padding:0.5ex 0.5em;text-align:center;vertical-align:top"|[[File:Java_prefs1.png|400px]]&lt;br/&gt;&amp;darr;&lt;br/&gt;[[File:Java_prefs2.png|400px]]
|}

;2) Press 'Delete Files...' button
:The [Delete Temporary Files] window, which asks which items are to remove, will be opened.

:[[File:Javacache_del_en.png]]

;3) Leave all the checkboxs on and click 'OK' button.

;4) In some case, restoring the Java environment to the default may be also required. 
:To do it, click "Restore Defaults" button in the Java Preferences (the following figure is the case of Mac OS X 10.6).
:[[File:Javapref_general_10_6.png]]

===remove local JOGL library===

Locally-installed JOGL libraries of different version cause conflicts with Java Web Start technology.
JOGL library files are different between operating systems.

'''Mac OS X'''

Open the [Macintosh HD]-[Library]-[Java]-[Extensions] folder.
If some of the following files

* jogl.jar
* gluegen-rt.jar
* libjogl.jnilib
* libjogl_awt.jnilib
* libjogl_cg.jnilib
* libgluegen-rt.jnilib

exist in the folder, remove them.
Here, this operation requires root privilege.

'''Windows'''

Files that should be removed are as follows.

* &lt;JRE&gt;\lib\ext\jogl.jar
* &lt;JRE&gt;\lib\ext\gluegen-rt.jar
* &lt;JRE&gt;\bin\jogl.dll
* &lt;JRE&gt;\bin\jogl_cg.dll
* &lt;JRE&gt;\bin\jogl_awt.dll
* &lt;JRE&gt;\bin\gluegen-rt.dll

Here, &lt;JRE&gt; denotes the folder that JRE has been installed; typically &lt;JRE&gt;=C:\Program Files\Java\jre6.

'''Linux'''

Files that should be removed are as follows.

* &lt;JRE&gt;/lib/ext/jogl.jar
* &lt;JRE&gt;/lib/ext/gluegen-rt.jar
* &lt;JRE&gt;/lib/&lt;arch&gt;/libjogl.so
* &lt;JRE&gt;/lib/&lt;arch&gt;/libjogl_cg.so
* &lt;JRE&gt;/lib/&lt;arch&gt;/libjogl_awt.so
* &lt;JRE&gt;/lib/&lt;arch&gt;/libjogl_drihack.so
* &lt;JRE&gt;/lib/&lt;arch&gt;/libgluegen-rt.so

Here, &lt;JRE&gt; denotes the directory that JRE has been installed; typically &lt;JRE&gt;=/usr/java/jdk1.6.0_17/jre,
and &lt;arch&gt; the processor architecture such as &lt;arch&gt;=i386.

== jV applet with Internet Explorer ==

When visiting a web page that contains a jV applet with Internet Explorer, there sometimes occurs trouble in working with native JOGL libraries especially on Windows Vista. Please use Firefox web browser in that case.

== Class not found error on applet ==

When you use JRE6 Update21 (1.6.0_21) with the next-generation Java Plug-in enabled on Windows or Linux, 
the following error occurs for the combination of jV applet and applet-launcher.

 Error: Class not found: org.pdbj.viewer.gui.ViewerApplet

You can avoid this problem by disabling the next-generation Java Plug-in.
[http://www.java.com/en/download/help/new_plugin.xml Here] is how to do that for Windows users.
On Linux platform, users can manually replace the symbolic link to new plug-in &lt;tt&gt;libnpjp2.so&lt;/tt&gt;
with the symbolic link to classic plug-in &lt;tt&gt;libjavaplugin_oji.so&lt;/tt&gt;
(see [http://www.oracle.com/technetwork/java/javase/manual-plugin-install-linux-136395.html this page] for help).
If you are using firefox 3.6 or later, however, you need to downgrade JRE to 1.6.0_20
because firefox of those versions run applets only with the new Java Plug-in.
To get JRE 1.6.0_20, see [https://cds.sun.com/is-bin/INTERSHOP.enfinity/WFS/CDS-CDS_Developer-Site/en_US/-/USD/ViewProductDetail-Start?ProductRef=jre-6u20-oth-JPR@CDS-CDS_Developer this page].


== The jV applet can't display on Mac + Firefox/Safari ==
The Mac OS and browser described below can't display jV applets.
To display them, please downgrade the browser or use another browser such as Opera, Camino, Shiira.
We are sorry for the inconvenient.
;OS
:Mac OS X 10.5 update 4 or later
;Browser
* Firefox 6.0 or later
* Safari 5.1 or later
;Reason
:You can specify which Java Plug-in is to use at the Java Preferences. If you select 'In their own process' to use new Java Plug-in, and select 'Within the browser process' to use classic Java Plug-in. But none the less, Firefox 6.0 or later and Safari 5.1 or later forces to use new Java Plug-in. Currently the new Java Plug-in for Mac doesn't support hardware-accelerated technologies like JOGL and Java3D[http://developer.apple.com/library/mac/#releasenotes/CrossPlatform/JavaSnowLeopardUpdate2LeopardUpdate7RN/NewandNoteworthy/NewandNoteworthy.html#//apple_ref/doc/uid/TP40009967-CH4-SW1], so the jV applet under these environment can't be displayed.

* The Windows and Linux users don't affect this problem.
* The Firefox 5.0 or older can display jV applets even if on Mac OS.
* The Safari 5.0 or older can display jV applets even if on Mac OS.</text>
    <sha1>554cb9421c1b0a762021d683c3b95c70ad30b0e1</sha1>
  </revision>
  <revision>
    <id>474</id>
    <parentid>473</parentid>
    <timestamp>2011-09-05T07:07:39Z</timestamp>
    <contributor>
      <username>Cudo29</username>
      <id>5</id>
    </contributor>
    <comment>/* The jV applet can't display on Mac + Firefox/Safari */ Modified.</comment>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="6988" xml:space="preserve">{| style="left"
 |__TOC__
 |}

== Certificate error on applet ==

When you use JRE6 Update15 (1.6.0_15) or JRE6 Update16 (1.6.0_16) on Windows or Linux,
jV applet and applet-launcher fail to start up with the following error.

 Error:java.io.IOException:Cannot find certificates for JNLP AppletLauncher class

Please use JRE6 Update17 (1.6.0_17) or later.

== JOGL library conflict ==

If you cannot start jV via Java Web Start or view jV applets due to a failure of locating the JOGL library, try the followings.

===clear cached files===

On JRE of version 1.6.0_15 and 1.6.0_16, previously cached JOGL files cause a problem
even if newer files are placed on the server.
JRE of version 1.6.0_17 or later is recommended.
On Mac OS X Snow Leopard, however, the latest JRE is of version 1.6.0_15 at the moment.
The following steps show how to clear cached files.

;1) Open the Java Preferences window
:Double-click the [Java Preferences] icon, then the Java Preferences window appears. The place of [Java Preferences] depends on the version of Mac OS as following:
:{|style="border:1px solid gray;border-collapse:collapse"
!style="border:1px solid gray;padding:0 0.5em;background-color:lightyellow"|Max OS X version
!style="border:1px solid gray;padding:0 0.5em;background-color:lightyellow"|place
|-
|style="border:1px solid gray;padding:0 0.5em"|10.4
|style="border:1px solid gray;padding:0 0.5em"|[Applications]-[Utilities]-[Java]-[J2SE 5.0]
|-
|style="border:1px solid gray;padding:0 0.5em"|10.5 (before installing Java for Mac OS X 10.5 Update 4)
|style="border:1px solid gray;padding:0 0.5em"|[Applications]-[Utilities]-[Java]
|-
|style="border:1px solid gray;padding:0 0.5em"|10.5 (after installing Java for Mac OS X 10.5 Update 4 or later)
|style="border:1px solid gray;padding:0 0.5em"|[Applications]-[Utilities]
|-
|style="border:1px solid gray;padding:0 0.5em"|10.6
|style="border:1px solid gray;padding:0 0.5em"|[Applications]-[Utilities]
|}
:The contents of the [Java Preferences] differ for the version of Mac OS. In case 10.4, use the [General] tab, which is default displayed. In case 10.5 or later, click to display [Network] tab.
:{|style="border:1px solid gray;border-collapse:collapse"
!style="border:1px solid gray;padding:0 0.5em;background-color:lightyellow"|Max OS X 10.4
!style="border:1px solid gray;padding:0 0.5em;background-color:lightyellow"|Max OS X 10.5 or later
|-
|style="border:1px solid gray;padding:0.5ex 0.5em;text-align:center;vertical-align:top"|[[File:Javapref_tiger.png|400px]]
|style="border:1px solid gray;padding:0.5ex 0.5em;text-align:center;vertical-align:top"|[[File:Java_prefs1.png|400px]]&lt;br/&gt;&amp;darr;&lt;br/&gt;[[File:Java_prefs2.png|400px]]
|}

;2) Press 'Delete Files...' button
:The [Delete Temporary Files] window, which asks which items are to remove, will be opened.

:[[File:Javacache_del_en.png]]

;3) Leave all the checkboxs on and click 'OK' button.

;4) In some case, restoring the Java environment to the default may be also required. 
:To do it, click "Restore Defaults" button in the Java Preferences (the following figure is the case of Mac OS X 10.6).
:[[File:Javapref_general_10_6.png]]

===remove local JOGL library===

Locally-installed JOGL libraries of different version cause conflicts with Java Web Start technology.
JOGL library files are different between operating systems.

'''Mac OS X'''

Open the [Macintosh HD]-[Library]-[Java]-[Extensions] folder.
If some of the following files

* jogl.jar
* gluegen-rt.jar
* libjogl.jnilib
* libjogl_awt.jnilib
* libjogl_cg.jnilib
* libgluegen-rt.jnilib

exist in the folder, remove them.
Here, this operation requires root privilege.

'''Windows'''

Files that should be removed are as follows.

* &lt;JRE&gt;\lib\ext\jogl.jar
* &lt;JRE&gt;\lib\ext\gluegen-rt.jar
* &lt;JRE&gt;\bin\jogl.dll
* &lt;JRE&gt;\bin\jogl_cg.dll
* &lt;JRE&gt;\bin\jogl_awt.dll
* &lt;JRE&gt;\bin\gluegen-rt.dll

Here, &lt;JRE&gt; denotes the folder that JRE has been installed; typically &lt;JRE&gt;=C:\Program Files\Java\jre6.

'''Linux'''

Files that should be removed are as follows.

* &lt;JRE&gt;/lib/ext/jogl.jar
* &lt;JRE&gt;/lib/ext/gluegen-rt.jar
* &lt;JRE&gt;/lib/&lt;arch&gt;/libjogl.so
* &lt;JRE&gt;/lib/&lt;arch&gt;/libjogl_cg.so
* &lt;JRE&gt;/lib/&lt;arch&gt;/libjogl_awt.so
* &lt;JRE&gt;/lib/&lt;arch&gt;/libjogl_drihack.so
* &lt;JRE&gt;/lib/&lt;arch&gt;/libgluegen-rt.so

Here, &lt;JRE&gt; denotes the directory that JRE has been installed; typically &lt;JRE&gt;=/usr/java/jdk1.6.0_17/jre,
and &lt;arch&gt; the processor architecture such as &lt;arch&gt;=i386.

== jV applet with Internet Explorer ==

When visiting a web page that contains a jV applet with Internet Explorer, there sometimes occurs trouble in working with native JOGL libraries especially on Windows Vista. Please use Firefox web browser in that case.

== Class not found error on applet ==

When you use JRE6 Update21 (1.6.0_21) with the next-generation Java Plug-in enabled on Windows or Linux, 
the following error occurs for the combination of jV applet and applet-launcher.

 Error: Class not found: org.pdbj.viewer.gui.ViewerApplet

You can avoid this problem by disabling the next-generation Java Plug-in.
[http://www.java.com/en/download/help/new_plugin.xml Here] is how to do that for Windows users.
On Linux platform, users can manually replace the symbolic link to new plug-in &lt;tt&gt;libnpjp2.so&lt;/tt&gt;
with the symbolic link to classic plug-in &lt;tt&gt;libjavaplugin_oji.so&lt;/tt&gt;
(see [http://www.oracle.com/technetwork/java/javase/manual-plugin-install-linux-136395.html this page] for help).
If you are using firefox 3.6 or later, however, you need to downgrade JRE to 1.6.0_20
because firefox of those versions run applets only with the new Java Plug-in.
To get JRE 1.6.0_20, see [https://cds.sun.com/is-bin/INTERSHOP.enfinity/WFS/CDS-CDS_Developer-Site/en_US/-/USD/ViewProductDetail-Start?ProductRef=jre-6u20-oth-JPR@CDS-CDS_Developer this page].


== The jV applet can't be displayed on Mac + Firefox/Safari ==
The Mac OS and browser described below can't display jV applets.
To display them, please downgrade the browser or use another browser such as Opera, Camino, Shiira.
We are sorry for the inconvenient.
;OS
:Mac OS X 10.5 update 4 or later
;Browser
* Firefox 6.0 or later
* Safari 5.1 or later
;Reason
:You can specify which Java Plug-in is to use at the Java Preferences. If you select 'In their own process' to use new Java Plug-in, and select 'Within the browser process' to use classic Java Plug-in. But none the less, Firefox 6.0 or later and Safari 5.1 or later forces to use new Java Plug-in. Currently the new Java Plug-in for Mac doesn't support hardware-accelerated technologies like JOGL and Java3D[http://developer.apple.com/library/mac/#releasenotes/CrossPlatform/JavaSnowLeopardUpdate2LeopardUpdate7RN/NewandNoteworthy/NewandNoteworthy.html#//apple_ref/doc/uid/TP40009967-CH4-SW1], so the jV applet under these environment can't be displayed.

* The Windows and Linux users don't affect this problem.
* The Firefox 5.0 or older can display jV applets even if on Mac OS.
* The Safari 5.0 or older can display jV applets even if on Mac OS.</text>
    <sha1>b528f7dfe9bdba8efc91d475ec49820006a03ebb</sha1>
  </revision>
  <revision>
    <id>475</id>
    <parentid>474</parentid>
    <timestamp>2011-09-05T07:14:30Z</timestamp>
    <contributor>
      <username>Cudo29</username>
      <id>5</id>
    </contributor>
    <comment>/* The jV applet can't be displayed on Mac + Firefox/Safari */ Google Chrome was added.</comment>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="7018" xml:space="preserve">{| style="left"
 |__TOC__
 |}

== Certificate error on applet ==

When you use JRE6 Update15 (1.6.0_15) or JRE6 Update16 (1.6.0_16) on Windows or Linux,
jV applet and applet-launcher fail to start up with the following error.

 Error:java.io.IOException:Cannot find certificates for JNLP AppletLauncher class

Please use JRE6 Update17 (1.6.0_17) or later.

== JOGL library conflict ==

If you cannot start jV via Java Web Start or view jV applets due to a failure of locating the JOGL library, try the followings.

===clear cached files===

On JRE of version 1.6.0_15 and 1.6.0_16, previously cached JOGL files cause a problem
even if newer files are placed on the server.
JRE of version 1.6.0_17 or later is recommended.
On Mac OS X Snow Leopard, however, the latest JRE is of version 1.6.0_15 at the moment.
The following steps show how to clear cached files.

;1) Open the Java Preferences window
:Double-click the [Java Preferences] icon, then the Java Preferences window appears. The place of [Java Preferences] depends on the version of Mac OS as following:
:{|style="border:1px solid gray;border-collapse:collapse"
!style="border:1px solid gray;padding:0 0.5em;background-color:lightyellow"|Max OS X version
!style="border:1px solid gray;padding:0 0.5em;background-color:lightyellow"|place
|-
|style="border:1px solid gray;padding:0 0.5em"|10.4
|style="border:1px solid gray;padding:0 0.5em"|[Applications]-[Utilities]-[Java]-[J2SE 5.0]
|-
|style="border:1px solid gray;padding:0 0.5em"|10.5 (before installing Java for Mac OS X 10.5 Update 4)
|style="border:1px solid gray;padding:0 0.5em"|[Applications]-[Utilities]-[Java]
|-
|style="border:1px solid gray;padding:0 0.5em"|10.5 (after installing Java for Mac OS X 10.5 Update 4 or later)
|style="border:1px solid gray;padding:0 0.5em"|[Applications]-[Utilities]
|-
|style="border:1px solid gray;padding:0 0.5em"|10.6
|style="border:1px solid gray;padding:0 0.5em"|[Applications]-[Utilities]
|}
:The contents of the [Java Preferences] differ for the version of Mac OS. In case 10.4, use the [General] tab, which is default displayed. In case 10.5 or later, click to display [Network] tab.
:{|style="border:1px solid gray;border-collapse:collapse"
!style="border:1px solid gray;padding:0 0.5em;background-color:lightyellow"|Max OS X 10.4
!style="border:1px solid gray;padding:0 0.5em;background-color:lightyellow"|Max OS X 10.5 or later
|-
|style="border:1px solid gray;padding:0.5ex 0.5em;text-align:center;vertical-align:top"|[[File:Javapref_tiger.png|400px]]
|style="border:1px solid gray;padding:0.5ex 0.5em;text-align:center;vertical-align:top"|[[File:Java_prefs1.png|400px]]&lt;br/&gt;&amp;darr;&lt;br/&gt;[[File:Java_prefs2.png|400px]]
|}

;2) Press 'Delete Files...' button
:The [Delete Temporary Files] window, which asks which items are to remove, will be opened.

:[[File:Javacache_del_en.png]]

;3) Leave all the checkboxs on and click 'OK' button.

;4) In some case, restoring the Java environment to the default may be also required. 
:To do it, click "Restore Defaults" button in the Java Preferences (the following figure is the case of Mac OS X 10.6).
:[[File:Javapref_general_10_6.png]]

===remove local JOGL library===

Locally-installed JOGL libraries of different version cause conflicts with Java Web Start technology.
JOGL library files are different between operating systems.

'''Mac OS X'''

Open the [Macintosh HD]-[Library]-[Java]-[Extensions] folder.
If some of the following files

* jogl.jar
* gluegen-rt.jar
* libjogl.jnilib
* libjogl_awt.jnilib
* libjogl_cg.jnilib
* libgluegen-rt.jnilib

exist in the folder, remove them.
Here, this operation requires root privilege.

'''Windows'''

Files that should be removed are as follows.

* &lt;JRE&gt;\lib\ext\jogl.jar
* &lt;JRE&gt;\lib\ext\gluegen-rt.jar
* &lt;JRE&gt;\bin\jogl.dll
* &lt;JRE&gt;\bin\jogl_cg.dll
* &lt;JRE&gt;\bin\jogl_awt.dll
* &lt;JRE&gt;\bin\gluegen-rt.dll

Here, &lt;JRE&gt; denotes the folder that JRE has been installed; typically &lt;JRE&gt;=C:\Program Files\Java\jre6.

'''Linux'''

Files that should be removed are as follows.

* &lt;JRE&gt;/lib/ext/jogl.jar
* &lt;JRE&gt;/lib/ext/gluegen-rt.jar
* &lt;JRE&gt;/lib/&lt;arch&gt;/libjogl.so
* &lt;JRE&gt;/lib/&lt;arch&gt;/libjogl_cg.so
* &lt;JRE&gt;/lib/&lt;arch&gt;/libjogl_awt.so
* &lt;JRE&gt;/lib/&lt;arch&gt;/libjogl_drihack.so
* &lt;JRE&gt;/lib/&lt;arch&gt;/libgluegen-rt.so

Here, &lt;JRE&gt; denotes the directory that JRE has been installed; typically &lt;JRE&gt;=/usr/java/jdk1.6.0_17/jre,
and &lt;arch&gt; the processor architecture such as &lt;arch&gt;=i386.

== jV applet with Internet Explorer ==

When visiting a web page that contains a jV applet with Internet Explorer, there sometimes occurs trouble in working with native JOGL libraries especially on Windows Vista. Please use Firefox web browser in that case.

== Class not found error on applet ==

When you use JRE6 Update21 (1.6.0_21) with the next-generation Java Plug-in enabled on Windows or Linux, 
the following error occurs for the combination of jV applet and applet-launcher.

 Error: Class not found: org.pdbj.viewer.gui.ViewerApplet

You can avoid this problem by disabling the next-generation Java Plug-in.
[http://www.java.com/en/download/help/new_plugin.xml Here] is how to do that for Windows users.
On Linux platform, users can manually replace the symbolic link to new plug-in &lt;tt&gt;libnpjp2.so&lt;/tt&gt;
with the symbolic link to classic plug-in &lt;tt&gt;libjavaplugin_oji.so&lt;/tt&gt;
(see [http://www.oracle.com/technetwork/java/javase/manual-plugin-install-linux-136395.html this page] for help).
If you are using firefox 3.6 or later, however, you need to downgrade JRE to 1.6.0_20
because firefox of those versions run applets only with the new Java Plug-in.
To get JRE 1.6.0_20, see [https://cds.sun.com/is-bin/INTERSHOP.enfinity/WFS/CDS-CDS_Developer-Site/en_US/-/USD/ViewProductDetail-Start?ProductRef=jre-6u20-oth-JPR@CDS-CDS_Developer this page].


== The jV applet can't be displayed on Mac + Firefox/Safari/Google Chrome ==
The Mac OS and browser described below can't display jV applets.
To display them, please downgrade the browser or use another browser such as Opera, Camino, Shiira.
We are sorry for the inconvenient.
;OS
:Mac OS X 10.5 update 4 or later
;Browser
* Firefox 6.0 or later
* Safari 5.1 or later
* Google Chrome
;Reason
:You can specify which Java Plug-in is to use at the Java Preferences. If you select 'In their own process' to use new Java Plug-in, and select 'Within the browser process' to use classic Java Plug-in. But none the less, Firefox 6.0 or later and Safari 5.1 or later forces to use new Java Plug-in. Currently the new Java Plug-in for Mac doesn't support hardware-accelerated technologies like JOGL and Java3D[http://developer.apple.com/library/mac/#releasenotes/CrossPlatform/JavaSnowLeopardUpdate2LeopardUpdate7RN/NewandNoteworthy/NewandNoteworthy.html#//apple_ref/doc/uid/TP40009967-CH4-SW1], so the jV applet under these environment can't be displayed.

* The Windows and Linux users don't affect this problem.
* The Firefox 5.0 or older can display jV applets even if on Mac OS.
* The Safari 5.0 or older can display jV applets even if on Mac OS.</text>
    <sha1>96bc808661e9075ba4f53f6b50d4594c19092db7</sha1>
  </revision>
  <revision>
    <id>476</id>
    <parentid>475</parentid>
    <timestamp>2011-09-05T07:15:38Z</timestamp>
    <contributor>
      <username>Cudo29</username>
      <id>5</id>
    </contributor>
    <minor/>
    <comment>/* The jV applet can't be displayed on Mac + Firefox/Safari/Google Chrome */ Edited.</comment>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="7032" xml:space="preserve">{| style="left"
 |__TOC__
 |}

== Certificate error on applet ==

When you use JRE6 Update15 (1.6.0_15) or JRE6 Update16 (1.6.0_16) on Windows or Linux,
jV applet and applet-launcher fail to start up with the following error.

 Error:java.io.IOException:Cannot find certificates for JNLP AppletLauncher class

Please use JRE6 Update17 (1.6.0_17) or later.

== JOGL library conflict ==

If you cannot start jV via Java Web Start or view jV applets due to a failure of locating the JOGL library, try the followings.

===clear cached files===

On JRE of version 1.6.0_15 and 1.6.0_16, previously cached JOGL files cause a problem
even if newer files are placed on the server.
JRE of version 1.6.0_17 or later is recommended.
On Mac OS X Snow Leopard, however, the latest JRE is of version 1.6.0_15 at the moment.
The following steps show how to clear cached files.

;1) Open the Java Preferences window
:Double-click the [Java Preferences] icon, then the Java Preferences window appears. The place of [Java Preferences] depends on the version of Mac OS as following:
:{|style="border:1px solid gray;border-collapse:collapse"
!style="border:1px solid gray;padding:0 0.5em;background-color:lightyellow"|Max OS X version
!style="border:1px solid gray;padding:0 0.5em;background-color:lightyellow"|place
|-
|style="border:1px solid gray;padding:0 0.5em"|10.4
|style="border:1px solid gray;padding:0 0.5em"|[Applications]-[Utilities]-[Java]-[J2SE 5.0]
|-
|style="border:1px solid gray;padding:0 0.5em"|10.5 (before installing Java for Mac OS X 10.5 Update 4)
|style="border:1px solid gray;padding:0 0.5em"|[Applications]-[Utilities]-[Java]
|-
|style="border:1px solid gray;padding:0 0.5em"|10.5 (after installing Java for Mac OS X 10.5 Update 4 or later)
|style="border:1px solid gray;padding:0 0.5em"|[Applications]-[Utilities]
|-
|style="border:1px solid gray;padding:0 0.5em"|10.6
|style="border:1px solid gray;padding:0 0.5em"|[Applications]-[Utilities]
|}
:The contents of the [Java Preferences] differ for the version of Mac OS. In case 10.4, use the [General] tab, which is default displayed. In case 10.5 or later, click to display [Network] tab.
:{|style="border:1px solid gray;border-collapse:collapse"
!style="border:1px solid gray;padding:0 0.5em;background-color:lightyellow"|Max OS X 10.4
!style="border:1px solid gray;padding:0 0.5em;background-color:lightyellow"|Max OS X 10.5 or later
|-
|style="border:1px solid gray;padding:0.5ex 0.5em;text-align:center;vertical-align:top"|[[File:Javapref_tiger.png|400px]]
|style="border:1px solid gray;padding:0.5ex 0.5em;text-align:center;vertical-align:top"|[[File:Java_prefs1.png|400px]]&lt;br/&gt;&amp;darr;&lt;br/&gt;[[File:Java_prefs2.png|400px]]
|}

;2) Press 'Delete Files...' button
:The [Delete Temporary Files] window, which asks which items are to remove, will be opened.

:[[File:Javacache_del_en.png]]

;3) Leave all the checkboxs on and click 'OK' button.

;4) In some case, restoring the Java environment to the default may be also required. 
:To do it, click "Restore Defaults" button in the Java Preferences (the following figure is the case of Mac OS X 10.6).
:[[File:Javapref_general_10_6.png]]

===remove local JOGL library===

Locally-installed JOGL libraries of different version cause conflicts with Java Web Start technology.
JOGL library files are different between operating systems.

'''Mac OS X'''

Open the [Macintosh HD]-[Library]-[Java]-[Extensions] folder.
If some of the following files

* jogl.jar
* gluegen-rt.jar
* libjogl.jnilib
* libjogl_awt.jnilib
* libjogl_cg.jnilib
* libgluegen-rt.jnilib

exist in the folder, remove them.
Here, this operation requires root privilege.

'''Windows'''

Files that should be removed are as follows.

* &lt;JRE&gt;\lib\ext\jogl.jar
* &lt;JRE&gt;\lib\ext\gluegen-rt.jar
* &lt;JRE&gt;\bin\jogl.dll
* &lt;JRE&gt;\bin\jogl_cg.dll
* &lt;JRE&gt;\bin\jogl_awt.dll
* &lt;JRE&gt;\bin\gluegen-rt.dll

Here, &lt;JRE&gt; denotes the folder that JRE has been installed; typically &lt;JRE&gt;=C:\Program Files\Java\jre6.

'''Linux'''

Files that should be removed are as follows.

* &lt;JRE&gt;/lib/ext/jogl.jar
* &lt;JRE&gt;/lib/ext/gluegen-rt.jar
* &lt;JRE&gt;/lib/&lt;arch&gt;/libjogl.so
* &lt;JRE&gt;/lib/&lt;arch&gt;/libjogl_cg.so
* &lt;JRE&gt;/lib/&lt;arch&gt;/libjogl_awt.so
* &lt;JRE&gt;/lib/&lt;arch&gt;/libjogl_drihack.so
* &lt;JRE&gt;/lib/&lt;arch&gt;/libgluegen-rt.so

Here, &lt;JRE&gt; denotes the directory that JRE has been installed; typically &lt;JRE&gt;=/usr/java/jdk1.6.0_17/jre,
and &lt;arch&gt; the processor architecture such as &lt;arch&gt;=i386.

== jV applet with Internet Explorer ==

When visiting a web page that contains a jV applet with Internet Explorer, there sometimes occurs trouble in working with native JOGL libraries especially on Windows Vista. Please use Firefox web browser in that case.

== Class not found error on applet ==

When you use JRE6 Update21 (1.6.0_21) with the next-generation Java Plug-in enabled on Windows or Linux, 
the following error occurs for the combination of jV applet and applet-launcher.

 Error: Class not found: org.pdbj.viewer.gui.ViewerApplet

You can avoid this problem by disabling the next-generation Java Plug-in.
[http://www.java.com/en/download/help/new_plugin.xml Here] is how to do that for Windows users.
On Linux platform, users can manually replace the symbolic link to new plug-in &lt;tt&gt;libnpjp2.so&lt;/tt&gt;
with the symbolic link to classic plug-in &lt;tt&gt;libjavaplugin_oji.so&lt;/tt&gt;
(see [http://www.oracle.com/technetwork/java/javase/manual-plugin-install-linux-136395.html this page] for help).
If you are using firefox 3.6 or later, however, you need to downgrade JRE to 1.6.0_20
because firefox of those versions run applets only with the new Java Plug-in.
To get JRE 1.6.0_20, see [https://cds.sun.com/is-bin/INTERSHOP.enfinity/WFS/CDS-CDS_Developer-Site/en_US/-/USD/ViewProductDetail-Start?ProductRef=jre-6u20-oth-JPR@CDS-CDS_Developer this page].


== The jV applet can't be displayed on Mac + Firefox/Safari/Google Chrome ==
The Mac OS and browser described below can't display jV applets.
To display them, please downgrade the browser or use another browser such as Opera, Camino, Shiira.
We are sorry for the inconvenient.
;OS
:Mac OS X 10.5 update 4 or later
;Browser
* Firefox 6.0 or later
* Safari 5.1 or later
* Google Chrome
;Reason
:You can specify which Java Plug-in is to use at the Java Preferences. If you select 'In their own process' to use new Java Plug-in, and select 'Within the browser process' to use classic Java Plug-in. But none the less, Firefox 6.0 or later, Safari 5.1 or later and Google Chrome force to use new Java Plug-in. Currently the new Java Plug-in for Mac doesn't support hardware-accelerated technologies like JOGL and Java3D[http://developer.apple.com/library/mac/#releasenotes/CrossPlatform/JavaSnowLeopardUpdate2LeopardUpdate7RN/NewandNoteworthy/NewandNoteworthy.html#//apple_ref/doc/uid/TP40009967-CH4-SW1], so the jV applet under these environment can't be displayed.

* The Windows and Linux users don't affect this problem.
* The Firefox 5.0 or older can display jV applets even if on Mac OS.
* The Safari 5.0 or older can display jV applets even if on Mac OS.</text>
    <sha1>a08674b6d80fdfc70cddf4ae76f2aa2794890509</sha1>
  </revision>
  <revision>
    <id>477</id>
    <parentid>476</parentid>
    <timestamp>2011-11-22T06:02:35Z</timestamp>
    <contributor>
      <username>Cudo29</username>
      <id>5</id>
    </contributor>
    <comment>/* The jV applet can't be displayed on Mac + Firefox/Safari/Google Chrome */ URLs were added.</comment>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="7128" xml:space="preserve">{| style="left"
 |__TOC__
 |}

== Certificate error on applet ==

When you use JRE6 Update15 (1.6.0_15) or JRE6 Update16 (1.6.0_16) on Windows or Linux,
jV applet and applet-launcher fail to start up with the following error.

 Error:java.io.IOException:Cannot find certificates for JNLP AppletLauncher class

Please use JRE6 Update17 (1.6.0_17) or later.

== JOGL library conflict ==

If you cannot start jV via Java Web Start or view jV applets due to a failure of locating the JOGL library, try the followings.

===clear cached files===

On JRE of version 1.6.0_15 and 1.6.0_16, previously cached JOGL files cause a problem
even if newer files are placed on the server.
JRE of version 1.6.0_17 or later is recommended.
On Mac OS X Snow Leopard, however, the latest JRE is of version 1.6.0_15 at the moment.
The following steps show how to clear cached files.

;1) Open the Java Preferences window
:Double-click the [Java Preferences] icon, then the Java Preferences window appears. The place of [Java Preferences] depends on the version of Mac OS as following:
:{|style="border:1px solid gray;border-collapse:collapse"
!style="border:1px solid gray;padding:0 0.5em;background-color:lightyellow"|Max OS X version
!style="border:1px solid gray;padding:0 0.5em;background-color:lightyellow"|place
|-
|style="border:1px solid gray;padding:0 0.5em"|10.4
|style="border:1px solid gray;padding:0 0.5em"|[Applications]-[Utilities]-[Java]-[J2SE 5.0]
|-
|style="border:1px solid gray;padding:0 0.5em"|10.5 (before installing Java for Mac OS X 10.5 Update 4)
|style="border:1px solid gray;padding:0 0.5em"|[Applications]-[Utilities]-[Java]
|-
|style="border:1px solid gray;padding:0 0.5em"|10.5 (after installing Java for Mac OS X 10.5 Update 4 or later)
|style="border:1px solid gray;padding:0 0.5em"|[Applications]-[Utilities]
|-
|style="border:1px solid gray;padding:0 0.5em"|10.6
|style="border:1px solid gray;padding:0 0.5em"|[Applications]-[Utilities]
|}
:The contents of the [Java Preferences] differ for the version of Mac OS. In case 10.4, use the [General] tab, which is default displayed. In case 10.5 or later, click to display [Network] tab.
:{|style="border:1px solid gray;border-collapse:collapse"
!style="border:1px solid gray;padding:0 0.5em;background-color:lightyellow"|Max OS X 10.4
!style="border:1px solid gray;padding:0 0.5em;background-color:lightyellow"|Max OS X 10.5 or later
|-
|style="border:1px solid gray;padding:0.5ex 0.5em;text-align:center;vertical-align:top"|[[File:Javapref_tiger.png|400px]]
|style="border:1px solid gray;padding:0.5ex 0.5em;text-align:center;vertical-align:top"|[[File:Java_prefs1.png|400px]]&lt;br/&gt;&amp;darr;&lt;br/&gt;[[File:Java_prefs2.png|400px]]
|}

;2) Press 'Delete Files...' button
:The [Delete Temporary Files] window, which asks which items are to remove, will be opened.

:[[File:Javacache_del_en.png]]

;3) Leave all the checkboxs on and click 'OK' button.

;4) In some case, restoring the Java environment to the default may be also required. 
:To do it, click "Restore Defaults" button in the Java Preferences (the following figure is the case of Mac OS X 10.6).
:[[File:Javapref_general_10_6.png]]

===remove local JOGL library===

Locally-installed JOGL libraries of different version cause conflicts with Java Web Start technology.
JOGL library files are different between operating systems.

'''Mac OS X'''

Open the [Macintosh HD]-[Library]-[Java]-[Extensions] folder.
If some of the following files

* jogl.jar
* gluegen-rt.jar
* libjogl.jnilib
* libjogl_awt.jnilib
* libjogl_cg.jnilib
* libgluegen-rt.jnilib

exist in the folder, remove them.
Here, this operation requires root privilege.

'''Windows'''

Files that should be removed are as follows.

* &lt;JRE&gt;\lib\ext\jogl.jar
* &lt;JRE&gt;\lib\ext\gluegen-rt.jar
* &lt;JRE&gt;\bin\jogl.dll
* &lt;JRE&gt;\bin\jogl_cg.dll
* &lt;JRE&gt;\bin\jogl_awt.dll
* &lt;JRE&gt;\bin\gluegen-rt.dll

Here, &lt;JRE&gt; denotes the folder that JRE has been installed; typically &lt;JRE&gt;=C:\Program Files\Java\jre6.

'''Linux'''

Files that should be removed are as follows.

* &lt;JRE&gt;/lib/ext/jogl.jar
* &lt;JRE&gt;/lib/ext/gluegen-rt.jar
* &lt;JRE&gt;/lib/&lt;arch&gt;/libjogl.so
* &lt;JRE&gt;/lib/&lt;arch&gt;/libjogl_cg.so
* &lt;JRE&gt;/lib/&lt;arch&gt;/libjogl_awt.so
* &lt;JRE&gt;/lib/&lt;arch&gt;/libjogl_drihack.so
* &lt;JRE&gt;/lib/&lt;arch&gt;/libgluegen-rt.so

Here, &lt;JRE&gt; denotes the directory that JRE has been installed; typically &lt;JRE&gt;=/usr/java/jdk1.6.0_17/jre,
and &lt;arch&gt; the processor architecture such as &lt;arch&gt;=i386.

== jV applet with Internet Explorer ==

When visiting a web page that contains a jV applet with Internet Explorer, there sometimes occurs trouble in working with native JOGL libraries especially on Windows Vista. Please use Firefox web browser in that case.

== Class not found error on applet ==

When you use JRE6 Update21 (1.6.0_21) with the next-generation Java Plug-in enabled on Windows or Linux, 
the following error occurs for the combination of jV applet and applet-launcher.

 Error: Class not found: org.pdbj.viewer.gui.ViewerApplet

You can avoid this problem by disabling the next-generation Java Plug-in.
[http://www.java.com/en/download/help/new_plugin.xml Here] is how to do that for Windows users.
On Linux platform, users can manually replace the symbolic link to new plug-in &lt;tt&gt;libnpjp2.so&lt;/tt&gt;
with the symbolic link to classic plug-in &lt;tt&gt;libjavaplugin_oji.so&lt;/tt&gt;
(see [http://www.oracle.com/technetwork/java/javase/manual-plugin-install-linux-136395.html this page] for help).
If you are using firefox 3.6 or later, however, you need to downgrade JRE to 1.6.0_20
because firefox of those versions run applets only with the new Java Plug-in.
To get JRE 1.6.0_20, see [https://cds.sun.com/is-bin/INTERSHOP.enfinity/WFS/CDS-CDS_Developer-Site/en_US/-/USD/ViewProductDetail-Start?ProductRef=jre-6u20-oth-JPR@CDS-CDS_Developer this page].


== The jV applet can't be displayed on Mac + Firefox/Safari/Google Chrome ==
The Mac OS and browser described below can't display jV applets.
To display them, please downgrade the browser or use another browser such as [http://www.opera.com/ Opera], [http://caminobrowser.org/ Camino], or [http://sourceforge.jp/projects/shiira/ Shiira].
We are sorry for the inconvenient.
;OS
:Mac OS X 10.5 update 4 or later
;Browser
* Firefox 6.0 or later
* Safari 5.1 or later
* Google Chrome
;Reason
:You can specify which Java Plug-in is to use at the Java Preferences. If you select 'In their own process' to use new Java Plug-in, and select 'Within the browser process' to use classic Java Plug-in. But none the less, Firefox 6.0 or later, Safari 5.1 or later and Google Chrome force to use new Java Plug-in. Currently the new Java Plug-in for Mac doesn't support hardware-accelerated technologies like JOGL and Java3D[http://developer.apple.com/library/mac/#releasenotes/CrossPlatform/JavaSnowLeopardUpdate2LeopardUpdate7RN/NewandNoteworthy/NewandNoteworthy.html#//apple_ref/doc/uid/TP40009967-CH4-SW1], so the jV applet under these environment can't be displayed.

* The Windows and Linux users don't affect this problem.
* The Firefox 5.0 or older can display jV applets even if on Mac OS.
* The Safari 5.0 or older can display jV applets even if on Mac OS.</text>
    <sha1>25a1aa3f5c0ad2afaea142d10b6109f49e98fc37</sha1>
  </revision>
  <revision>
    <id>478</id>
    <parentid>477</parentid>
    <timestamp>2011-12-01T08:11:18Z</timestamp>
    <contributor>
      <username>IMSsato</username>
      <id>4</id>
    </contributor>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="7577" xml:space="preserve">{| style="left"
 |__TOC__
 |}

== Certificate error on applet ==

When you use JRE6 Update15 (1.6.0_15) or JRE6 Update16 (1.6.0_16) on Windows or Linux,
jV applet and applet-launcher fail to start up with the following error.

 Error:java.io.IOException:Cannot find certificates for JNLP AppletLauncher class

Please use JRE6 Update17 (1.6.0_17) or later.

== JOGL library conflict ==

If you cannot start jV via Java Web Start or view jV applets due to a failure of locating the JOGL library, try the followings.

===clear cached files===

On JRE of version 1.6.0_15 and 1.6.0_16, previously cached JOGL files cause a problem
even if newer files are placed on the server.
JRE of version 1.6.0_17 or later is recommended.
On Mac OS X Snow Leopard, however, the latest JRE is of version 1.6.0_15 at the moment.
The following steps show how to clear cached files.

;1) Open the Java Preferences window
:Double-click the [Java Preferences] icon, then the Java Preferences window appears. The place of [Java Preferences] depends on the version of Mac OS as following:
:{|style="border:1px solid gray;border-collapse:collapse"
!style="border:1px solid gray;padding:0 0.5em;background-color:lightyellow"|Max OS X version
!style="border:1px solid gray;padding:0 0.5em;background-color:lightyellow"|place
|-
|style="border:1px solid gray;padding:0 0.5em"|10.4
|style="border:1px solid gray;padding:0 0.5em"|[Applications]-[Utilities]-[Java]-[J2SE 5.0]
|-
|style="border:1px solid gray;padding:0 0.5em"|10.5 (before installing Java for Mac OS X 10.5 Update 4)
|style="border:1px solid gray;padding:0 0.5em"|[Applications]-[Utilities]-[Java]
|-
|style="border:1px solid gray;padding:0 0.5em"|10.5 (after installing Java for Mac OS X 10.5 Update 4 or later)
|style="border:1px solid gray;padding:0 0.5em"|[Applications]-[Utilities]
|-
|style="border:1px solid gray;padding:0 0.5em"|10.6
|style="border:1px solid gray;padding:0 0.5em"|[Applications]-[Utilities]
|}
:The contents of the [Java Preferences] differ for the version of Mac OS. In case 10.4, use the [General] tab, which is default displayed. In case 10.5 or later, click to display [Network] tab.
:{|style="border:1px solid gray;border-collapse:collapse"
!style="border:1px solid gray;padding:0 0.5em;background-color:lightyellow"|Max OS X 10.4
!style="border:1px solid gray;padding:0 0.5em;background-color:lightyellow"|Max OS X 10.5 or later
|-
|style="border:1px solid gray;padding:0.5ex 0.5em;text-align:center;vertical-align:top"|[[File:Javapref_tiger.png|400px]]
|style="border:1px solid gray;padding:0.5ex 0.5em;text-align:center;vertical-align:top"|[[File:Java_prefs1.png|400px]]&lt;br/&gt;&amp;darr;&lt;br/&gt;[[File:Java_prefs2.png|400px]]
|}

;2) Press 'Delete Files...' button
:The [Delete Temporary Files] window, which asks which items are to remove, will be opened.

:[[File:Javacache_del_en.png]]

;3) Leave all the checkboxs on and click 'OK' button.

;4) In some case, restoring the Java environment to the default may be also required. 
:To do it, click "Restore Defaults" button in the Java Preferences (the following figure is the case of Mac OS X 10.6).
:[[File:Javapref_general_10_6.png]]

===remove local JOGL library===

Locally-installed JOGL libraries of different version cause conflicts with Java Web Start technology.
JOGL library files are different between operating systems.

'''Mac OS X'''

Open the [Macintosh HD]-[Library]-[Java]-[Extensions] folder.
If some of the following files

* jogl.jar
* gluegen-rt.jar
* libjogl.jnilib
* libjogl_awt.jnilib
* libjogl_cg.jnilib
* libgluegen-rt.jnilib

exist in the folder, remove them.
Here, this operation requires root privilege.

'''Windows'''

Files that should be removed are as follows.

* &lt;JRE&gt;\lib\ext\jogl.jar
* &lt;JRE&gt;\lib\ext\gluegen-rt.jar
* &lt;JRE&gt;\bin\jogl.dll
* &lt;JRE&gt;\bin\jogl_cg.dll
* &lt;JRE&gt;\bin\jogl_awt.dll
* &lt;JRE&gt;\bin\gluegen-rt.dll

Here, &lt;JRE&gt; denotes the folder that JRE has been installed; typically &lt;JRE&gt;=C:\Program Files\Java\jre6.

'''Linux'''

Files that should be removed are as follows.

* &lt;JRE&gt;/lib/ext/jogl.jar
* &lt;JRE&gt;/lib/ext/gluegen-rt.jar
* &lt;JRE&gt;/lib/&lt;arch&gt;/libjogl.so
* &lt;JRE&gt;/lib/&lt;arch&gt;/libjogl_cg.so
* &lt;JRE&gt;/lib/&lt;arch&gt;/libjogl_awt.so
* &lt;JRE&gt;/lib/&lt;arch&gt;/libjogl_drihack.so
* &lt;JRE&gt;/lib/&lt;arch&gt;/libgluegen-rt.so

Here, &lt;JRE&gt; denotes the directory that JRE has been installed; typically &lt;JRE&gt;=/usr/java/jdk1.6.0_17/jre,
and &lt;arch&gt; the processor architecture such as &lt;arch&gt;=i386.

== jV applet with Internet Explorer ==

When visiting a web page that contains a jV applet with Internet Explorer, there sometimes occurs trouble in working with native JOGL libraries especially on Windows Vista. Please use Firefox web browser in that case.

== Class not found error on applet ==

When you use JRE6 Update21 (1.6.0_21) with the next-generation Java Plug-in enabled on Windows or Linux, 
the following error occurs for the combination of jV applet and applet-launcher.

 Error: Class not found: org.pdbj.viewer.gui.ViewerApplet

You can avoid this problem by disabling the next-generation Java Plug-in.
[http://www.java.com/en/download/help/new_plugin.xml Here] is how to do that for Windows users.
On Linux platform, users can manually replace the symbolic link to new plug-in &lt;tt&gt;libnpjp2.so&lt;/tt&gt;
with the symbolic link to classic plug-in &lt;tt&gt;libjavaplugin_oji.so&lt;/tt&gt;
(see [http://www.oracle.com/technetwork/java/javase/manual-plugin-install-linux-136395.html this page] for help).
If you are using firefox 3.6 or later, however, you need to downgrade JRE to 1.6.0_20
because firefox of those versions run applets only with the new Java Plug-in.
To get JRE 1.6.0_20, see [https://cds.sun.com/is-bin/INTERSHOP.enfinity/WFS/CDS-CDS_Developer-Site/en_US/-/USD/ViewProductDetail-Start?ProductRef=jre-6u20-oth-JPR@CDS-CDS_Developer this page].


== The jV applet can't be displayed on Mac + Firefox/Safari/Google Chrome ==
The Mac OS and browser described below can't display jV applets.
To display them, please downgrade the browser or use another browser such as [http://www.opera.com/ Opera], [http://caminobrowser.org/ Camino], or [http://sourceforge.jp/projects/shiira/ Shiira].
We are sorry for the inconvenient.
;OS
:Mac OS X 10.5 update 4 or later
;Browser
* Firefox 6.0 or later
* Safari 5.1 or later
* Google Chrome
;Reason
:You can specify which Java Plug-in is to use at the Java Preferences. If you select 'In their own process' to use new Java Plug-in, and select 'Within the browser process' to use classic Java Plug-in. But none the less, Firefox 6.0 or later, Safari 5.1 or later and Google Chrome force to use new Java Plug-in. Currently the new Java Plug-in for Mac doesn't support hardware-accelerated technologies like JOGL and Java3D[http://developer.apple.com/library/mac/#releasenotes/CrossPlatform/JavaSnowLeopardUpdate2LeopardUpdate7RN/NewandNoteworthy/NewandNoteworthy.html#//apple_ref/doc/uid/TP40009967-CH4-SW1], so the jV applet under these environment can't be displayed.

* The Windows and Linux users don't affect this problem.
* The Firefox 5.0 or older can display jV applets even if on Mac OS.
* The Safari 5.0 or older can display jV applets even if on Mac OS.


== The jV applet can't be displayed on Mac with JRE 1.6.0_29 ==
The Mac OS with JRE6 Update29 (1.6.0_29) cannot display jV applets on any browser at the moment.
In JRE 1.6.0_29, the classic Java Plug-in has been removed and only new Java Plug-in is available. 
However, the current version of JOGL library does not work with the new Java Plug-in.
The issue will be resolved by the next release of JOGL library.
We are sorry for the inconvenience.</text>
    <sha1>6f5879f5b93601f5a973d2472ac12c5a9284111e</sha1>
  </revision>
  <revision>
    <id>492</id>
    <parentid>478</parentid>
    <timestamp>2011-12-22T06:05:29Z</timestamp>
    <contributor>
      <username>IMSsato</username>
      <id>4</id>
    </contributor>
    <comment>/* The jV applet can't be displayed on Mac with JRE 1.6.0_29 */</comment>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="7640" xml:space="preserve">{| style="left"
 |__TOC__
 |}

== Certificate error on applet ==

When you use JRE6 Update15 (1.6.0_15) or JRE6 Update16 (1.6.0_16) on Windows or Linux,
jV applet and applet-launcher fail to start up with the following error.

 Error:java.io.IOException:Cannot find certificates for JNLP AppletLauncher class

Please use JRE6 Update17 (1.6.0_17) or later.

== JOGL library conflict ==

If you cannot start jV via Java Web Start or view jV applets due to a failure of locating the JOGL library, try the followings.

===clear cached files===

On JRE of version 1.6.0_15 and 1.6.0_16, previously cached JOGL files cause a problem
even if newer files are placed on the server.
JRE of version 1.6.0_17 or later is recommended.
On Mac OS X Snow Leopard, however, the latest JRE is of version 1.6.0_15 at the moment.
The following steps show how to clear cached files.

;1) Open the Java Preferences window
:Double-click the [Java Preferences] icon, then the Java Preferences window appears. The place of [Java Preferences] depends on the version of Mac OS as following:
:{|style="border:1px solid gray;border-collapse:collapse"
!style="border:1px solid gray;padding:0 0.5em;background-color:lightyellow"|Max OS X version
!style="border:1px solid gray;padding:0 0.5em;background-color:lightyellow"|place
|-
|style="border:1px solid gray;padding:0 0.5em"|10.4
|style="border:1px solid gray;padding:0 0.5em"|[Applications]-[Utilities]-[Java]-[J2SE 5.0]
|-
|style="border:1px solid gray;padding:0 0.5em"|10.5 (before installing Java for Mac OS X 10.5 Update 4)
|style="border:1px solid gray;padding:0 0.5em"|[Applications]-[Utilities]-[Java]
|-
|style="border:1px solid gray;padding:0 0.5em"|10.5 (after installing Java for Mac OS X 10.5 Update 4 or later)
|style="border:1px solid gray;padding:0 0.5em"|[Applications]-[Utilities]
|-
|style="border:1px solid gray;padding:0 0.5em"|10.6
|style="border:1px solid gray;padding:0 0.5em"|[Applications]-[Utilities]
|}
:The contents of the [Java Preferences] differ for the version of Mac OS. In case 10.4, use the [General] tab, which is default displayed. In case 10.5 or later, click to display [Network] tab.
:{|style="border:1px solid gray;border-collapse:collapse"
!style="border:1px solid gray;padding:0 0.5em;background-color:lightyellow"|Max OS X 10.4
!style="border:1px solid gray;padding:0 0.5em;background-color:lightyellow"|Max OS X 10.5 or later
|-
|style="border:1px solid gray;padding:0.5ex 0.5em;text-align:center;vertical-align:top"|[[File:Javapref_tiger.png|400px]]
|style="border:1px solid gray;padding:0.5ex 0.5em;text-align:center;vertical-align:top"|[[File:Java_prefs1.png|400px]]&lt;br/&gt;&amp;darr;&lt;br/&gt;[[File:Java_prefs2.png|400px]]
|}

;2) Press 'Delete Files...' button
:The [Delete Temporary Files] window, which asks which items are to remove, will be opened.

:[[File:Javacache_del_en.png]]

;3) Leave all the checkboxs on and click 'OK' button.

;4) In some case, restoring the Java environment to the default may be also required. 
:To do it, click "Restore Defaults" button in the Java Preferences (the following figure is the case of Mac OS X 10.6).
:[[File:Javapref_general_10_6.png]]

===remove local JOGL library===

Locally-installed JOGL libraries of different version cause conflicts with Java Web Start technology.
JOGL library files are different between operating systems.

'''Mac OS X'''

Open the [Macintosh HD]-[Library]-[Java]-[Extensions] folder.
If some of the following files

* jogl.jar
* gluegen-rt.jar
* libjogl.jnilib
* libjogl_awt.jnilib
* libjogl_cg.jnilib
* libgluegen-rt.jnilib

exist in the folder, remove them.
Here, this operation requires root privilege.

'''Windows'''

Files that should be removed are as follows.

* &lt;JRE&gt;\lib\ext\jogl.jar
* &lt;JRE&gt;\lib\ext\gluegen-rt.jar
* &lt;JRE&gt;\bin\jogl.dll
* &lt;JRE&gt;\bin\jogl_cg.dll
* &lt;JRE&gt;\bin\jogl_awt.dll
* &lt;JRE&gt;\bin\gluegen-rt.dll

Here, &lt;JRE&gt; denotes the folder that JRE has been installed; typically &lt;JRE&gt;=C:\Program Files\Java\jre6.

'''Linux'''

Files that should be removed are as follows.

* &lt;JRE&gt;/lib/ext/jogl.jar
* &lt;JRE&gt;/lib/ext/gluegen-rt.jar
* &lt;JRE&gt;/lib/&lt;arch&gt;/libjogl.so
* &lt;JRE&gt;/lib/&lt;arch&gt;/libjogl_cg.so
* &lt;JRE&gt;/lib/&lt;arch&gt;/libjogl_awt.so
* &lt;JRE&gt;/lib/&lt;arch&gt;/libjogl_drihack.so
* &lt;JRE&gt;/lib/&lt;arch&gt;/libgluegen-rt.so

Here, &lt;JRE&gt; denotes the directory that JRE has been installed; typically &lt;JRE&gt;=/usr/java/jdk1.6.0_17/jre,
and &lt;arch&gt; the processor architecture such as &lt;arch&gt;=i386.

== jV applet with Internet Explorer ==

When visiting a web page that contains a jV applet with Internet Explorer, there sometimes occurs trouble in working with native JOGL libraries especially on Windows Vista. Please use Firefox web browser in that case.

== Class not found error on applet ==

When you use JRE6 Update21 (1.6.0_21) with the next-generation Java Plug-in enabled on Windows or Linux, 
the following error occurs for the combination of jV applet and applet-launcher.

 Error: Class not found: org.pdbj.viewer.gui.ViewerApplet

You can avoid this problem by disabling the next-generation Java Plug-in.
[http://www.java.com/en/download/help/new_plugin.xml Here] is how to do that for Windows users.
On Linux platform, users can manually replace the symbolic link to new plug-in &lt;tt&gt;libnpjp2.so&lt;/tt&gt;
with the symbolic link to classic plug-in &lt;tt&gt;libjavaplugin_oji.so&lt;/tt&gt;
(see [http://www.oracle.com/technetwork/java/javase/manual-plugin-install-linux-136395.html this page] for help).
If you are using firefox 3.6 or later, however, you need to downgrade JRE to 1.6.0_20
because firefox of those versions run applets only with the new Java Plug-in.
To get JRE 1.6.0_20, see [https://cds.sun.com/is-bin/INTERSHOP.enfinity/WFS/CDS-CDS_Developer-Site/en_US/-/USD/ViewProductDetail-Start?ProductRef=jre-6u20-oth-JPR@CDS-CDS_Developer this page].


== The jV applet can't be displayed on Mac + Firefox/Safari/Google Chrome ==
The Mac OS and browser described below can't display jV applets.
To display them, please downgrade the browser or use another browser such as [http://www.opera.com/ Opera], [http://caminobrowser.org/ Camino], or [http://sourceforge.jp/projects/shiira/ Shiira].
We are sorry for the inconvenient.
;OS
:Mac OS X 10.5 update 4 or later
;Browser
* Firefox 6.0 or later
* Safari 5.1 or later
* Google Chrome
;Reason
:You can specify which Java Plug-in is to use at the Java Preferences. If you select 'In their own process' to use new Java Plug-in, and select 'Within the browser process' to use classic Java Plug-in. But none the less, Firefox 6.0 or later, Safari 5.1 or later and Google Chrome force to use new Java Plug-in. Currently the new Java Plug-in for Mac doesn't support hardware-accelerated technologies like JOGL and Java3D[http://developer.apple.com/library/mac/#releasenotes/CrossPlatform/JavaSnowLeopardUpdate2LeopardUpdate7RN/NewandNoteworthy/NewandNoteworthy.html#//apple_ref/doc/uid/TP40009967-CH4-SW1], so the jV applet under these environment can't be displayed.

* The Windows and Linux users don't affect this problem.
* The Firefox 5.0 or older can display jV applets even if on Mac OS.
* The Safari 5.0 or older can display jV applets even if on Mac OS.


== The jV applet can't be displayed on Mac with JRE 1.6.0_29 ==
The Mac OS with JRE6 Update29 (1.6.0_29) cannot display jV applets on any browser at the moment.
In JRE 1.6.0_29, the classic Java Plug-in has been removed and only new Java Plug-in is available. 
However, the current version of JOGL library does not work with the new Java Plug-in.
The issue will be resolved by the next release of JOGL library.
We are sorry for the inconvenience.

'''Resolved''': jV version 4.1 runs on Mac with JRE 1.6.0_29.</text>
    <sha1>89e9c6d995488148c9505cf7c7fcd42a2100fadb</sha1>
  </revision>
  <revision>
    <id>493</id>
    <parentid>492</parentid>
    <timestamp>2011-12-22T06:06:32Z</timestamp>
    <contributor>
      <username>IMSsato</username>
      <id>4</id>
    </contributor>
    <comment>/* The jV applet can't be displayed on Mac + Firefox/Safari/Google Chrome */</comment>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="7724" xml:space="preserve">{| style="left"
 |__TOC__
 |}

== Certificate error on applet ==

When you use JRE6 Update15 (1.6.0_15) or JRE6 Update16 (1.6.0_16) on Windows or Linux,
jV applet and applet-launcher fail to start up with the following error.

 Error:java.io.IOException:Cannot find certificates for JNLP AppletLauncher class

Please use JRE6 Update17 (1.6.0_17) or later.

== JOGL library conflict ==

If you cannot start jV via Java Web Start or view jV applets due to a failure of locating the JOGL library, try the followings.

===clear cached files===

On JRE of version 1.6.0_15 and 1.6.0_16, previously cached JOGL files cause a problem
even if newer files are placed on the server.
JRE of version 1.6.0_17 or later is recommended.
On Mac OS X Snow Leopard, however, the latest JRE is of version 1.6.0_15 at the moment.
The following steps show how to clear cached files.

;1) Open the Java Preferences window
:Double-click the [Java Preferences] icon, then the Java Preferences window appears. The place of [Java Preferences] depends on the version of Mac OS as following:
:{|style="border:1px solid gray;border-collapse:collapse"
!style="border:1px solid gray;padding:0 0.5em;background-color:lightyellow"|Max OS X version
!style="border:1px solid gray;padding:0 0.5em;background-color:lightyellow"|place
|-
|style="border:1px solid gray;padding:0 0.5em"|10.4
|style="border:1px solid gray;padding:0 0.5em"|[Applications]-[Utilities]-[Java]-[J2SE 5.0]
|-
|style="border:1px solid gray;padding:0 0.5em"|10.5 (before installing Java for Mac OS X 10.5 Update 4)
|style="border:1px solid gray;padding:0 0.5em"|[Applications]-[Utilities]-[Java]
|-
|style="border:1px solid gray;padding:0 0.5em"|10.5 (after installing Java for Mac OS X 10.5 Update 4 or later)
|style="border:1px solid gray;padding:0 0.5em"|[Applications]-[Utilities]
|-
|style="border:1px solid gray;padding:0 0.5em"|10.6
|style="border:1px solid gray;padding:0 0.5em"|[Applications]-[Utilities]
|}
:The contents of the [Java Preferences] differ for the version of Mac OS. In case 10.4, use the [General] tab, which is default displayed. In case 10.5 or later, click to display [Network] tab.
:{|style="border:1px solid gray;border-collapse:collapse"
!style="border:1px solid gray;padding:0 0.5em;background-color:lightyellow"|Max OS X 10.4
!style="border:1px solid gray;padding:0 0.5em;background-color:lightyellow"|Max OS X 10.5 or later
|-
|style="border:1px solid gray;padding:0.5ex 0.5em;text-align:center;vertical-align:top"|[[File:Javapref_tiger.png|400px]]
|style="border:1px solid gray;padding:0.5ex 0.5em;text-align:center;vertical-align:top"|[[File:Java_prefs1.png|400px]]&lt;br/&gt;&amp;darr;&lt;br/&gt;[[File:Java_prefs2.png|400px]]
|}

;2) Press 'Delete Files...' button
:The [Delete Temporary Files] window, which asks which items are to remove, will be opened.

:[[File:Javacache_del_en.png]]

;3) Leave all the checkboxs on and click 'OK' button.

;4) In some case, restoring the Java environment to the default may be also required. 
:To do it, click "Restore Defaults" button in the Java Preferences (the following figure is the case of Mac OS X 10.6).
:[[File:Javapref_general_10_6.png]]

===remove local JOGL library===

Locally-installed JOGL libraries of different version cause conflicts with Java Web Start technology.
JOGL library files are different between operating systems.

'''Mac OS X'''

Open the [Macintosh HD]-[Library]-[Java]-[Extensions] folder.
If some of the following files

* jogl.jar
* gluegen-rt.jar
* libjogl.jnilib
* libjogl_awt.jnilib
* libjogl_cg.jnilib
* libgluegen-rt.jnilib

exist in the folder, remove them.
Here, this operation requires root privilege.

'''Windows'''

Files that should be removed are as follows.

* &lt;JRE&gt;\lib\ext\jogl.jar
* &lt;JRE&gt;\lib\ext\gluegen-rt.jar
* &lt;JRE&gt;\bin\jogl.dll
* &lt;JRE&gt;\bin\jogl_cg.dll
* &lt;JRE&gt;\bin\jogl_awt.dll
* &lt;JRE&gt;\bin\gluegen-rt.dll

Here, &lt;JRE&gt; denotes the folder that JRE has been installed; typically &lt;JRE&gt;=C:\Program Files\Java\jre6.

'''Linux'''

Files that should be removed are as follows.

* &lt;JRE&gt;/lib/ext/jogl.jar
* &lt;JRE&gt;/lib/ext/gluegen-rt.jar
* &lt;JRE&gt;/lib/&lt;arch&gt;/libjogl.so
* &lt;JRE&gt;/lib/&lt;arch&gt;/libjogl_cg.so
* &lt;JRE&gt;/lib/&lt;arch&gt;/libjogl_awt.so
* &lt;JRE&gt;/lib/&lt;arch&gt;/libjogl_drihack.so
* &lt;JRE&gt;/lib/&lt;arch&gt;/libgluegen-rt.so

Here, &lt;JRE&gt; denotes the directory that JRE has been installed; typically &lt;JRE&gt;=/usr/java/jdk1.6.0_17/jre,
and &lt;arch&gt; the processor architecture such as &lt;arch&gt;=i386.

== jV applet with Internet Explorer ==

When visiting a web page that contains a jV applet with Internet Explorer, there sometimes occurs trouble in working with native JOGL libraries especially on Windows Vista. Please use Firefox web browser in that case.

== Class not found error on applet ==

When you use JRE6 Update21 (1.6.0_21) with the next-generation Java Plug-in enabled on Windows or Linux, 
the following error occurs for the combination of jV applet and applet-launcher.

 Error: Class not found: org.pdbj.viewer.gui.ViewerApplet

You can avoid this problem by disabling the next-generation Java Plug-in.
[http://www.java.com/en/download/help/new_plugin.xml Here] is how to do that for Windows users.
On Linux platform, users can manually replace the symbolic link to new plug-in &lt;tt&gt;libnpjp2.so&lt;/tt&gt;
with the symbolic link to classic plug-in &lt;tt&gt;libjavaplugin_oji.so&lt;/tt&gt;
(see [http://www.oracle.com/technetwork/java/javase/manual-plugin-install-linux-136395.html this page] for help).
If you are using firefox 3.6 or later, however, you need to downgrade JRE to 1.6.0_20
because firefox of those versions run applets only with the new Java Plug-in.
To get JRE 1.6.0_20, see [https://cds.sun.com/is-bin/INTERSHOP.enfinity/WFS/CDS-CDS_Developer-Site/en_US/-/USD/ViewProductDetail-Start?ProductRef=jre-6u20-oth-JPR@CDS-CDS_Developer this page].


== The jV applet can't be displayed on Mac + Firefox/Safari/Google Chrome ==
The Mac OS and browser described below can't display jV applets.
To display them, please downgrade the browser or use another browser such as [http://www.opera.com/ Opera], [http://caminobrowser.org/ Camino], or [http://sourceforge.jp/projects/shiira/ Shiira].
We are sorry for the inconvenient.
;OS
:Mac OS X 10.5 update 4 or later
;Browser
* Firefox 6.0 or later
* Safari 5.1 or later
* Google Chrome
;Reason
:You can specify which Java Plug-in is to use at the Java Preferences. If you select 'In their own process' to use new Java Plug-in, and select 'Within the browser process' to use classic Java Plug-in. But none the less, Firefox 6.0 or later, Safari 5.1 or later and Google Chrome force to use new Java Plug-in. Currently the new Java Plug-in for Mac doesn't support hardware-accelerated technologies like JOGL and Java3D[http://developer.apple.com/library/mac/#releasenotes/CrossPlatform/JavaSnowLeopardUpdate2LeopardUpdate7RN/NewandNoteworthy/NewandNoteworthy.html#//apple_ref/doc/uid/TP40009967-CH4-SW1], so the jV applet under these environment can't be displayed.

* The Windows and Linux users don't affect this problem.
* The Firefox 5.0 or older can display jV applets even if on Mac OS.
* The Safari 5.0 or older can display jV applets even if on Mac OS.


'''Resolved''': jV version 4.1 runs on Mac + latest Firefox/Safari/Google Chrome .

== The jV applet can't be displayed on Mac with JRE 1.6.0_29 ==
The Mac OS with JRE6 Update29 (1.6.0_29) cannot display jV applets on any browser at the moment.
In JRE 1.6.0_29, the classic Java Plug-in has been removed and only new Java Plug-in is available. 
However, the current version of JOGL library does not work with the new Java Plug-in.
The issue will be resolved by the next release of JOGL library.
We are sorry for the inconvenience.

'''Resolved''': jV version 4.1 runs on Mac with JRE 1.6.0_29.</text>
    <sha1>597a6d8ccf692b8bc3c4b6ea15c51f7e81478458</sha1>
  </revision>
  <revision>
    <id>494</id>
    <parentid>493</parentid>
    <timestamp>2011-12-22T06:06:42Z</timestamp>
    <contributor>
      <username>IMSsato</username>
      <id>4</id>
    </contributor>
    <comment>/* The jV applet can't be displayed on Mac + Firefox/Safari/Google Chrome */</comment>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="7723" xml:space="preserve">{| style="left"
 |__TOC__
 |}

== Certificate error on applet ==

When you use JRE6 Update15 (1.6.0_15) or JRE6 Update16 (1.6.0_16) on Windows or Linux,
jV applet and applet-launcher fail to start up with the following error.

 Error:java.io.IOException:Cannot find certificates for JNLP AppletLauncher class

Please use JRE6 Update17 (1.6.0_17) or later.

== JOGL library conflict ==

If you cannot start jV via Java Web Start or view jV applets due to a failure of locating the JOGL library, try the followings.

===clear cached files===

On JRE of version 1.6.0_15 and 1.6.0_16, previously cached JOGL files cause a problem
even if newer files are placed on the server.
JRE of version 1.6.0_17 or later is recommended.
On Mac OS X Snow Leopard, however, the latest JRE is of version 1.6.0_15 at the moment.
The following steps show how to clear cached files.

;1) Open the Java Preferences window
:Double-click the [Java Preferences] icon, then the Java Preferences window appears. The place of [Java Preferences] depends on the version of Mac OS as following:
:{|style="border:1px solid gray;border-collapse:collapse"
!style="border:1px solid gray;padding:0 0.5em;background-color:lightyellow"|Max OS X version
!style="border:1px solid gray;padding:0 0.5em;background-color:lightyellow"|place
|-
|style="border:1px solid gray;padding:0 0.5em"|10.4
|style="border:1px solid gray;padding:0 0.5em"|[Applications]-[Utilities]-[Java]-[J2SE 5.0]
|-
|style="border:1px solid gray;padding:0 0.5em"|10.5 (before installing Java for Mac OS X 10.5 Update 4)
|style="border:1px solid gray;padding:0 0.5em"|[Applications]-[Utilities]-[Java]
|-
|style="border:1px solid gray;padding:0 0.5em"|10.5 (after installing Java for Mac OS X 10.5 Update 4 or later)
|style="border:1px solid gray;padding:0 0.5em"|[Applications]-[Utilities]
|-
|style="border:1px solid gray;padding:0 0.5em"|10.6
|style="border:1px solid gray;padding:0 0.5em"|[Applications]-[Utilities]
|}
:The contents of the [Java Preferences] differ for the version of Mac OS. In case 10.4, use the [General] tab, which is default displayed. In case 10.5 or later, click to display [Network] tab.
:{|style="border:1px solid gray;border-collapse:collapse"
!style="border:1px solid gray;padding:0 0.5em;background-color:lightyellow"|Max OS X 10.4
!style="border:1px solid gray;padding:0 0.5em;background-color:lightyellow"|Max OS X 10.5 or later
|-
|style="border:1px solid gray;padding:0.5ex 0.5em;text-align:center;vertical-align:top"|[[File:Javapref_tiger.png|400px]]
|style="border:1px solid gray;padding:0.5ex 0.5em;text-align:center;vertical-align:top"|[[File:Java_prefs1.png|400px]]&lt;br/&gt;&amp;darr;&lt;br/&gt;[[File:Java_prefs2.png|400px]]
|}

;2) Press 'Delete Files...' button
:The [Delete Temporary Files] window, which asks which items are to remove, will be opened.

:[[File:Javacache_del_en.png]]

;3) Leave all the checkboxs on and click 'OK' button.

;4) In some case, restoring the Java environment to the default may be also required. 
:To do it, click "Restore Defaults" button in the Java Preferences (the following figure is the case of Mac OS X 10.6).
:[[File:Javapref_general_10_6.png]]

===remove local JOGL library===

Locally-installed JOGL libraries of different version cause conflicts with Java Web Start technology.
JOGL library files are different between operating systems.

'''Mac OS X'''

Open the [Macintosh HD]-[Library]-[Java]-[Extensions] folder.
If some of the following files

* jogl.jar
* gluegen-rt.jar
* libjogl.jnilib
* libjogl_awt.jnilib
* libjogl_cg.jnilib
* libgluegen-rt.jnilib

exist in the folder, remove them.
Here, this operation requires root privilege.

'''Windows'''

Files that should be removed are as follows.

* &lt;JRE&gt;\lib\ext\jogl.jar
* &lt;JRE&gt;\lib\ext\gluegen-rt.jar
* &lt;JRE&gt;\bin\jogl.dll
* &lt;JRE&gt;\bin\jogl_cg.dll
* &lt;JRE&gt;\bin\jogl_awt.dll
* &lt;JRE&gt;\bin\gluegen-rt.dll

Here, &lt;JRE&gt; denotes the folder that JRE has been installed; typically &lt;JRE&gt;=C:\Program Files\Java\jre6.

'''Linux'''

Files that should be removed are as follows.

* &lt;JRE&gt;/lib/ext/jogl.jar
* &lt;JRE&gt;/lib/ext/gluegen-rt.jar
* &lt;JRE&gt;/lib/&lt;arch&gt;/libjogl.so
* &lt;JRE&gt;/lib/&lt;arch&gt;/libjogl_cg.so
* &lt;JRE&gt;/lib/&lt;arch&gt;/libjogl_awt.so
* &lt;JRE&gt;/lib/&lt;arch&gt;/libjogl_drihack.so
* &lt;JRE&gt;/lib/&lt;arch&gt;/libgluegen-rt.so

Here, &lt;JRE&gt; denotes the directory that JRE has been installed; typically &lt;JRE&gt;=/usr/java/jdk1.6.0_17/jre,
and &lt;arch&gt; the processor architecture such as &lt;arch&gt;=i386.

== jV applet with Internet Explorer ==

When visiting a web page that contains a jV applet with Internet Explorer, there sometimes occurs trouble in working with native JOGL libraries especially on Windows Vista. Please use Firefox web browser in that case.

== Class not found error on applet ==

When you use JRE6 Update21 (1.6.0_21) with the next-generation Java Plug-in enabled on Windows or Linux, 
the following error occurs for the combination of jV applet and applet-launcher.

 Error: Class not found: org.pdbj.viewer.gui.ViewerApplet

You can avoid this problem by disabling the next-generation Java Plug-in.
[http://www.java.com/en/download/help/new_plugin.xml Here] is how to do that for Windows users.
On Linux platform, users can manually replace the symbolic link to new plug-in &lt;tt&gt;libnpjp2.so&lt;/tt&gt;
with the symbolic link to classic plug-in &lt;tt&gt;libjavaplugin_oji.so&lt;/tt&gt;
(see [http://www.oracle.com/technetwork/java/javase/manual-plugin-install-linux-136395.html this page] for help).
If you are using firefox 3.6 or later, however, you need to downgrade JRE to 1.6.0_20
because firefox of those versions run applets only with the new Java Plug-in.
To get JRE 1.6.0_20, see [https://cds.sun.com/is-bin/INTERSHOP.enfinity/WFS/CDS-CDS_Developer-Site/en_US/-/USD/ViewProductDetail-Start?ProductRef=jre-6u20-oth-JPR@CDS-CDS_Developer this page].


== The jV applet can't be displayed on Mac + Firefox/Safari/Google Chrome ==
The Mac OS and browser described below can't display jV applets.
To display them, please downgrade the browser or use another browser such as [http://www.opera.com/ Opera], [http://caminobrowser.org/ Camino], or [http://sourceforge.jp/projects/shiira/ Shiira].
We are sorry for the inconvenient.
;OS
:Mac OS X 10.5 update 4 or later
;Browser
* Firefox 6.0 or later
* Safari 5.1 or later
* Google Chrome
;Reason
:You can specify which Java Plug-in is to use at the Java Preferences. If you select 'In their own process' to use new Java Plug-in, and select 'Within the browser process' to use classic Java Plug-in. But none the less, Firefox 6.0 or later, Safari 5.1 or later and Google Chrome force to use new Java Plug-in. Currently the new Java Plug-in for Mac doesn't support hardware-accelerated technologies like JOGL and Java3D[http://developer.apple.com/library/mac/#releasenotes/CrossPlatform/JavaSnowLeopardUpdate2LeopardUpdate7RN/NewandNoteworthy/NewandNoteworthy.html#//apple_ref/doc/uid/TP40009967-CH4-SW1], so the jV applet under these environment can't be displayed.

* The Windows and Linux users don't affect this problem.
* The Firefox 5.0 or older can display jV applets even if on Mac OS.
* The Safari 5.0 or older can display jV applets even if on Mac OS.

'''Resolved''': jV version 4.1 runs on Mac + latest Firefox/Safari/Google Chrome .

== The jV applet can't be displayed on Mac with JRE 1.6.0_29 ==
The Mac OS with JRE6 Update29 (1.6.0_29) cannot display jV applets on any browser at the moment.
In JRE 1.6.0_29, the classic Java Plug-in has been removed and only new Java Plug-in is available. 
However, the current version of JOGL library does not work with the new Java Plug-in.
The issue will be resolved by the next release of JOGL library.
We are sorry for the inconvenience.

'''Resolved''': jV version 4.1 runs on Mac with JRE 1.6.0_29.</text>
    <sha1>0aafedb08ab34d7ccbd0e9737372b53d26ad0c55</sha1>
  </revision>
</page>
<page arvcontinue="20110106074224|454">
  <title>File:Javacache del en.png</title>
  <ns>6</ns>
  <id>71</id>
  <revision>
    <id>463</id>
    <timestamp>2011-04-14T08:20:06Z</timestamp>
    <contributor>
      <username>Cudo29</username>
      <id>5</id>
    </contributor>
    <comment>The window to inquiring target to delete when java cache file removing on Mac OS X. The English version of File:Javacache_del.png.</comment>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="130" xml:space="preserve">The window to inquiring target to delete when java cache file removing on Mac OS X. The English version of File:Javacache_del.png.</text>
    <sha1>1087255c487773d3b7a54a34422daadddd7cc14d</sha1>
  </revision>
</page>
<page arvcontinue="20110106074224|454">
  <title>File:Javapref general 10 6.png</title>
  <ns>6</ns>
  <id>72</id>
  <revision>
    <id>465</id>
    <timestamp>2011-04-28T02:16:02Z</timestamp>
    <contributor>
      <username>Cudo29</username>
      <id>5</id>
    </contributor>
    <comment>Restore Defaults button of Java Preferences (Mac OS X 10.6).</comment>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="60" xml:space="preserve">Restore Defaults button of Java Preferences (Mac OS X 10.6).</text>
    <sha1>a0d0efe32e11fdf1d7f88cf299a5cf8054ec892c</sha1>
  </revision>
</page>
<page arvcontinue="20110106074224|454">
  <title>Atom Expression</title>
  <ns>0</ns>
  <id>21</id>
  <revision>
    <id>468</id>
    <parentid>428</parentid>
    <timestamp>2011-07-11T07:14:05Z</timestamp>
    <contributor>
      <username>IMSsato</username>
      <id>4</id>
    </contributor>
    <comment>/* primitive expression */</comment>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="12340" xml:space="preserve">{| style="float:right"
 |__TOC__
 |}
In order to specify a group of atoms in a molecule, the following five expressions are available.

The standard boolean connectives 'and', 'or' and 'not', and brackets can be used to construct a complex expression. The boolean connectives may be abbreviated as '&amp;', '|', and '!', respectively. 

== predefined set ==
=== element name ===
Element names, such as carbon or nitrogen, can be used to select atoms. 
=== set based on residue property ===
a) amino acids in protein molecule
&lt;table border="1"&gt;
&lt;tr&gt;
&lt;td&gt;&lt;/td&gt;
&lt;td&gt;ALA&lt;/td&gt;&lt;td&gt;ARG&lt;/td&gt;&lt;td&gt;ASN&lt;/td&gt;&lt;td&gt;ASP&lt;/td&gt;&lt;td&gt;CYS&lt;/td&gt;
&lt;td&gt;GLU&lt;/td&gt;&lt;td&gt;GLN&lt;/td&gt;&lt;td&gt;GLY&lt;/td&gt;&lt;td&gt;HIS&lt;/td&gt;&lt;td&gt;ILE&lt;/td&gt;
&lt;td&gt;LEU&lt;/td&gt;&lt;td&gt;LYS&lt;/td&gt;&lt;td&gt;MET&lt;/td&gt;&lt;td&gt;PHE&lt;/td&gt;&lt;td&gt;PRO&lt;/td&gt;
&lt;td&gt;SER&lt;/td&gt;&lt;td&gt;THR&lt;/td&gt;&lt;td&gt;TRP&lt;/td&gt;&lt;td&gt;TYR&lt;/td&gt;&lt;td&gt;VAL&lt;/td&gt;
&lt;/tr&gt;
&lt;tr&gt;
&lt;td&gt;Acidic&lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;/tr&gt;
&lt;tr&gt;
&lt;td&gt;Acyclic&lt;/td&gt;
&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;
&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;
&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;&lt;/td&gt;&lt;td&gt;&lt;/td&gt;
&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;&lt;/td&gt;&lt;td&gt;&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;
&lt;/tr&gt;
&lt;tr&gt;
&lt;td&gt;Aliphatic&lt;/td&gt;
&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;
&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;
&lt;/tr&gt;
&lt;tr&gt;
&lt;td&gt;Aromatic&lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;/tr&gt;
&lt;tr&gt;
&lt;td&gt;Basic&lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;/tr&gt;
&lt;tr&gt;
&lt;td&gt;Buried&lt;/td&gt;
&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;
&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;
&lt;/tr&gt;
&lt;tr&gt;
&lt;td&gt;Charged&lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;/tr&gt;
&lt;tr&gt;
&lt;td&gt;Cyclic&lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;/tr&gt;
&lt;tr&gt;
&lt;td&gt;Hydrophobic&lt;/td&gt;
&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;
&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;
&lt;/tr&gt;
&lt;tr&gt;
&lt;td&gt;Large&lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;
&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;/tr&gt;
&lt;tr&gt;
&lt;td&gt;Medium&lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;
&lt;/tr&gt;
&lt;tr&gt;
&lt;td&gt;Negative&lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;/tr&gt;
&lt;tr&gt;
&lt;td&gt;Neutral&lt;/td&gt;
&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;
&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;
&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;
&lt;/tr&gt;
&lt;tr&gt;
&lt;td&gt;Polar&lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;
&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;/tr&gt;
&lt;tr&gt;
&lt;td&gt;Positive&lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;/tr&gt;
&lt;tr&gt;
&lt;td&gt;Small&lt;/td&gt;
&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;/tr&gt;
&lt;tr&gt;
&lt;td&gt;Surface&lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;
&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;/tr&gt;
&lt;tr&gt;
&lt;td&gt;Cysteine&lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;/tr&gt;
&lt;tr&gt;
&lt;td&gt;Amino&lt;/td&gt;
&lt;td colspan="20"&gt;above 20 amino acids + other amino acids&lt;/td&gt;
&lt;/tr&gt;
&lt;tr&gt;
&lt;td&gt;Protein&lt;/td&gt;
&lt;td colspan="20"&gt;above 'Amino' set + UNK, ACE + FOR (PDB version 2.3 only)&lt;/td&gt;
&lt;/tr&gt;
&lt;/table&gt;
Here, 'other amino acids' stands for components whose type is one of the followings in [http://remediation.wwpdb.org/ccd.html Chemical Component Dictionary].&lt;br/&gt;
D-PEPTIDE LINKING&lt;br/&gt;
D-PEPTIDE NH3 AMINO TERMINUS&lt;br/&gt;
L-PEPTIDE COOH CARBOXY TERMINUS&lt;br/&gt;
L-PEPTIDE LINKING&lt;br/&gt;
L-PEPTIDE NH3 AMINO TERMINUS&lt;br/&gt;
PEPTIDE LINKING&lt;br/&gt;
PEPTIDE-LIKE&lt;br/&gt;

b1) nucleotides (for PDB version 2.3)
&lt;table border="1"&gt;
&lt;tr&gt;
&lt;td&gt;&lt;/td&gt;
&lt;td&gt;  A&lt;/td&gt;&lt;td&gt;  C&lt;/td&gt;&lt;td&gt;  G&lt;/td&gt;&lt;td&gt;  T&lt;/td&gt;&lt;td&gt;  U&lt;/td&gt;
&lt;td&gt; +U&lt;/td&gt;&lt;td&gt;  I&lt;/td&gt;&lt;td&gt;1MA&lt;/td&gt;&lt;td&gt;5MC&lt;/td&gt;&lt;td&gt;OMC&lt;/td&gt;
&lt;td&gt;1MG&lt;/td&gt;&lt;td&gt;2MG&lt;/td&gt;&lt;td&gt;M2G&lt;/td&gt;&lt;td&gt;7MG&lt;/td&gt;&lt;td&gt;OMG&lt;/td&gt;
&lt;td&gt; YG&lt;/td&gt;&lt;td&gt;H2U&lt;/td&gt;&lt;td&gt;5MU&lt;/td&gt;&lt;td&gt;PSU&lt;/td&gt;
&lt;/tr&gt;
&lt;tr&gt;
&lt;td&gt;AT&lt;/td&gt;
&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;/tr&gt;
&lt;tr&gt;
&lt;td&gt;CG&lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;/tr&gt;
&lt;tr&gt;
&lt;td&gt;Purine&lt;/td&gt;
&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;/tr&gt;
&lt;tr&gt;
&lt;td&gt;Pyrimidine&lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;/tr&gt;
&lt;tr&gt;
&lt;td&gt;DNA&lt;/td&gt;
&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;/tr&gt;
&lt;tr&gt;
&lt;td&gt;RNA&lt;/td&gt;
&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;
&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;
&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;
&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;
&lt;/tr&gt;
&lt;tr&gt;
&lt;td&gt;Nucleic&lt;/td&gt;
&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;
&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;
&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;
&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;
&lt;/tr&gt;
&lt;/table&gt;

b2) nucleotides (for PDB version 3)
&lt;table border="1"&gt;
&lt;tr&gt;
&lt;td&gt;&lt;/td&gt;
&lt;td&gt; DA&lt;/td&gt;&lt;td&gt; DC&lt;/td&gt;&lt;td&gt; DG&lt;/td&gt;&lt;td&gt; DT&lt;/td&gt;
&lt;td&gt;  A&lt;/td&gt;&lt;td&gt;  C&lt;/td&gt;&lt;td&gt;  G&lt;/td&gt;&lt;td&gt;  U&lt;/td&gt;
&lt;td&gt;other DNA&lt;/td&gt;&lt;td&gt;other RNA&lt;/td&gt;
&lt;/tr&gt;
&lt;tr&gt;
&lt;td&gt;AT&lt;/td&gt;
&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;/tr&gt;
&lt;tr&gt;
&lt;td&gt;CG&lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;/tr&gt;
&lt;tr&gt;
&lt;td&gt;Purine&lt;/td&gt;
&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;/tr&gt;
&lt;tr&gt;
&lt;td&gt;Pyrimidine&lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;/tr&gt;
&lt;tr&gt;
&lt;td&gt;DNA&lt;/td&gt;
&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;/tr&gt;
&lt;tr&gt;
&lt;td&gt;RNA&lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;
&lt;/tr&gt;
&lt;tr&gt;
&lt;td&gt;Nucleic&lt;/td&gt;
&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;
&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;
&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;
&lt;/tr&gt;
&lt;/table&gt;
Here, 'other DNA' and 'other RNA' stand for components whose type is 
DNA LINKING and RNA LINKING respectively in [http://remediation.wwpdb.org/ccd.html Chemical Component Dictionary].&lt;br/&gt;

c) others
&lt;table border="1"&gt;
&lt;tr&gt;
&lt;td&gt;&lt;/td&gt;
&lt;td&gt;HOH&lt;/td&gt;&lt;td&gt;DOD&lt;/td&gt;&lt;td&gt;SO4&lt;/td&gt;&lt;td&gt;PO4&lt;/td&gt;
&lt;/tr&gt;
&lt;tr&gt;
&lt;td&gt;Water&lt;/td&gt;
&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;/tr&gt;
&lt;tr&gt;
&lt;td&gt;Ions&lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;
&lt;/tr&gt;
&lt;tr&gt;
&lt;td&gt;Solvent&lt;/td&gt;
&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;
&lt;/tr&gt;
&lt;/table&gt;

=== others ===
&lt;table border="1"&gt;
&lt;tr&gt;
&lt;td&gt;Alpha&lt;/td&gt;
&lt;td&gt;
atoms whose name is CA.
&lt;/td&gt;
&lt;/tr&gt;
&lt;tr&gt;
&lt;td&gt;Hetero&lt;/td&gt;
&lt;td&gt;
atoms written as HETATM in PDB files or atoms in Solvent set.
&lt;/td&gt;
&lt;/tr&gt;
&lt;tr&gt;
&lt;td&gt;Ligand&lt;/td&gt;
&lt;td&gt;
atoms in Hetero set and not in Solvent set.
&lt;/td&gt;
&lt;/tr&gt;
&lt;tr&gt;
&lt;td&gt;Backbone&lt;br&gt;Mainchain&lt;/td&gt;
&lt;td&gt;
atoms in Amino set whose name is N, CA, C or O, or atoms in Nuceic set
whose name is P,O1P,O2P,O5*,C5*,C4*,O4*,C3*,O3*,C2*,O2* or C1*.
&lt;/td&gt;
&lt;/tr&gt;
&lt;tr&gt;
&lt;td&gt;Sidechain&lt;/td&gt;
&lt;td&gt;
atoms in Amino set or Nucleic set and not in Backbone set.
&lt;/td&gt;
&lt;/tr&gt;
&lt;tr&gt;
&lt;td&gt;Bonded&lt;/td&gt;
&lt;td&gt;
atoms that is connected to at least one other atom.
&lt;/td&gt;
&lt;/tr&gt;
&lt;tr&gt;
&lt;td&gt;Selected&lt;/td&gt;
&lt;td&gt;
atoms currently selected.
&lt;/td&gt;
&lt;/tr&gt;
&lt;tr&gt;
&lt;td&gt;Helix&lt;/td&gt;
&lt;td&gt;
atoms in the alpha-helix structure.
&lt;/td&gt;
&lt;/tr&gt;
&lt;tr&gt;
&lt;td&gt;Sheet&lt;/td&gt;
&lt;td&gt;
atoms in the beta-sheet structure.
&lt;/td&gt;
&lt;/tr&gt;
&lt;tr&gt;
&lt;td&gt;Turn&lt;/td&gt;
&lt;td&gt;
atoms in the turn structure.
&lt;/td&gt;
&lt;/tr&gt;
&lt;/table&gt;

== comparison operators ==
Parts of a molecule can be selected using equality, inequality and ordering operators on their properties. Possible operators are =, ==, &lt;&gt;, !=, /=, &lt;, &lt;=, &gt; and &gt;=, and possible property names are as follows.
{| border="1"
 |-
 | AtomNo || atom ID in PDB files.
 |-
 | ElemNo || atomic number.
 |-
 | ResNo || residue ID in PDB files.
 |-
 | Radius || radius of a ball image of atoms.
 |-
 | Temperature || temperature factor of atoms.
 |-
 | Model || model ID in PDB files.
 |-
 | File || File ID.
 |}

== residue range ==
A group of atoms in a molecule can be selected by the residue ID. For example, command 'select 3' selects atoms whose residue ID is 3, and 'select 3-10' selects atoms whose residue ID is larger than or equal to 3 and smaller than or equal to 10. 
Optionally, the chain ID can be specified after residue range with a colon.
For example, command 'select 3:A' selects atoms
whose residue ID is 3 in the A chain.

== within expression ==
A within expression selects atoms that exist within a specified distance from another set of atoms. For example, 'select within(3.0, backbone) selects atoms within a 3.0 Angstrom radius of any atom in a protein or nucleic acid backbone. 

== PDBj expression ==
A PDBj expression selects a group of atoms according to molecule's properties defined in the PDBMLplus file. It takes the following form;
 pdbj:keyword
For example, 'select pdbj:binding'. The keywords available for each molecule are obtained by the 'show pdbj' command.

== primitive expression ==
A primitive expression takes such a form as
 residue name[residue ID][:chain ID][.atom name][;alternate location][/model ID][@file ID]
Here, residue name and atom name are three letter and four letter name, respectively, and terms in square brackets can be omitted. For example, command 'select SER.CA' selects all alpha carbon atoms in serine.
Residue names that contain numeric characters should be enclosed in square brackets such as '[SO4]'.
Expressions are treated in a case-insensitive manner.
However, the chain ID can be specified case-sensitively such as 'a_A' or 'a_a',
where these mean the chains whose auth_asym_id is 'A' or 'a', respectively. 
In the same way, you can use label_asym_id to specify chains case-sensitively such as 'l_A'.
Note that the label_asym_id is available only for PDBML files and not for PDB flat files.</text>
    <sha1>32884eeb718f8851afba2d9e6fd44b99d06f2e5c</sha1>
  </revision>
  <revision>
    <id>469</id>
    <parentid>468</parentid>
    <timestamp>2011-07-11T07:16:01Z</timestamp>
    <contributor>
      <username>IMSsato</username>
      <id>4</id>
    </contributor>
    <comment>/* residue range */</comment>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="12440" xml:space="preserve">{| style="float:right"
 |__TOC__
 |}
In order to specify a group of atoms in a molecule, the following five expressions are available.

The standard boolean connectives 'and', 'or' and 'not', and brackets can be used to construct a complex expression. The boolean connectives may be abbreviated as '&amp;', '|', and '!', respectively. 

== predefined set ==
=== element name ===
Element names, such as carbon or nitrogen, can be used to select atoms. 
=== set based on residue property ===
a) amino acids in protein molecule
&lt;table border="1"&gt;
&lt;tr&gt;
&lt;td&gt;&lt;/td&gt;
&lt;td&gt;ALA&lt;/td&gt;&lt;td&gt;ARG&lt;/td&gt;&lt;td&gt;ASN&lt;/td&gt;&lt;td&gt;ASP&lt;/td&gt;&lt;td&gt;CYS&lt;/td&gt;
&lt;td&gt;GLU&lt;/td&gt;&lt;td&gt;GLN&lt;/td&gt;&lt;td&gt;GLY&lt;/td&gt;&lt;td&gt;HIS&lt;/td&gt;&lt;td&gt;ILE&lt;/td&gt;
&lt;td&gt;LEU&lt;/td&gt;&lt;td&gt;LYS&lt;/td&gt;&lt;td&gt;MET&lt;/td&gt;&lt;td&gt;PHE&lt;/td&gt;&lt;td&gt;PRO&lt;/td&gt;
&lt;td&gt;SER&lt;/td&gt;&lt;td&gt;THR&lt;/td&gt;&lt;td&gt;TRP&lt;/td&gt;&lt;td&gt;TYR&lt;/td&gt;&lt;td&gt;VAL&lt;/td&gt;
&lt;/tr&gt;
&lt;tr&gt;
&lt;td&gt;Acidic&lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;/tr&gt;
&lt;tr&gt;
&lt;td&gt;Acyclic&lt;/td&gt;
&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;
&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;
&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;&lt;/td&gt;&lt;td&gt;&lt;/td&gt;
&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;&lt;/td&gt;&lt;td&gt;&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;
&lt;/tr&gt;
&lt;tr&gt;
&lt;td&gt;Aliphatic&lt;/td&gt;
&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;
&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;
&lt;/tr&gt;
&lt;tr&gt;
&lt;td&gt;Aromatic&lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;/tr&gt;
&lt;tr&gt;
&lt;td&gt;Basic&lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;/tr&gt;
&lt;tr&gt;
&lt;td&gt;Buried&lt;/td&gt;
&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;
&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;
&lt;/tr&gt;
&lt;tr&gt;
&lt;td&gt;Charged&lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;/tr&gt;
&lt;tr&gt;
&lt;td&gt;Cyclic&lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;/tr&gt;
&lt;tr&gt;
&lt;td&gt;Hydrophobic&lt;/td&gt;
&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;
&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;
&lt;/tr&gt;
&lt;tr&gt;
&lt;td&gt;Large&lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;
&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;/tr&gt;
&lt;tr&gt;
&lt;td&gt;Medium&lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;
&lt;/tr&gt;
&lt;tr&gt;
&lt;td&gt;Negative&lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;/tr&gt;
&lt;tr&gt;
&lt;td&gt;Neutral&lt;/td&gt;
&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;
&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;
&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;
&lt;/tr&gt;
&lt;tr&gt;
&lt;td&gt;Polar&lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;
&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;/tr&gt;
&lt;tr&gt;
&lt;td&gt;Positive&lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;/tr&gt;
&lt;tr&gt;
&lt;td&gt;Small&lt;/td&gt;
&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;/tr&gt;
&lt;tr&gt;
&lt;td&gt;Surface&lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;
&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;/tr&gt;
&lt;tr&gt;
&lt;td&gt;Cysteine&lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;/tr&gt;
&lt;tr&gt;
&lt;td&gt;Amino&lt;/td&gt;
&lt;td colspan="20"&gt;above 20 amino acids + other amino acids&lt;/td&gt;
&lt;/tr&gt;
&lt;tr&gt;
&lt;td&gt;Protein&lt;/td&gt;
&lt;td colspan="20"&gt;above 'Amino' set + UNK, ACE + FOR (PDB version 2.3 only)&lt;/td&gt;
&lt;/tr&gt;
&lt;/table&gt;
Here, 'other amino acids' stands for components whose type is one of the followings in [http://remediation.wwpdb.org/ccd.html Chemical Component Dictionary].&lt;br/&gt;
D-PEPTIDE LINKING&lt;br/&gt;
D-PEPTIDE NH3 AMINO TERMINUS&lt;br/&gt;
L-PEPTIDE COOH CARBOXY TERMINUS&lt;br/&gt;
L-PEPTIDE LINKING&lt;br/&gt;
L-PEPTIDE NH3 AMINO TERMINUS&lt;br/&gt;
PEPTIDE LINKING&lt;br/&gt;
PEPTIDE-LIKE&lt;br/&gt;

b1) nucleotides (for PDB version 2.3)
&lt;table border="1"&gt;
&lt;tr&gt;
&lt;td&gt;&lt;/td&gt;
&lt;td&gt;  A&lt;/td&gt;&lt;td&gt;  C&lt;/td&gt;&lt;td&gt;  G&lt;/td&gt;&lt;td&gt;  T&lt;/td&gt;&lt;td&gt;  U&lt;/td&gt;
&lt;td&gt; +U&lt;/td&gt;&lt;td&gt;  I&lt;/td&gt;&lt;td&gt;1MA&lt;/td&gt;&lt;td&gt;5MC&lt;/td&gt;&lt;td&gt;OMC&lt;/td&gt;
&lt;td&gt;1MG&lt;/td&gt;&lt;td&gt;2MG&lt;/td&gt;&lt;td&gt;M2G&lt;/td&gt;&lt;td&gt;7MG&lt;/td&gt;&lt;td&gt;OMG&lt;/td&gt;
&lt;td&gt; YG&lt;/td&gt;&lt;td&gt;H2U&lt;/td&gt;&lt;td&gt;5MU&lt;/td&gt;&lt;td&gt;PSU&lt;/td&gt;
&lt;/tr&gt;
&lt;tr&gt;
&lt;td&gt;AT&lt;/td&gt;
&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;/tr&gt;
&lt;tr&gt;
&lt;td&gt;CG&lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;/tr&gt;
&lt;tr&gt;
&lt;td&gt;Purine&lt;/td&gt;
&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;/tr&gt;
&lt;tr&gt;
&lt;td&gt;Pyrimidine&lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;/tr&gt;
&lt;tr&gt;
&lt;td&gt;DNA&lt;/td&gt;
&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;/tr&gt;
&lt;tr&gt;
&lt;td&gt;RNA&lt;/td&gt;
&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;
&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;
&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;
&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;
&lt;/tr&gt;
&lt;tr&gt;
&lt;td&gt;Nucleic&lt;/td&gt;
&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;
&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;
&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;
&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;
&lt;/tr&gt;
&lt;/table&gt;

b2) nucleotides (for PDB version 3)
&lt;table border="1"&gt;
&lt;tr&gt;
&lt;td&gt;&lt;/td&gt;
&lt;td&gt; DA&lt;/td&gt;&lt;td&gt; DC&lt;/td&gt;&lt;td&gt; DG&lt;/td&gt;&lt;td&gt; DT&lt;/td&gt;
&lt;td&gt;  A&lt;/td&gt;&lt;td&gt;  C&lt;/td&gt;&lt;td&gt;  G&lt;/td&gt;&lt;td&gt;  U&lt;/td&gt;
&lt;td&gt;other DNA&lt;/td&gt;&lt;td&gt;other RNA&lt;/td&gt;
&lt;/tr&gt;
&lt;tr&gt;
&lt;td&gt;AT&lt;/td&gt;
&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;/tr&gt;
&lt;tr&gt;
&lt;td&gt;CG&lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;/tr&gt;
&lt;tr&gt;
&lt;td&gt;Purine&lt;/td&gt;
&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;/tr&gt;
&lt;tr&gt;
&lt;td&gt;Pyrimidine&lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;/tr&gt;
&lt;tr&gt;
&lt;td&gt;DNA&lt;/td&gt;
&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;/tr&gt;
&lt;tr&gt;
&lt;td&gt;RNA&lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;
&lt;/tr&gt;
&lt;tr&gt;
&lt;td&gt;Nucleic&lt;/td&gt;
&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;
&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;
&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;
&lt;/tr&gt;
&lt;/table&gt;
Here, 'other DNA' and 'other RNA' stand for components whose type is 
DNA LINKING and RNA LINKING respectively in [http://remediation.wwpdb.org/ccd.html Chemical Component Dictionary].&lt;br/&gt;

c) others
&lt;table border="1"&gt;
&lt;tr&gt;
&lt;td&gt;&lt;/td&gt;
&lt;td&gt;HOH&lt;/td&gt;&lt;td&gt;DOD&lt;/td&gt;&lt;td&gt;SO4&lt;/td&gt;&lt;td&gt;PO4&lt;/td&gt;
&lt;/tr&gt;
&lt;tr&gt;
&lt;td&gt;Water&lt;/td&gt;
&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;/tr&gt;
&lt;tr&gt;
&lt;td&gt;Ions&lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;
&lt;/tr&gt;
&lt;tr&gt;
&lt;td&gt;Solvent&lt;/td&gt;
&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;
&lt;/tr&gt;
&lt;/table&gt;

=== others ===
&lt;table border="1"&gt;
&lt;tr&gt;
&lt;td&gt;Alpha&lt;/td&gt;
&lt;td&gt;
atoms whose name is CA.
&lt;/td&gt;
&lt;/tr&gt;
&lt;tr&gt;
&lt;td&gt;Hetero&lt;/td&gt;
&lt;td&gt;
atoms written as HETATM in PDB files or atoms in Solvent set.
&lt;/td&gt;
&lt;/tr&gt;
&lt;tr&gt;
&lt;td&gt;Ligand&lt;/td&gt;
&lt;td&gt;
atoms in Hetero set and not in Solvent set.
&lt;/td&gt;
&lt;/tr&gt;
&lt;tr&gt;
&lt;td&gt;Backbone&lt;br&gt;Mainchain&lt;/td&gt;
&lt;td&gt;
atoms in Amino set whose name is N, CA, C or O, or atoms in Nuceic set
whose name is P,O1P,O2P,O5*,C5*,C4*,O4*,C3*,O3*,C2*,O2* or C1*.
&lt;/td&gt;
&lt;/tr&gt;
&lt;tr&gt;
&lt;td&gt;Sidechain&lt;/td&gt;
&lt;td&gt;
atoms in Amino set or Nucleic set and not in Backbone set.
&lt;/td&gt;
&lt;/tr&gt;
&lt;tr&gt;
&lt;td&gt;Bonded&lt;/td&gt;
&lt;td&gt;
atoms that is connected to at least one other atom.
&lt;/td&gt;
&lt;/tr&gt;
&lt;tr&gt;
&lt;td&gt;Selected&lt;/td&gt;
&lt;td&gt;
atoms currently selected.
&lt;/td&gt;
&lt;/tr&gt;
&lt;tr&gt;
&lt;td&gt;Helix&lt;/td&gt;
&lt;td&gt;
atoms in the alpha-helix structure.
&lt;/td&gt;
&lt;/tr&gt;
&lt;tr&gt;
&lt;td&gt;Sheet&lt;/td&gt;
&lt;td&gt;
atoms in the beta-sheet structure.
&lt;/td&gt;
&lt;/tr&gt;
&lt;tr&gt;
&lt;td&gt;Turn&lt;/td&gt;
&lt;td&gt;
atoms in the turn structure.
&lt;/td&gt;
&lt;/tr&gt;
&lt;/table&gt;

== comparison operators ==
Parts of a molecule can be selected using equality, inequality and ordering operators on their properties. Possible operators are =, ==, &lt;&gt;, !=, /=, &lt;, &lt;=, &gt; and &gt;=, and possible property names are as follows.
{| border="1"
 |-
 | AtomNo || atom ID in PDB files.
 |-
 | ElemNo || atomic number.
 |-
 | ResNo || residue ID in PDB files.
 |-
 | Radius || radius of a ball image of atoms.
 |-
 | Temperature || temperature factor of atoms.
 |-
 | Model || model ID in PDB files.
 |-
 | File || File ID.
 |}

== residue range ==
A group of atoms in a molecule can be selected by the residue ID. For example, command 'select 3' selects atoms whose residue ID is 3, and 'select 3-10' selects atoms whose residue ID is larger than or equal to 3 and smaller than or equal to 10. 
Optionally, the chain ID can be specified after residue range with a colon.
For example, command 'select 3:A' selects atoms
whose residue ID is 3 in the A chain.
The chain ID can be specified in several ways (see [[#primitive_expression|primitive expression]]).

== within expression ==
A within expression selects atoms that exist within a specified distance from another set of atoms. For example, 'select within(3.0, backbone) selects atoms within a 3.0 Angstrom radius of any atom in a protein or nucleic acid backbone. 

== PDBj expression ==
A PDBj expression selects a group of atoms according to molecule's properties defined in the PDBMLplus file. It takes the following form;
 pdbj:keyword
For example, 'select pdbj:binding'. The keywords available for each molecule are obtained by the 'show pdbj' command.

== primitive expression ==
A primitive expression takes such a form as
 residue name[residue ID][:chain ID][.atom name][;alternate location][/model ID][@file ID]
Here, residue name and atom name are three letter and four letter name, respectively, and terms in square brackets can be omitted. For example, command 'select SER.CA' selects all alpha carbon atoms in serine.
Residue names that contain numeric characters should be enclosed in square brackets such as '[SO4]'.
Expressions are treated in a case-insensitive manner.
However, the chain ID can be specified case-sensitively such as 'a_A' or 'a_a',
where these mean the chains whose auth_asym_id is 'A' or 'a', respectively. 
In the same way, you can use label_asym_id to specify chains case-sensitively such as 'l_A'.
Note that the label_asym_id is available only for PDBML files and not for PDB flat files.</text>
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  <title>Installation of jV3</title>
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    <text bytes="365" xml:space="preserve">* contents
** How to use|How to use
** Installation_of_jV | Installation
** Trouble shooting|Trouble shooting
** Links|Links
** old version|Old version
* navigation
** mainpage|mainpage-description
** portal-url|portal
** currentevents-url|currentevents
** recentchanges-url|recentchanges
** randompage-url|randompage
** helppage|help
* SEARCH
* TOOLBOX
* LANGUAGES</text>
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  <title>Command List</title>
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  |__TOC__
  |}
Command usage of jV follows that of [http://www.rasmol.org/ Rasmol] with some modifications. In the following part, command arguments that can take an arbitrary value are denoted as &lt;value&gt; for example, arguments restricted to several possible values are listed with / as a delimiter, and arguments that can be omitted are put in brackets {}. Commands, [[#exit|exit]], [[#load|load]], [[#quit|quit]], [[#save|save]], [[#script|script]], and [[#write|write]], are not available in applet circumstance.

== add_backboe ==
 add_backbone {&lt;residue_name&gt; {&lt;atom_names&gt;}}
Adds backbone atom names to predefined ones for the specified residue. The &lt;atom_names&gt; is a comma-delimited list of atom names. Omitting the &lt;atom_names&gt; means to reset the residue to the initial setting. When no arguments are given, the current settings are shown.

== anim ==
 anim forward {&lt;value&gt;}
Starts animation forward. If the &lt;value&gt; is given, just move frames forward by the specified amount.

 anim backward {&lt;value&gt;}
Starts animation backward. If the &lt;value&gt; is given, just move frames backward by the specified amount.

 anim stop
Stops animation.

== animframe ==
 animframe &lt;frame&gt; {&lt;file_ID&gt;}
Sets the frame of all animation files for the specified value. When &lt;file_ID&gt; is given, only the specified file is processed.

== animmode ==
 animmode once
Sets the behavior of animation for 'once'. When the frame reaches the last one, animation is stopped.

 animmode loop
Sets the behavior of animation for 'loop'. When the frame reaches the last one, animation is reset to the first frame and continues playing.

 animmode swing
Sets the behavior of animation for 'swing'. When the frame reaches the last one, the direction of animation is reversed.

== animrange ==
 animrange &lt;init_frame&gt;-&lt;term_frame&gt; {&lt;file_IDs&gt;}
Sets the range of all animation files. When is given, only the specified file is processed.

== animselect ==
 animselect {-a/-r} &lt;file_IDs&gt;
Selects the specified files and makes the others not selected. More than one file IDs can be specified by putting commas as the delimiter. When the option -a or -r is specified, only the selection status of the specified files are modified, selected or not selected, respectively, and the others remain unchanged.

== animspeed ==
 animspeed &lt;speed&gt;
Sets the animation speed. The argument should be an integer value from 1 to 20.

== animstep ==
 animstep &lt;step&gt; {&lt;file_ID&gt;}
Sets the step of all animation files for the specified value. When &lt;file_ID&gt; is given, only the specified file is processed.

== backbone ==
 backbone {on/true}
Turns on the selected backbone bonds.

 backbone off/false
Turns off the selected backbone bonds.

 backbone &lt;radius&gt;
Turns on the selected backbone bonds with the specified raidus (angstrom or Rasmol unit). The maximum parameter value is 2.0.

== background ==
 background &lt;color&gt;
Changes the background color. The color may be given as RGB values [r,g,b], or predefined color names.

== ball_and_stick ==
 ball_and_stick {on/true}
Turns on the ball and stick image of the selected atoms with ball radius 0.5 and stick radius 0.2 in angstrom.

 ball_and_stick off/false
Turns off the ball and stick image of the selected atoms.

 ball_and_stick &lt;ball_radius&gt; &lt;stick_radius&gt;
Turns on the ball and stick image of the selected atoms with the specified ball radius and stick radius (angstrom or Rasmol unit). The maximum parameter value is 3.0 and 2.0, respectively.

== cartoon ==
 cartoon {on/true}
Turns on the thick ribbons for the selected residues. When a chain does not have enough atoms to draw the ribbon model, a backbone will be shown instead.

 cartoon off/false
Turns off the thick ribbons for the selected residues.

 cartoon &lt;half_width&gt;
Turns on the thick ribbons for the selected residues with the specified half width (angstrom or Rasmol unit). The maximum parameter value is 4.0.

== center ==
 center {-r/-s} {&lt;atom_expression&gt;}
Sets the center of rotation and the center of the screen to the center of a group of atoms specified by the [[Atom Expression|atom expression]]. When the option -r or -s is specified, only the center of rotation or the center of the screen is modified, respectively.

 center {-r} [x, y, z]
Moves the center of rotation and the center of the screen from the current position by the specified amount. When the option -r is specified, only the center of rotation is modified.

 center {-r} {x, y, z}
Sets the center of rotation and the center of the screen to the specified coordinates. When the option -r is specified, only the center of rotation is modified.

 center -s [x, y]
Moves the center of the screen from the current position by the specified amount.

 center -s {x, y}
Sets the center of the screen to the specified coordinates.

== color ==
 color {atoms} &lt;color&gt;
Sets the color of the selected atoms. The color may be given as RGB values [r,g,b], predefined color names, or predefined color schemes; amino, chain, charge, cpk, group, shapely, structure, and temperature.

 color bonds/backbone/ribbons/hbonds/ssbonds &lt;color&gt;
Sets the color of the specified object. The color may be given as RGB values [r,g,b] or predefined color names. For hydrogen bonds, color scheme 'type' can be specified.

 color bonds/backbone/ribbons/hbonds/ssbonds none
Resets the color of the specified object.

== colorvertex ==
 colorvertex &lt;color&gt;
Sets the color of the selected vertices. The color may be given as RGB values [r,g,b] or predefined color names.

 colorvertex none
Resets the color of the selected vertices.

== cpk ==
 cpk
A synonym of the [[#spacefill|spacefill]] command.

== define ==
 define &lt;name&gt; &lt;atom_expression&gt;
Associates an arbitrary set of atoms specified by the [[Atom Expression|atom expression]] with a unique name.

== display ==
 display all
Displays the image of all files.

 display none
Turns off the image of all files.

 display {-a/-r} &lt;file_IDs&gt;
Displays the image of the specified files and turns off the others. More than one file IDs can be specified by putting commas as the delimiter. When the option -a or -r is specified, turns the image of the specified files on or off, respectively, and the others remain unchanged.

== displayatom ==
 displayatom {on/true}
Displays the selected atoms.

 displayatom off/false
Turns off the selected atoms.

== displayvertex ==
 displayvertex {on/true}
Displays the selected vertices.

 displayvertex off/false
Turns off the selected vertices.

== echo ==
 echo &lt;string&gt;
Echoes the specified message back to the message area.

== exit ==
 exit
Terminates the application.

== fit ==
 fit &lt;file1_ID&gt; &lt;file2_ID&gt;
Sets the transform matrix of file1 identical to that of file2. 

== fselect ==
 fselect all
Selects all files.

 fselect none
Selects no files.

 fselect {-a/-r} &lt;file_IDs&gt;
Selects the specified files and makes the others not selected. More than one file IDs can be specified by putting commas as the delimiter. When the option -a or -r is specified, only the selection status of the specified files are modified, selected or not selected, respectively, and the others remain unchanged.

== hbonds ==
 hbonds {on/true}
Turns on the selected hydrogen bonds.

 hbonds off/false
Turns off the selected hydrogen bonds.

 hbonds &lt;radius&gt;
Turns on the selected hydrogen bonds with the specified raidus (angstrom or Rasmol unit). The maximum parameter value is 2.0. 

== load ==
 load {pdbml} &lt;filename&gt; {fit &lt;file_ID&gt;}
Opens a PDBML file. URL can be used to open a remote file. On loading, the transform matrix can be set identical to that of the specified file.

 load pdb &lt;filename&gt; {fit &lt;file_ID&gt;}
Opens a PDB file. URL can be used to open a remote file. On loading, the transform matrix can be set identical to that of the specified file.

 load polygon &lt;filename&gt; {fit &lt;file_ID&gt;}
Opens a polygon file. URL can be used to open a remote file. On loading, the transform matrix can be set identical to that of the specified file.

 load animation &lt;filename&gt; {fit &lt;file_ID&gt;}
Opens an animation file. URL can be used to open a remote file. On loading, the transform matrix can be set identical to that of the specified file.

 load ftp &lt;PDB_code&gt; {fit &lt;file_ID&gt;}
Retrieves a PDBML file from the PDBj FTP site and opens it. On loading, the transform matrix can be set identical to that of the specified file. 

== pause ==
 pause
Stops the execution of a script file until any key is pressed to restart. 

== pdbj_describe ==
 pdbj_describe &lt;file_id&gt; {&lt;name&gt;} 
Shows the document for the jV_command in PDBMLplus specified by file ID and name. When the name is not specified, all available names are listed.

== pdbj_execute ==
 pdbj_execute &lt;file_id&gt; &lt;name&gt; 
Executes the jV_command in PDBMLplus specified by file ID and name.

== quit ==
 quit
A synonym of the [[#exit|exit]] command.

== refresh ==
 refresh
Redraws all images. 

== reset ==
=== default ===
 reset
Restores the original viewing transformation of all images, the center of rotation, and the view point. 

=== cartoon ===
 reset cartoon
Restores the thickness of the cartoon representation. 

=== line_width ===
 reset line_width
Restores the width of lines in polygon images. 

=== pickradius ===
 reset pickradius
Restores the mouse-pickable region of each atom. 

=== point_size ===
 reset point_size
Restores the size of points in polygon images. 

=== polyline_width ===
 reset polyline_width
Restores the width of polylines in polygon images. 

=== transparency ===
 reset transparency
Restores the transparency of polygon images.

 reset point_transparency
Restores the transparency of points in polygon images.

 reset line_transparency
Restores the transparency of lines in polygon images.

 reset triangle_transparency
Restores the transparency of triangles in polygon images.

 reset quad_transparency
Restores the transparency of quads in polygon images.

 reset polyline_transparency
Restores the transparency of polylines in polygon images. 

== ribbons ==
 ribbons {on/true}
Turns on the ribbon surfaces for the selected residues. When a chain does not have enough atoms to draw the ribbon model, a backbone will be shown instead.

 ribbons off/false
Turns off the ribbon surfaces for the selected residues.

 ribbons &lt;half_width&gt;
Turns on the ribbon surfaces for the selected residues with the specified half width (angstrom or Rasmol unit). The maximum parameter value is 4.0.

== rotate ==
 rotate x/y/z &lt;angle&gt;
Rotates images about the specified axis by the specified angle in degrees. 

== save ==
 save {pdb} &lt;filename&gt;
Saves the currently selected set of atoms in a PDB format file.

 save script &lt;filename&gt;
Creates a script file that reproduces the currently displayed image.

 save png &lt;filename&gt;
Creates a PNG image file of the currently displayed image.

 save jpeg &lt;filename&gt; {&lt;quality&gt;}
Creates a JPEG image file of the currently displayed image. The compression quality can be specified, 0 &lt; quality &lt;= 1, where 'quality = 1' means no compression. 

== script ==
 script &lt;filename&gt;
Opens and executes the specified script file. URL can be used to open a remote file. 

== select ==
 select
Selects all atoms. Whether hetero atoms and hydrogens are selected or not depends on the internal parameters, hetero and hydrogen, respectively.

 select all
Selects all atoms including hetero atoms and hydrogens.

 select none
Selects no atoms.

 select &lt;atom_expression&gt;
Selects a group of atoms specified by the [[Atom Expression|atom expression]].

== selectvertex ==
 selectvertex {all}
Selects all vertices.

 selectvertex none
Selects no vertices.

 selectvertex &lt;vertex_expression&gt;
Selects a group of vertices specified by the [[Vertex Expression|vertex expression]].

== set ==
=== ambient ===
 set ambient {&lt;value&gt;}
Sets the amount of ambient light. The value must be between 0 and 100. When the parameter is not specified, it is restored to the default value 33.

=== adjustview ===
 set adjustview on
The view point is automatically adjusted when a new file is loaded.

 set adjustview off
The view point is kept unchanged when a new file is loaded. 

=== background ===
 set background &lt;color&gt;
Changes the background color. The color may be given as RGB values [r,g,b], or predefined color names. 

=== bondmode ===
 set bondmode and
Specifies how to select an individual bonds. A bond is selected when both atoms connected by the bond are selected.

 set bondmode or
Specifies how to select an individual bonds. A bond is selected when either of the connected atoms is selected. 

=== cartoon ===
 set cartoon {&lt;value&gt;}
Specifies the thickness of the cartoon representation (angstrom or Rasmol unit). The maximum parameter value is 2.0. When the parameter is not specified, it is restored to the default value. 

=== cartoon_loop_tube ===
 set cartoon_loop_tube on
The loop region is drawn as tube in the cartoon representation.

 set cartoon_loop_tube off
The loop region is drawn as square pillar in the cartoon representation.

=== cartoon_round ===
 set cartoon_round on
Square pillar with round edge is drawn in the cartoon representation (except beta strands). 

 set cartoon_round off
Square pillar is drawn in the cartoon representation.

=== center ===
 set center &lt;atom_expression&gt;
Sets the default center of the selected files to the center of a group of atoms specified by the [[Atom Expression|atom expression]].

 set center [x, y, z]
Sets the default center of the selected files to the specified coordinates.

=== diffuse1 ===
 set diffuse1 {&lt;value&gt;}
Sets the amount of the first diffuse light. The value must be between 0 and 100. When the parameter is not specified, it is restored to the default value 50.

=== diffuse1_direction ===
 set diffuse1_direction {[x, y, z]}
Sets the direction of the first diffuse light. When the parameter is not specified, it is restored to the default value [-1, -1, -1].

=== diffuse2 ===
 set diffuse2 {&lt;value&gt;}
Sets the amount of the second diffuse light. The value must be between 0 and 100. When the parameter is not specified, it is restored to the default value 50.

=== diffuse2_direction ===
 set diffuse2_direction {[x, y, z]}
Sets the direction of the second diffuse light. When the parameter is not specified, it is restored to the default value [-1, -1, -1].

=== drawlevel ===
 set drawlevel &lt;value&gt;
Specifies precision of the rendering of spheres and cylinders. The value may be given as an integer (minimum 5) that stands for the number of straight line segments to represent an arc of 180 degrees. 

=== efsite_url ===
 set efsite_url &lt;URL&gt;
Sets the URL for eF-site.

=== ext_site_url ===
 set ext_site_url &lt;prefix&gt; &lt;URL&gt;
Sets the URL for an external database site.

=== hbonds ===
 set hbonds backbone
Hydrogen bonds are displayed between backbones.

 set hbonds sidechain
Hydrogen bonds are displayed between sidechains. 

=== hetero ===
 set hetero on
Sets the default behavior of the select command such that hetero atoms are selected.

 set hetero off
Sets the default behavior of the select command such that hetero atoms are not selected. 

=== hydrogen ===
 set hydrogen on
Sets the default behavior of the select command such that hydrogens are selected.

 set hydrogen off
Sets the default behavior of the select command such that hydrogens are not selected. 

=== imagesize ===
 set imagesize &lt;width&gt; &lt;height&gt;
Sets the size of the 3D-rendering panel in pixels. The size will be set within the screen size with the width being an even integer. 

=== line_width ===
 set line_width &lt;value&gt;
Sets the width of lines in polygon images. The &lt;value&gt; should be larger than 0. 

=== loadcenter ===
 set loadcenter on
When a file is opened, sets the default center of that file to the center of all files that have already opened.

 set loadcenter off
When a file is opened, sets the default center of that file according to its own coordiantes. 

=== pdbml_noatom_url ===
 set pdbml_noatom_url &lt;URL&gt;
Sets the URL for PDBML noatom files.

=== pdbml_extatom_url ===
 set pdbml_extatom_url &lt;URL&gt;
Sets the URL for PDBML extatom files.

=== pdbml_plus_url ===
 set pdbml_plus_url &lt;URL&gt;
Sets the URL for PDBMLplus files.

=== picking ===
 set picking off
Turns off the mouse picking.

 set picking ident
Sets the mouse picking behavior to show atom identification.

 set picking coord
Sets the mouse picking behavior to show atom coordinates with identification.

 set picking distance
Sets the mouse picking behavior to show the distance between atoms successively picked.

 set picking center
Sets the mouse picking behavior to specify the center of rotation and center of the screen.

 set picking select
Sets the mouse picking behavior to select the file that contains the atom picked. 

=== pickradius ===
 set pickradius &lt;value&gt;
Sets the mouse-pickable region of each atom to be the sphere centered to each atom with the specified radius (angstrom or Rasmol unit). 

=== point_size ===
 set point_size &lt;value&gt;
Sets the size of points in polygon images. The &lt;value&gt; should be larger than 0. 

=== polyline_width ===
 set polyline_width &lt;value&gt;
Sets the width of polylines in polygon images. The &lt;value&gt; should be larger than 0. 

=== projection ===
 set projection perspective
Sets the projection mode for a perspective projection.

 set projection parallel {&lt;size&gt;}
Sets the projection mode for a parallel projection. The size of image (fit to the height of the screen) can be specified (angstrom or Rasmol unit). 

=== ribbonback ===
 set ribbonback &lt;color&gt;
Sets the color of the back of ribbon models. The color may be given as RGB values [r,g,b] or predefined color names.

 set ribbonback none
Resets the color of the back of ribbon models.

=== specular ===
 set specular on/true
Enables the display of specular highlights on solid objects.

 set specular off/false
Disables the display of specular highlights on solid objects.

 set specular &lt;value&gt;
Enables the display of specular highlights on solid objects. The value between 0 and 100 specifies the specular color in gray scale with 0 and 100 being black and white, respectively. The default value is 50.0. 

=== specpower ===
 set specpower &lt;value&gt;
Sets the shininess of solid objects. The value between 0 and 100 specifies a material reflection coefficient with 0 being diffuse surfaces and 100 being shiny surfaces. 

=== ssbonds ===
 set ssbonds backbone
Disulfide bonds are displayed between backbones.

 set ssbonds sidechain
Disulfide bonds are displayed between sidechains. 

=== stereo ===
 set stereo
A synonym of the [[#stereo_2|stereo]] command.

=== transparency ===
 set transparency &lt;value&gt;
Sets the transparency of polygon images.

 set point_transparency &lt;value&gt;
Sets the transparency of points in polygon images.

 set line_transparency &lt;value&gt;
Sets the transparency of lines in polygon images.

 set triangle_transparency &lt;value&gt;
Sets the transparency of triangles in polygon images.

 set quad_transparency &lt;value&gt;
Sets the transparency of quads in polygon images.

 set polyline_transparency &lt;value&gt;
Sets the transparency of polylines in polygon images. 

=== viewpoint ===
 set viewpoint {x, y, z}
Sets the viewpoint to the specified coordinates. 

== show ==
 show godata
Displays gene ontology data of molecules.

 show imagesize
Displays the size of the 3D-rendering panel.

 show information
Displays a detail discription of molecules.

 show site {&lt;prefix&gt;:&lt;db&gt;:&lt;category&gt;}
Displays site information in an external database.

 show transform
Displays the transform matrix of molecules.

 show viewpoint
Displays the current viewpoint.

 show pdbj
Displays keywords available in [[Atom Expression#PDBj expression|PDBj expression]].

== slab ==
 slab {on/true}
Enables the z-clipping plane of molecules and polygons.

 slab off/false
Disables the z-clipping plane of molecules and polygons.

 slab &lt;ratio&gt;
Sets the position of the z-clipping plane of molecules and polygons. The parameter may be given as a number from 0 to 100. The values 0 and 100 represent that image as a whole is completely invisible and visible, respectively.

 slab -v &lt;value&gt;
Sets the position of the z-clipping plane of molecules and polygons by specifying the z coordinate value. 

== spacefill ==
 spacefill {on/true}
Turns on the ball image of the selected atoms.

 spacefill off/false
Turns off the ball image of the selected atoms.

 spacefill &lt;radius&gt;
Turns on the ball image of the selected atoms with the specified radius (angstrom or Rasmol unit). The maximum parameter value is 3.0.

 spacefill temperature
Turns on the ball image of the selected atoms using the temperature factor as radius. 

== ssbonds ==
 ssbonds {on/true}
Turns on the selected disulfide bonds.

 ssbonds off/false
Turns off the selected disulfide bonds.

 ssbonds &lt;radius&gt;
Turns on the selected disulfide bonds with the specified raidus (angstrom or Rasmol unit). The maximum parameter value is 2.0. 

== stereo ==
 stereo {on/true}
Enables stereo display. This command without arguments cycles three state; 'stereo off', 'stereo on' in cross-eyed mode and 'stereo on' in parallel-eyed mode.

 stereo off/false
Disables stereo display.

 stereo &lt;angle&gt;
Enables stereo display with the specified separation angle. Positive and negative values represent cross-eyed and parallel-eyed viewing, respectively.


== structure ==
 structure
Estimates the secondary structure using Kabsch and Sander's DSSP algorithm. 

== trace ==
 trace {on/true}
Turns on a tube representation for the selected residues. When a chain does not have enough atoms to draw the tube model, a backbone will be shown instead.

 trace off/false
Turns off a tube representation for the selected residues.

 trace &lt;radius&gt;
Turns on a tube representation for the selected residues with the specified radius (angstrom or Rasmol unit). The maximum parameter value is 2.0.

== translate ==
 translate x/y/z &lt;value&gt;
Moves images along the specified axis by the specified amount (angstrom). 

== wireframe ==
 wireframe {on/true}
Turns on the selected bonds.

 wireframe off/false
Turns off the selected bonds.

 wireframe &lt;radius&gt;
Turns on the selected bonds with the specified raidus (angstrom or Rasmol unit). The maximum parameter value is 2.0. 

== write ==
 write
A synonym of the [[#save|save]] command.

== zap ==
 zap {&lt;file_IDs&gt;}
Closes the specified files. More than one file IDs can be specified by putting commas as the delimiter. When the paraneter is absent, all files are closed. 

== zoom ==
 zoom {&lt;value&gt;}
Sets the magnification of the image as a whole. The value stands for the magnification as a percentage of the current scale. The minimum parameter value is 10.0.</text>
    <sha1>ead0d63ee6458949040ebdeb585fa873638ef310</sha1>
  </revision>
</page>
<page arvcontinue="20110106074224|454">
  <title>Use as Applet</title>
  <ns>0</ns>
  <id>24</id>
  <revision>
    <id>486</id>
    <parentid>336</parentid>
    <timestamp>2011-12-22T05:19:27Z</timestamp>
    <contributor>
      <username>IMSsato</username>
      <id>4</id>
    </contributor>
    <comment>/* Parameters */</comment>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="4484" xml:space="preserve">{| style="float:right"
 |__TOC__
 |}

== Introduction ==
In order to use jV as an applet, [http://java.sun.com/products/plugin/ Java Plug-in] must be installed on client computers. The applet is called from usual APPLET tags, or OBJECT and EMBED tags in HTML (see [http://java.sun.com/products/plugin/ Java Plug-in] homepage), where class name that should be called is "org.pdbj.viewer.gui.ViewerApplet" class. The program has following features.
* whether to use the command line interface or not can be specified
* whether to use the file control panel or not can be specified
* whether to use the popup menu or not can be specified
* witihin applets in the same web page, mouse events can be shared
* applet can receive a command string from JaveScript
* applet can send information about mouse-picked atoms to JavaScript.

== Parameters ==
To initialize the applet, the following parameters can be specified in HTML.
{| class="wikitable" border="1"
 ! parameter !! value 
 |-
 | pdbmlURL || URL of the PDBML files to be loaded (delimited by comma for more than one files).
 |-
 | pdbURL || URL of the PDB files to be loaded (delimited by comma for more than one files).
 |-
 | polygonURL || URL of the polygon files to be loaded (delimited by comma for more than one files).
 |-
 | animURL || URL of the animation files to be loaded (delimited by comma for more than one files).
 |-
 | command_area || whether to use the command line interface or not (true or false).
 |-
 | file_control || whether to use the file control panel or not (true or false).
 |-
 | popup_menu || whether to use the popup menu or not (true or false).
 |-
 | mouse_send_to || name property of applets with which mouse events are shared (delimited by comma for more than one applets).
 |-
 | commands || initial commands that are executed when the applet starts (delimited by semicolon for more than one commands).
 |-
 | report_picking || whether to send information about mouse-picked atoms to JavaScript or not (true or false).
 |-
 | picking_receiver || JavaScript function name that receives mouse-picking data.
 |-
 | file_load_message || whether to show a message dialog while loading a file (true or false).
 |-
 | call_on_start || whether to call a JavaScript function when the applet started (true or false).
 |-
 | newt || whether to use JOGL's native windowing toolkit (true or false). At the current version, applets on Mac need this parameter set to true. On other platforms, however, this parameter must be set to fasle. Therefore the parameter should be dynamically determined in applet tags in HTML based on the platform. When set to true, two other parameters, command_area and file_control, are automatically set to false and the stereo command becomes unavailable.
|}

== JavaScript-to-Applet Communication ==
The ViewerApplet class has some public methods, which can be called from JavaScript.

 void executeCommand(String commands)

Through this method, the applet can receive some arbitrary commands (delimited by semicolon).

 void loadPDB(String fileLocation)
 void loadPDBML(String fileLocation)
 void loadPolygon(String fileLocation)
 void loadAnim(String fileLocation)

Using these methods, PDB file, PDBML file, polygon file, and animation file specified by URL can be loaded respectively.

 void loadPDB(String fileLocation, int fitTo)
 void loadPDBML(String fileLocation, int fitTo)
 void loadPolygon(String fileLocation, int fitTo)
 void loadAnim(String fileLocation, int fitTo)

When these methods are used, the transform matrix of the loaded file is set identical to that of the specified file. 

== Applet-to-JavaScript Communication ==
In order to send the result of mouse-picking to JavaScript, the following function must be defined in JavaScript.

 function receiveMousePick(file, model, chain, res, atom, altloc, resName, atomName, x, y, z)

The function name 'receiveMousePick' is a default name. It can be changed by specifying the 'picking_receiver' parameter in APPLET or OBJECT/EMBED tags.

When the applet started, it invokes the following JavScript function 

 function jvOnStart(name)

if it is configured to do so by the applet parameter 'call_on_start'. Here the function receives the name of the applet as its argument. 

In order to enable applet-to-JavaScript communications, a new attribute 'MAYSCRIPT' is required in APPLET or OBJECT/EMBED tags (see [http://java.sun.com/j2se/1.4.2/docs/guide/plugin/developer_guide/java_js.html Java Plug-in guide]).</text>
    <sha1>e57632b38c8a363ab6ec793f90efe1e9c343311d</sha1>
  </revision>
  <revision>
    <id>500</id>
    <parentid>486</parentid>
    <timestamp>2012-01-26T01:17:54Z</timestamp>
    <contributor>
      <username>Cudo29</username>
      <id>5</id>
    </contributor>
    <comment>A link to the page with available applet code for each environment was added.</comment>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="4649" xml:space="preserve">{| style="float:right"
 |__TOC__
 |}

== Introduction ==
In order to use jV as an applet, [http://java.sun.com/products/plugin/ Java Plug-in] must be installed on client computers. The applet is called from usual APPLET tags, or OBJECT and EMBED tags in HTML (see [http://java.sun.com/products/plugin/ Java Plug-in] homepage), where class name that should be called is "org.pdbj.viewer.gui.ViewerApplet" class. The program has following features.
* whether to use the command line interface or not can be specified
* whether to use the file control panel or not can be specified
* whether to use the popup menu or not can be specified
* witihin applets in the same web page, mouse events can be shared
* applet can receive a command string from JaveScript
* applet can send information about mouse-picked atoms to JavaScript.

== Parameters ==
To initialize the applet, the following parameters can be specified in HTML.
{| class="wikitable" border="1"
 ! parameter !! value 
 |-
 | pdbmlURL || URL of the PDBML files to be loaded (delimited by comma for more than one files).
 |-
 | pdbURL || URL of the PDB files to be loaded (delimited by comma for more than one files).
 |-
 | polygonURL || URL of the polygon files to be loaded (delimited by comma for more than one files).
 |-
 | animURL || URL of the animation files to be loaded (delimited by comma for more than one files).
 |-
 | command_area || whether to use the command line interface or not (true or false).
 |-
 | file_control || whether to use the file control panel or not (true or false).
 |-
 | popup_menu || whether to use the popup menu or not (true or false).
 |-
 | mouse_send_to || name property of applets with which mouse events are shared (delimited by comma for more than one applets).
 |-
 | commands || initial commands that are executed when the applet starts (delimited by semicolon for more than one commands).
 |-
 | report_picking || whether to send information about mouse-picked atoms to JavaScript or not (true or false).
 |-
 | picking_receiver || JavaScript function name that receives mouse-picking data.
 |-
 | file_load_message || whether to show a message dialog while loading a file (true or false).
 |-
 | call_on_start || whether to call a JavaScript function when the applet started (true or false).
 |-
 | newt || whether to use JOGL's native windowing toolkit (true or false). At the current version, applets on Mac need this parameter set to true. On other platforms, however, this parameter must be set to fasle. Therefore the parameter should be dynamically determined in applet tags in HTML based on the platform. When set to true, two other parameters, command_area and file_control, are automatically set to false and the stereo command becomes unavailable.
|}

== JavaScript-to-Applet Communication ==
The ViewerApplet class has some public methods, which can be called from JavaScript.

 void executeCommand(String commands)

Through this method, the applet can receive some arbitrary commands (delimited by semicolon).

 void loadPDB(String fileLocation)
 void loadPDBML(String fileLocation)
 void loadPolygon(String fileLocation)
 void loadAnim(String fileLocation)

Using these methods, PDB file, PDBML file, polygon file, and animation file specified by URL can be loaded respectively.

 void loadPDB(String fileLocation, int fitTo)
 void loadPDBML(String fileLocation, int fitTo)
 void loadPolygon(String fileLocation, int fitTo)
 void loadAnim(String fileLocation, int fitTo)

When these methods are used, the transform matrix of the loaded file is set identical to that of the specified file. 

== Applet-to-JavaScript Communication ==
In order to send the result of mouse-picking to JavaScript, the following function must be defined in JavaScript.

 function receiveMousePick(file, model, chain, res, atom, altloc, resName, atomName, x, y, z)

The function name 'receiveMousePick' is a default name. It can be changed by specifying the 'picking_receiver' parameter in APPLET or OBJECT/EMBED tags.

When the applet started, it invokes the following JavScript function 

 function jvOnStart(name)

if it is configured to do so by the applet parameter 'call_on_start'. Here the function receives the name of the applet as its argument. 

In order to enable applet-to-JavaScript communications, a new attribute 'MAYSCRIPT' is required in APPLET or OBJECT/EMBED tags (see [http://java.sun.com/j2se/1.4.2/docs/guide/plugin/developer_guide/java_js.html Java Plug-in guide]).

== Available applet code for each environment ==
Which type of applet code works or not in each environment is described [http://pdbj.org/jv/test/applet.php here].</text>
    <sha1>4fb530e355a03cfc95b775e198303e6f31c615b2</sha1>
  </revision>
</page>
<page arvcontinue="20110106074224|454">
  <title>Use jV applet with JNLP file</title>
  <ns>0</ns>
  <id>68</id>
  <revision>
    <id>487</id>
    <parentid>451</parentid>
    <timestamp>2011-12-22T05:28:47Z</timestamp>
    <contributor>
      <username>IMSsato</username>
      <id>4</id>
    </contributor>
    <comment>/* Example */</comment>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="1768" xml:space="preserve">A brief introduction to use jV as applet with next-generation Java Plug-in.
Note that Mac users cannnot utilize the next-generation Java Plug-in at the moment.

== Example ==
The following code snippet shows how to embed jV applet in a web page.

 &lt;applet name="jVwindow" height="600" width="600"&gt;
   &lt;param name="jnlp_href" value="jV-applet.jnlp"/&gt;
   &amp;lt;!-- replace the following with an appropriate URL --&gt;
   &lt;param name="pdbmlURL" value="http://eprots.protein.osaka-u.ac.jp/Rep_PDBML/1ashA1.xml.gz"&gt;
   &lt;param name="commands" value="cartoon;color group" name="commands"&gt;
 &lt;/applet&gt;

The example assumes that a file named jV-applet.jnlp is placed at the same location as the HTML file that contains above applet tag. The contents of jV-applet.jnlp is as follows.

 &lt;?xml version="1.0" encoding="UTF-8"?&gt;
 &lt;jnlp href="jV-applet.jnlp"&gt;
   &lt;information&gt;
     &lt;title&gt;jV&lt;/title&gt;
     &lt;vendor&gt;Protein Data Bank Japan&lt;/vendor&gt;
     &lt;homepage href="http://ef-site.hgc.jp/jV/"/&gt;
     &lt;description&gt;Program to display molecular graphics of proteins and nucleic acids&lt;/description&gt;
     &lt;description kind="short"&gt;&lt;/description&gt;
     &lt;offline-allowed/&gt;
   &lt;/information&gt;
   &lt;resources&gt;
     &lt;j2se href="http://java.sun.com/products/autodl/j2se" version="1.4+"/&gt;
     &lt;property name="sun.java2d.noddraw" value="true"/&gt;
     &lt;jar href="jv3_8_2.jar"/&gt;
     &lt;extension name="jogl-all-awt" href="http://jogamp.org/deployment/jogamp-current/jogl-all-awt.jnlp" /&gt;
   &lt;/resources&gt;
   &lt;applet-desc
       name="jV"
       main-class="org.pdbj.viewer.gui.ViewerApplet"
       width="500"
       height="500"&gt;
   &lt;/applet-desc&gt;
 &lt;/jnlp&gt;

Here, applet-desc tag has name, width and height attributes. These are required, however, their values are overridden by those of applet tag in HTML.</text>
    <sha1>5c39c3475f5aa37c5fa44e9c99cc13ff2109140a</sha1>
  </revision>
  <revision>
    <id>488</id>
    <parentid>487</parentid>
    <timestamp>2011-12-22T05:34:09Z</timestamp>
    <contributor>
      <username>IMSsato</username>
      <id>4</id>
    </contributor>
    <comment>/* Example */</comment>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="2051" xml:space="preserve">A brief introduction to use jV as applet with next-generation Java Plug-in.
Note that Mac users cannnot utilize the next-generation Java Plug-in at the moment.

== Example ==
The following code snippet shows how to embed jV applet in a web page.

 &lt;applet name="jVwindow" height="600" width="600"&gt;
   &lt;param name="jnlp_href" value="jV-applet.jnlp"/&gt;
   &amp;lt;!-- replace the following with an appropriate URL --&gt;
   &lt;param name="pdbmlURL" value="http://eprots.protein.osaka-u.ac.jp/Rep_PDBML/1ashA1.xml.gz"&gt;
   &lt;param name="commands" value="cartoon;color group" name="commands"&gt;
   &lt;script type="text/javascript"&gt;
   &amp;lt;!-- 
   if(navigator.userAgent.indexOf("Mac") != -1 ){
     document.write('&lt;param name="newt" value="true"/&gt;');
   }
   //--&gt;
   &lt;/script&gt;
 &lt;/applet&gt;

Note that jV version 4.1 requires an applet parameter newt set to true when the user's OS is Mac OS X.
The example assumes that a file named jV-applet.jnlp is placed at the same location as the HTML file that contains above applet tag. The contents of jV-applet.jnlp is as follows.

 &lt;?xml version="1.0" encoding="UTF-8"?&gt;
 &lt;jnlp href="jV-applet.jnlp"&gt;
   &lt;information&gt;
     &lt;title&gt;jV&lt;/title&gt;
     &lt;vendor&gt;Protein Data Bank Japan&lt;/vendor&gt;
     &lt;homepage href="http://ef-site.hgc.jp/jV/"/&gt;
     &lt;description&gt;Program to display molecular graphics of proteins and nucleic acids&lt;/description&gt;
     &lt;description kind="short"&gt;&lt;/description&gt;
     &lt;offline-allowed/&gt;
   &lt;/information&gt;
   &lt;resources&gt;
     &lt;j2se href="http://java.sun.com/products/autodl/j2se" version="1.4+"/&gt;
     &lt;property name="sun.java2d.noddraw" value="true"/&gt;
     &lt;jar href="jv4_1.jar"/&gt;
     &lt;extension name="jogl-all-awt" href="http://jogamp.org/deployment/jogamp-current/jogl-all-awt.jnlp" /&gt;
   &lt;/resources&gt;
   &lt;applet-desc
       name="jV"
       main-class="org.pdbj.viewer.gui.ViewerApplet"
       width="500"
       height="500"&gt;
   &lt;/applet-desc&gt;
 &lt;/jnlp&gt;

Here, applet-desc tag has name, width and height attributes. These are required, however, their values are overridden by those of applet tag in HTML.</text>
    <sha1>2176b70dd1dc9f3d30cea60a56870324eb2f6961</sha1>
  </revision>
  <revision>
    <id>498</id>
    <parentid>488</parentid>
    <timestamp>2012-01-12T05:50:50Z</timestamp>
    <contributor>
      <username>IMSsato</username>
      <id>4</id>
    </contributor>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="2150" xml:space="preserve">A brief introduction to use jV as applet with next-generation Java Plug-in.
Note that the next-generation Java Plug-in is available from JRE 1.6.0_10.

== Example ==
The following code snippet shows how to embed jV applet in a web page.

 &lt;applet name="jVwindow" height="600" width="600" code="org.pdbj.viewer.gui.ViewerApplet"&gt;
   &lt;param name="jnlp_href" value="jV-applet.jnlp"/&gt;
   &lt;param name="java_arguments" value="-Dsun.java2d.noddraw=true"/&gt;
   &amp;lt;!-- replace the following with an appropriate URL --&gt;
   &lt;param name="pdbmlURL" value="http://eprots.protein.osaka-u.ac.jp/Rep_PDBML/1ashA1.xml.gz"&gt;
   &lt;param name="commands" value="cartoon;color group" name="commands"&gt;
   &lt;script type="text/javascript"&gt;
   &amp;lt;!-- 
   if(navigator.userAgent.indexOf("Mac") != -1 ){
     document.write('&lt;param name="newt" value="true"/&gt;');
   }
   //--&gt;
   &lt;/script&gt;
 &lt;/applet&gt;

Note that jV version 4.1 requires an applet parameter newt set to true when the user's OS is Mac OS X.
The example assumes that a file named jV-applet.jnlp is placed at the same location as the HTML file that contains above applet tag. The contents of jV-applet.jnlp is as follows.

 &lt;?xml version="1.0" encoding="UTF-8"?&gt;
 &lt;jnlp href="jV-applet.jnlp"&gt;
   &lt;information&gt;
     &lt;title&gt;jV&lt;/title&gt;
     &lt;vendor&gt;Protein Data Bank Japan&lt;/vendor&gt;
     &lt;homepage href="http://ef-site.hgc.jp/jV/"/&gt;
     &lt;description&gt;Program to display molecular graphics of proteins and nucleic acids&lt;/description&gt;
     &lt;description kind="short"&gt;&lt;/description&gt;
     &lt;offline-allowed/&gt;
   &lt;/information&gt;
   &lt;resources&gt;
     &lt;j2se href="http://java.sun.com/products/autodl/j2se" version="1.4+"/&gt;
     &lt;property name="sun.java2d.noddraw" value="true"/&gt;
     &lt;jar href="jv4_1.jar"/&gt;
     &lt;extension name="jogl-all-awt" href="http://jogamp.org/deployment/jogamp-current/jogl-all-awt.jnlp" /&gt;
   &lt;/resources&gt;
   &lt;applet-desc
       name="jV"
       main-class="org.pdbj.viewer.gui.ViewerApplet"
       width="500"
       height="500"&gt;
   &lt;/applet-desc&gt;
 &lt;/jnlp&gt;

Here, applet-desc tag has name, width and height attributes. These are required, however, their values are overridden by those of applet tag in HTML.</text>
    <sha1>01bbc2d66934da42af103d1160843666a21ad358</sha1>
  </revision>
  <revision>
    <id>499</id>
    <parentid>498</parentid>
    <timestamp>2012-01-12T05:51:28Z</timestamp>
    <contributor>
      <username>IMSsato</username>
      <id>4</id>
    </contributor>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="2156" xml:space="preserve">A brief introduction to use jV as applet with next-generation Java Plug-in.
Note that the next-generation Java Plug-in is not available before JRE 1.6.0_10.

== Example ==
The following code snippet shows how to embed jV applet in a web page.

 &lt;applet name="jVwindow" height="600" width="600" code="org.pdbj.viewer.gui.ViewerApplet"&gt;
   &lt;param name="jnlp_href" value="jV-applet.jnlp"/&gt;
   &lt;param name="java_arguments" value="-Dsun.java2d.noddraw=true"/&gt;
   &amp;lt;!-- replace the following with an appropriate URL --&gt;
   &lt;param name="pdbmlURL" value="http://eprots.protein.osaka-u.ac.jp/Rep_PDBML/1ashA1.xml.gz"&gt;
   &lt;param name="commands" value="cartoon;color group" name="commands"&gt;
   &lt;script type="text/javascript"&gt;
   &amp;lt;!-- 
   if(navigator.userAgent.indexOf("Mac") != -1 ){
     document.write('&lt;param name="newt" value="true"/&gt;');
   }
   //--&gt;
   &lt;/script&gt;
 &lt;/applet&gt;

Note that jV version 4.1 requires an applet parameter newt set to true when the user's OS is Mac OS X.
The example assumes that a file named jV-applet.jnlp is placed at the same location as the HTML file that contains above applet tag. The contents of jV-applet.jnlp is as follows.

 &lt;?xml version="1.0" encoding="UTF-8"?&gt;
 &lt;jnlp href="jV-applet.jnlp"&gt;
   &lt;information&gt;
     &lt;title&gt;jV&lt;/title&gt;
     &lt;vendor&gt;Protein Data Bank Japan&lt;/vendor&gt;
     &lt;homepage href="http://ef-site.hgc.jp/jV/"/&gt;
     &lt;description&gt;Program to display molecular graphics of proteins and nucleic acids&lt;/description&gt;
     &lt;description kind="short"&gt;&lt;/description&gt;
     &lt;offline-allowed/&gt;
   &lt;/information&gt;
   &lt;resources&gt;
     &lt;j2se href="http://java.sun.com/products/autodl/j2se" version="1.4+"/&gt;
     &lt;property name="sun.java2d.noddraw" value="true"/&gt;
     &lt;jar href="jv4_1.jar"/&gt;
     &lt;extension name="jogl-all-awt" href="http://jogamp.org/deployment/jogamp-current/jogl-all-awt.jnlp" /&gt;
   &lt;/resources&gt;
   &lt;applet-desc
       name="jV"
       main-class="org.pdbj.viewer.gui.ViewerApplet"
       width="500"
       height="500"&gt;
   &lt;/applet-desc&gt;
 &lt;/jnlp&gt;

Here, applet-desc tag has name, width and height attributes. These are required, however, their values are overridden by those of applet tag in HTML.</text>
    <sha1>35843c4f6475270cf57d8571d672bf9b41d2f7b1</sha1>
  </revision>
</page>
<page arvcontinue="20110106074224|454">
  <title>Use jV applet with applet launcher</title>
  <ns>0</ns>
  <id>16</id>
  <revision>
    <id>489</id>
    <parentid>448</parentid>
    <timestamp>2011-12-22T05:50:44Z</timestamp>
    <contributor>
      <username>IMSsato</username>
      <id>4</id>
    </contributor>
    <comment>/* Minimum Example */</comment>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="2187" xml:space="preserve">A brief introduction to use jV in applet.

== Minimum Example ==
One way to use jV applet is to use with applet-launcher. jV after v3.6 is fully compatible with applet-launcher.

 &lt;applet
   hspace="0" vspace="0" align="middle"
   name="jVwindow" height="600" width="600"
   archive="http://jogamp.org/deployment/jogamp-current/jar/applet-launcher.jar,
            http://jogamp.org/deployment/jogamp-current/jar/jogl.all.jar,
            http://jogamp.org/deployment/jogamp-current/jar/gluegen-rt.jar,
            '''jv4_1.jar'''"
   code="org.jdesktop.applet.util.JNLPAppletLauncher"&gt;
 &amp;lt;!-- param for applet-launcher --&gt;
   &lt;param name="subapplet.classname" value="'''org.pdbj.viewer.gui.ViewerApplet'''"&gt;
   &lt;param name="subapplet.displayname" value="jV applet"&gt;
   &lt;param name="noddraw.check" value="true"/&gt;
   &lt;param name="noddraw.check.silent" value="true"/&gt;
   &lt;param name="java_arguments" value="-Dsun.java2d.noddraw=true"/&gt;
   &lt;param name="progressbar" value="true"/&gt;
   &lt;param name="jnlpNumExtensions" value="1"/&gt;
   &lt;param name="jnlpExtension1"
    value="http://jogamp.org/deployment/jogamp-current/jogl-all-awt.jnlp"/&gt;
 '''&amp;lt;!-- param for jV --&gt;'''
   '''&lt;param value="" name="pdbURL"&gt;'''
    '''&amp;lt;!-- replace the following with an appropriate URL --&gt;'''
   '''&lt;param name="pdbmlURL" value="http://eprots.protein.osaka-u.ac.jp/Rep_PDBML/1ashA1.xml.gz"&gt;'''
   '''&lt;param value="" name="polygonURL"&gt;'''
   '''&lt;param value="set picking ident;background black;wireframe off;cartoon;color group" name="commands"&gt;'''
   '''&lt;script type="text/javascript"&gt;'''
   '''&amp;lt;!--'''
   '''if(navigator.userAgent.indexOf("Mac") != -1 ){'''
   '''  document.write('&lt;param name="newt" value="true"/&gt;');'''
   '''}'''
   '''//--&gt;'''
   '''&lt;/script&gt;'''
 &lt;/applet&gt;

Upper part is almost same as the usual usage of applet launcher. See the [http://jogamp.org/applet-launcher/www/ applet-launcher page] for details. The latter part is for jV parameters.

Only the &lt;B&gt;bold face&lt;/B&gt; part is specific for jV.

To use this template, you need to get applet-launcher.jar from http://download.java.net/media/applet-launcher/applet-launcher.jar, and put it in the same server that jv.jar is placed.</text>
    <sha1>1f7456db096b19a656a77cebb899c5d37eb7b7df</sha1>
  </revision>
  <revision>
    <id>490</id>
    <parentid>489</parentid>
    <timestamp>2011-12-22T05:55:55Z</timestamp>
    <contributor>
      <username>IMSsato</username>
      <id>4</id>
    </contributor>
    <comment>/* Minimum Example */</comment>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="2290" xml:space="preserve">A brief introduction to use jV in applet.

== Minimum Example ==
One way to use jV applet is to use with applet-launcher. jV after v3.6 is fully compatible with applet-launcher.

 &lt;applet
   hspace="0" vspace="0" align="middle"
   name="jVwindow" height="600" width="600"
   archive="http://jogamp.org/deployment/jogamp-current/jar/applet-launcher.jar,
            http://jogamp.org/deployment/jogamp-current/jar/jogl.all.jar,
            http://jogamp.org/deployment/jogamp-current/jar/gluegen-rt.jar,
            '''jv4_1.jar'''"
   code="org.jdesktop.applet.util.JNLPAppletLauncher"&gt;
 &amp;lt;!-- param for applet-launcher --&gt;
   &lt;param name="subapplet.classname" value="'''org.pdbj.viewer.gui.ViewerApplet'''"&gt;
   &lt;param name="subapplet.displayname" value="jV applet"&gt;
   &lt;param name="noddraw.check" value="true"/&gt;
   &lt;param name="noddraw.check.silent" value="true"/&gt;
   &lt;param name="java_arguments" value="-Dsun.java2d.noddraw=true"/&gt;
   &lt;param name="progressbar" value="true"/&gt;
   &lt;param name="jnlpNumExtensions" value="1"/&gt;
   &lt;param name="jnlpExtension1"
    value="http://jogamp.org/deployment/jogamp-current/jogl-all-awt.jnlp"/&gt;
 '''&amp;lt;!-- param for jV --&gt;'''
   '''&lt;param value="" name="pdbURL"&gt;'''
    '''&amp;lt;!-- replace the following with an appropriate URL --&gt;'''
   '''&lt;param name="pdbmlURL" value="http://eprots.protein.osaka-u.ac.jp/Rep_PDBML/1ashA1.xml.gz"&gt;'''
   '''&lt;param value="" name="polygonURL"&gt;'''
   '''&lt;param value="set picking ident;background black;wireframe off;cartoon;color group" name="commands"&gt;'''
   '''&lt;script type="text/javascript"&gt;'''
   '''&amp;lt;!--'''
   '''if(navigator.userAgent.indexOf("Mac") != -1 ){'''
   '''  document.write('&lt;param name="newt" value="true"/&gt;');'''
   '''}'''
   '''//--&gt;'''
   '''&lt;/script&gt;'''
 &lt;/applet&gt;

Upper part is almost same as the usual usage of applet launcher. See the [http://jogamp.org/applet-launcher/www/ applet-launcher page] for details. The latter part is for jV parameters. Note that jV version 4.1 requires an applet parameter newt set to true when the user's OS is Mac OS X.

Only the &lt;B&gt;bold face&lt;/B&gt; part is specific for jV.

To use this template, you need to get applet-launcher.jar from http://download.java.net/media/applet-launcher/applet-launcher.jar, and put it in the same server that jv.jar is placed.</text>
    <sha1>cb82678f703430612445a3c18a958b724c4acf40</sha1>
  </revision>
  <revision>
    <id>491</id>
    <parentid>490</parentid>
    <timestamp>2011-12-22T06:00:50Z</timestamp>
    <contributor>
      <username>IMSsato</username>
      <id>4</id>
    </contributor>
    <comment>/* Minimum Example */</comment>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="2105" xml:space="preserve">A brief introduction to use jV in applet.

== Minimum Example ==
One way to use jV applet is to use with applet-launcher. jV after v3.6 is fully compatible with applet-launcher.

 &lt;applet
   hspace="0" vspace="0" align="middle"
   name="jVwindow" height="600" width="600"
   archive="http://jogamp.org/deployment/jogamp-current/jar/applet-launcher.jar,
            http://jogamp.org/deployment/jogamp-current/jar/jogl.all.jar,
            http://jogamp.org/deployment/jogamp-current/jar/gluegen-rt.jar,
            '''jv4_1.jar'''"
   code="org.jdesktop.applet.util.JNLPAppletLauncher"&gt;
 &amp;lt;!-- param for applet-launcher --&gt;
   &lt;param name="subapplet.classname" value="'''org.pdbj.viewer.gui.ViewerApplet'''"&gt;
   &lt;param name="subapplet.displayname" value="jV applet"&gt;
   &lt;param name="noddraw.check" value="true"/&gt;
   &lt;param name="noddraw.check.silent" value="true"/&gt;
   &lt;param name="java_arguments" value="-Dsun.java2d.noddraw=true"/&gt;
   &lt;param name="progressbar" value="true"/&gt;
   &lt;param name="jnlpNumExtensions" value="1"/&gt;
   &lt;param name="jnlpExtension1"
    value="http://jogamp.org/deployment/jogamp-current/jogl-all-awt.jnlp"/&gt;
 '''&amp;lt;!-- param for jV --&gt;'''
   '''&lt;param value="" name="pdbURL"&gt;'''
    '''&amp;lt;!-- replace the following with an appropriate URL --&gt;'''
   '''&lt;param name="pdbmlURL" value="http://eprots.protein.osaka-u.ac.jp/Rep_PDBML/1ashA1.xml.gz"&gt;'''
   '''&lt;param value="" name="polygonURL"&gt;'''
   '''&lt;param value="set picking ident;background black;wireframe off;cartoon;color group" name="commands"&gt;'''
   '''&lt;script type="text/javascript"&gt;'''
   '''&amp;lt;!--'''
   '''if(navigator.userAgent.indexOf("Mac") != -1 ){'''
   '''  document.write('&lt;param name="newt" value="true"/&gt;');'''
   '''}'''
   '''//--&gt;'''
   '''&lt;/script&gt;'''
 &lt;/applet&gt;

Upper part is almost same as the usual usage of applet launcher. See the [http://jogamp.org/applet-launcher/www/ applet-launcher page] for details. The latter part is for jV parameters. Note that jV version 4.1 requires an applet parameter newt set to true when the user's OS is Mac OS X.

Only the &lt;B&gt;bold face&lt;/B&gt; part is specific for jV.</text>
    <sha1>22db916a2473d831f5dcf874aff1831d51635ec0</sha1>
  </revision>
</page>
<page arvcontinue="20110106074224|454">
  <title>Introduction</title>
  <ns>0</ns>
  <id>44</id>
  <revision>
    <id>496</id>
    <parentid>447</parentid>
    <timestamp>2011-12-22T06:09:39Z</timestamp>
    <contributor>
      <username>IMSsato</username>
      <id>4</id>
    </contributor>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="1899" xml:space="preserve">jV is an interactive 3D viewer program to visualize protein and nucleic acid molecules. The program reads in a PDBML file that is an XML format for PDB. Usual PDB format files are also accepted. More than one molecule files can be opened and displayed at the same time and their display models and transforms can be operated separately. In addition to molecule files, a polygon file written in XML can be read and displayed. More than one polygon files can be opened at the same time and superposed on molecule images. The [http://ef-site.hgc.jp/eF-site/schema/polygon12.xsd XML schema] of the polygon file is available. jV can perform an animation of molecules. The animation file is a PDB format file in which each frame is separated by a MODEL line.

jV runs on Java Runtime Environment ([http://java.sun.com/javase/ JRE]) and can be used both as a standalone program and an applet. The 3D rendering is performed with the use of [http://jogamp.org/jogl/www/ JOGL] API. The version requirements are as follows.

* JRE (includes Java Plug-in) 1.6 or later
* JOGL 2.0-rc4 or later

Here, [http://java.sun.com/products/plugin/ Java Plug-in] is required in order to use the program as an applet.

The program allows an interactive mouse control and command execution. The commnad syntax follows that of [http://www.rasmol.org/ Rasmol] with some modifications. In order to handle the transform of each molecule and polygon separately, every files are set to be either selected or not selected. The transform operation commands, such as rotate or translate, act only on selected files. On the other hand, every atoms in a molecule are also set to be either selected or not selected independently of whether the molecule itself is selected or not selected. Only selected atoms are the target of display model operations, such as wireframe or spacefill commands, and coloring operations.

[[Release note]]</text>
    <sha1>1838742b0e3a7e914c43d13af22b74bba4b65353</sha1>
  </revision>
</page>
<page arvcontinue="20120326072111|504">
  <title>Document type of the polygon file</title>
  <ns>0</ns>
  <id>35</id>
  <revision>
    <id>504</id>
    <parentid>239</parentid>
    <timestamp>2012-03-26T07:21:11Z</timestamp>
    <contributor>
      <username>IMSsato</username>
      <id>4</id>
    </contributor>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="4989" xml:space="preserve">The contents of a polygon file are organized as follows.

 &lt;?xml version="1.0"?&gt;
 &amp;nbsp;
 &lt;polygon&gt;
  &lt;vertices count="100" id_numbers=”use”&gt;            ←impossible to omit
    &lt;vertex id="1" image="x y z nx ny nz R G B"/&gt;
    &lt;vertex id="2" image="x y z nx ny nz R G B"/&gt;
    ・・・
  &lt;/vertices&gt;
 &amp;nbsp;
  &lt;point_array count="2" size=”3”&gt;                   ←possible to omit
    &lt;point id="1" vertex="v1"/&gt;
    &lt;point id="2" vertex="v1"/&gt;
  &lt;/point_array&gt;
 &amp;nbsp;
  &lt;line_array count="2" width=”2”&gt;                   ←possible to omit
    &lt;line id="1" vertex="v1 v2"/&gt;
    &lt;line id="2" vertex="v1 v2"/&gt;
  &lt;/line_array&gt;
 &amp;nbsp;
  &lt;triangle_array count="2" transparency=”0.5”&gt;      ←possible to omit
    &lt;triangle id="1" vertex="v1 v2 v3"/&gt;
    &lt;triangle id="2" vertex="v1 v2 v3"/&gt;
  &lt;/triangle_array&gt;
 &amp;nbsp;
  &lt;quad_array count="2"&gt;                               ←possible to omit
    &lt;quad id="1" vertex="v1 v2 v3 v4"/&gt;
    &lt;quad id="2" vertex="v1 v2 v3 v4"/&gt;
  &lt;/quad_array&gt;
 &amp;nbsp;
  &lt;polyline_array count="2" width=”1”&gt;               ←possible to omit
    &lt;polyline id="1" vertex="v1 v2 v3 v4 v5 ・・・"/&gt;
    &lt;polyline id="2" vertex="v1 v2 v3 v4 v5 ・・・"/&gt;
  &lt;/quad_array&gt;
 &amp;nbsp;
 &lt;/polygon&gt;

The ‘vertices’ element contains the sequence of vertices and the number of vertices is specified by the ‘count’ attribute. If the value of the ‘id_numbers’ attribute is ‘ignore’, the vertex id is automatically numbered starting from 1. If the ‘id_numbers’ attribute is set to be ‘use’, users can assign arbitrary numbers to each vertex id. In the ‘vertex’ element, x, y and z represent the x, y and z coordinates of the vertex, respectively, and nx, ny and nz represent the x, y and z components of the normal vector at the vertex, respectively. They are assigned real numbers. The color of each vertex is defined according to the RGB color scheme; R, G and B take the real numbers from 0 to 255. The ‘point_array’, ‘line_array’, ‘traiangle_array’, ‘quad_array’ and ‘polyline_array’ elements contain the sequence of polygons such as dots, lines, triangles, quadrangles and polylines, respectively. They can be omitted. The v1, v2, v3, v4 and v5 describe id of the vertices constructing the polygon. For these elements, the ‘transparency’ attribute that is omissible can be used to set the transparency of the image. To specify the size of dots and the width of lines, the ‘point_array’ element has the omissible ‘size’ attribute and ‘line_array’ and ‘polyline_array’ elements have the omissible ‘width’ attribute, respectively. The XML schema file that describes the type definitions and element declarations is published at http://www.pdbj.org/jv/polygonSchema. A simple example of a polygon is shown below. It represents a colored cube. The file is published at http://ef-site.hgc.jp/eF-site/jV/cube.xml. Before you open this polygon, you should close all files currently loaded to the application to get an appropriate viewpoint for the cube. To do this, you can use [File] – [Close] menu, or execute ‘zap’ in the command line.

 &lt;?xml version="1.0"?&gt;
 &amp;nbsp;
  &lt;polygon&gt;
   &lt;vertices count="24" id_numbers="use"&gt;
    &lt;vertex id="1"  image=" 1  1  1  0  0  1 255   0   0"/&gt;
    &lt;vertex id="2"  image="-1  1  1  0  0  1 255   0   0"/&gt;
    &lt;vertex id="3"  image="-1 -1  1  0  0  1 255   0   0"/&gt;
    &lt;vertex id="4"  image=" 1 -1  1  0  0  1 255   0   0"/&gt;
    &lt;vertex id="5"  image="-1  1 -1  0  0 -1   0 255 255"/&gt;
    &lt;vertex id="6"  image=" 1  1 -1  0  0 -1   0 255 255"/&gt;
    &lt;vertex id="7"  image=" 1 -1 -1  0  0 -1   0 255 255"/&gt;
    &lt;vertex id="8"  image="-1 -1 -1  0  0 -1   0 255 255"/&gt;
    &lt;vertex id="9"  image=" 1  1  1  1  0  0   0 255   0"/&gt;
    &lt;vertex id="10" image=" 1 -1  1  1  0  0   0 255   0"/&gt;
    &lt;vertex id="11" image=" 1 -1 -1  1  0  0   0 255   0"/&gt;
    &lt;vertex id="12" image=" 1  1 -1  1  0  0   0 255   0"/&gt;
    &lt;vertex id="13" image="-1  1 -1 -1  0  0 255   0 255"/&gt;
    &lt;vertex id="14" image="-1 -1 -1 -1  0  0 255   0 255"/&gt;
    &lt;vertex id="15" image="-1 -1  1 -1  0  0 255   0 255"/&gt;
    &lt;vertex id="16" image="-1  1  1 -1  0  0 255   0 255"/&gt;
    &lt;vertex id="17" image=" 1  1  1  0  1  0   0   0 255"/&gt;
    &lt;vertex id="18" image=" 1  1 -1  0  1  0   0   0 255"/&gt;
    &lt;vertex id="19" image="-1  1 -1  0  1  0   0   0 255"/&gt;
    &lt;vertex id="20" image="-1  1  1  0  1  0   0   0 255"/&gt;
    &lt;vertex id="21" image=" 1 -1 -1  0 -1  0 255 255   0"/&gt;
    &lt;vertex id="22" image=" 1 -1  1  0 -1  0 255 255   0"/&gt;
    &lt;vertex id="23" image="-1 -1  1  0 -1  0 255 255   0"/&gt;
    &lt;vertex id="24" image="-1 -1 -1  0 -1  0 255 255   0"/&gt;
   &lt;/vertices&gt;
   &lt;quad_array count="6"&gt;
    &lt;quad id="1" vertex=" 1  2  3  4"/&gt;
    &lt;quad id="2" vertex=" 5  6  7  8"/&gt;
    &lt;quad id="3" vertex=" 9 10 11 12"/&gt;
    &lt;quad id="4" vertex="13 14 15 16"/&gt;
    &lt;quad id="5" vertex="17 18 19 20"/&gt;
    &lt;quad id="6" vertex="21 22 23 24"/&gt;
   &lt;/quad_array&gt;
  &lt;/polygon&gt;</text>
    <sha1>230943f5d84d8e6261668edae0301b2a09ac978f</sha1>
  </revision>
</page>
<page arvcontinue="20120326072111|504">
  <title>Use as Applet</title>
  <ns>0</ns>
  <id>24</id>
  <revision>
    <id>505</id>
    <parentid>500</parentid>
    <timestamp>2012-03-29T03:05:51Z</timestamp>
    <contributor>
      <username>IMSsato</username>
      <id>4</id>
    </contributor>
    <comment>/* Parameters */</comment>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="4800" xml:space="preserve">{| style="float:right"
 |__TOC__
 |}

== Introduction ==
In order to use jV as an applet, [http://java.sun.com/products/plugin/ Java Plug-in] must be installed on client computers. The applet is called from usual APPLET tags, or OBJECT and EMBED tags in HTML (see [http://java.sun.com/products/plugin/ Java Plug-in] homepage), where class name that should be called is "org.pdbj.viewer.gui.ViewerApplet" class. The program has following features.
* whether to use the command line interface or not can be specified
* whether to use the file control panel or not can be specified
* whether to use the popup menu or not can be specified
* witihin applets in the same web page, mouse events can be shared
* applet can receive a command string from JaveScript
* applet can send information about mouse-picked atoms to JavaScript.

== Parameters ==
To initialize the applet, the following parameters can be specified in HTML.
{| class="wikitable" border="1"
 ! parameter !! value 
 |-
 | pdbid || PDB ID to be loaded from the PDBj FTP site (delimited by comma for more than one files). This parameter works only in a signed applet.
 |-
 | pdbmlURL || URL of the PDBML files to be loaded (delimited by comma for more than one files).
 |-
 | pdbURL || URL of the PDB files to be loaded (delimited by comma for more than one files).
 |-
 | polygonURL || URL of the polygon files to be loaded (delimited by comma for more than one files).
 |-
 | animURL || URL of the animation files to be loaded (delimited by comma for more than one files).
 |-
 | command_area || whether to use the command line interface or not (true or false).
 |-
 | file_control || whether to use the file control panel or not (true or false).
 |-
 | popup_menu || whether to use the popup menu or not (true or false).
 |-
 | mouse_send_to || name property of applets with which mouse events are shared (delimited by comma for more than one applets).
 |-
 | commands || initial commands that are executed when the applet starts (delimited by semicolon for more than one commands).
 |-
 | report_picking || whether to send information about mouse-picked atoms to JavaScript or not (true or false).
 |-
 | picking_receiver || JavaScript function name that receives mouse-picking data.
 |-
 | file_load_message || whether to show a message dialog while loading a file (true or false).
 |-
 | call_on_start || whether to call a JavaScript function when the applet started (true or false).
 |-
 | newt || whether to use JOGL's native windowing toolkit (true or false). At the current version, applets on Mac need this parameter set to true. On other platforms, however, this parameter must be set to fasle. Therefore the parameter should be dynamically determined in applet tags in HTML based on the platform. When set to true, two other parameters, command_area and file_control, are automatically set to false and the stereo command becomes unavailable.
|}

== JavaScript-to-Applet Communication ==
The ViewerApplet class has some public methods, which can be called from JavaScript.

 void executeCommand(String commands)

Through this method, the applet can receive some arbitrary commands (delimited by semicolon).

 void loadPDB(String fileLocation)
 void loadPDBML(String fileLocation)
 void loadPolygon(String fileLocation)
 void loadAnim(String fileLocation)

Using these methods, PDB file, PDBML file, polygon file, and animation file specified by URL can be loaded respectively.

 void loadPDB(String fileLocation, int fitTo)
 void loadPDBML(String fileLocation, int fitTo)
 void loadPolygon(String fileLocation, int fitTo)
 void loadAnim(String fileLocation, int fitTo)

When these methods are used, the transform matrix of the loaded file is set identical to that of the specified file. 

== Applet-to-JavaScript Communication ==
In order to send the result of mouse-picking to JavaScript, the following function must be defined in JavaScript.

 function receiveMousePick(file, model, chain, res, atom, altloc, resName, atomName, x, y, z)

The function name 'receiveMousePick' is a default name. It can be changed by specifying the 'picking_receiver' parameter in APPLET or OBJECT/EMBED tags.

When the applet started, it invokes the following JavScript function 

 function jvOnStart(name)

if it is configured to do so by the applet parameter 'call_on_start'. Here the function receives the name of the applet as its argument. 

In order to enable applet-to-JavaScript communications, a new attribute 'MAYSCRIPT' is required in APPLET or OBJECT/EMBED tags (see [http://java.sun.com/j2se/1.4.2/docs/guide/plugin/developer_guide/java_js.html Java Plug-in guide]).

== Available applet code for each environment ==
Which type of applet code works or not in each environment is described [http://pdbj.org/jv/test/applet.php here].</text>
    <sha1>883a6f550e4e7819889aaa2278eb9f14e01c7062</sha1>
  </revision>
  <revision>
    <id>506</id>
    <parentid>505</parentid>
    <timestamp>2012-03-29T03:07:28Z</timestamp>
    <contributor>
      <username>IMSsato</username>
      <id>4</id>
    </contributor>
    <comment>/* JavaScript-to-Applet Communication */</comment>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="5086" xml:space="preserve">{| style="float:right"
 |__TOC__
 |}

== Introduction ==
In order to use jV as an applet, [http://java.sun.com/products/plugin/ Java Plug-in] must be installed on client computers. The applet is called from usual APPLET tags, or OBJECT and EMBED tags in HTML (see [http://java.sun.com/products/plugin/ Java Plug-in] homepage), where class name that should be called is "org.pdbj.viewer.gui.ViewerApplet" class. The program has following features.
* whether to use the command line interface or not can be specified
* whether to use the file control panel or not can be specified
* whether to use the popup menu or not can be specified
* witihin applets in the same web page, mouse events can be shared
* applet can receive a command string from JaveScript
* applet can send information about mouse-picked atoms to JavaScript.

== Parameters ==
To initialize the applet, the following parameters can be specified in HTML.
{| class="wikitable" border="1"
 ! parameter !! value 
 |-
 | pdbid || PDB ID to be loaded from the PDBj FTP site (delimited by comma for more than one files). This parameter works only in a signed applet.
 |-
 | pdbmlURL || URL of the PDBML files to be loaded (delimited by comma for more than one files).
 |-
 | pdbURL || URL of the PDB files to be loaded (delimited by comma for more than one files).
 |-
 | polygonURL || URL of the polygon files to be loaded (delimited by comma for more than one files).
 |-
 | animURL || URL of the animation files to be loaded (delimited by comma for more than one files).
 |-
 | command_area || whether to use the command line interface or not (true or false).
 |-
 | file_control || whether to use the file control panel or not (true or false).
 |-
 | popup_menu || whether to use the popup menu or not (true or false).
 |-
 | mouse_send_to || name property of applets with which mouse events are shared (delimited by comma for more than one applets).
 |-
 | commands || initial commands that are executed when the applet starts (delimited by semicolon for more than one commands).
 |-
 | report_picking || whether to send information about mouse-picked atoms to JavaScript or not (true or false).
 |-
 | picking_receiver || JavaScript function name that receives mouse-picking data.
 |-
 | file_load_message || whether to show a message dialog while loading a file (true or false).
 |-
 | call_on_start || whether to call a JavaScript function when the applet started (true or false).
 |-
 | newt || whether to use JOGL's native windowing toolkit (true or false). At the current version, applets on Mac need this parameter set to true. On other platforms, however, this parameter must be set to fasle. Therefore the parameter should be dynamically determined in applet tags in HTML based on the platform. When set to true, two other parameters, command_area and file_control, are automatically set to false and the stereo command becomes unavailable.
|}

== JavaScript-to-Applet Communication ==
The ViewerApplet class has some public methods, which can be called from JavaScript.

 void executeCommand(String commands)

Through this method, the applet can receive some arbitrary commands (delimited by semicolon).

 void loadPDB(String fileLocation)
 void loadPDBML(String fileLocation)
 void loadFTP(String pdbId)
 void loadPolygon(String fileLocation)
 void loadPolygonCGO(String fileLocation)
 void loadAnim(String fileLocation)

Using these methods, PDB file, PDBML file, polygon file, and animation file specified by URL can be loaded respectively.
The loadFTP method receives a PDB ID and retrieves a PDBML file from the PDBj FTP site, which works only in a signed applet.

 void loadPDB(String fileLocation, int fitTo)
 void loadPDBML(String fileLocation, int fitTo)
 void loadFTP(String pdbId, int fitTo)
 void loadPolygon(String fileLocation, int fitTo)
 void loadPolygonCGO(String fileLocation, int fitTo)
 void loadAnim(String fileLocation, int fitTo)

When these methods are used, the transform matrix of the loaded file is set identical to that of the specified file.

== Applet-to-JavaScript Communication ==
In order to send the result of mouse-picking to JavaScript, the following function must be defined in JavaScript.

 function receiveMousePick(file, model, chain, res, atom, altloc, resName, atomName, x, y, z)

The function name 'receiveMousePick' is a default name. It can be changed by specifying the 'picking_receiver' parameter in APPLET or OBJECT/EMBED tags.

When the applet started, it invokes the following JavScript function 

 function jvOnStart(name)

if it is configured to do so by the applet parameter 'call_on_start'. Here the function receives the name of the applet as its argument. 

In order to enable applet-to-JavaScript communications, a new attribute 'MAYSCRIPT' is required in APPLET or OBJECT/EMBED tags (see [http://java.sun.com/j2se/1.4.2/docs/guide/plugin/developer_guide/java_js.html Java Plug-in guide]).

== Available applet code for each environment ==
Which type of applet code works or not in each environment is described [http://pdbj.org/jv/test/applet.php here].</text>
    <sha1>afc93b09496d5d61afccc3d409821298eddb0358</sha1>
  </revision>
</page>
<page arvcontinue="20120326072111|504">
  <title>Command List</title>
  <ns>0</ns>
  <id>20</id>
  <revision>
    <id>507</id>
    <parentid>485</parentid>
    <timestamp>2012-03-29T03:09:22Z</timestamp>
    <contributor>
      <username>IMSsato</username>
      <id>4</id>
    </contributor>
    <comment>/* load */</comment>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="22824" xml:space="preserve"> {| style="float:right"
  |__TOC__
  |}
Command usage of jV follows that of [http://www.rasmol.org/ Rasmol] with some modifications. In the following part, command arguments that can take an arbitrary value are denoted as &lt;value&gt; for example, arguments restricted to several possible values are listed with / as a delimiter, and arguments that can be omitted are put in brackets {}. Commands, [[#exit|exit]], [[#load|load]], [[#quit|quit]], [[#save|save]], [[#script|script]], and [[#write|write]], are not available in applet circumstance.

== add_backboe ==
 add_backbone {&lt;residue_name&gt; {&lt;atom_names&gt;}}
Adds backbone atom names to predefined ones for the specified residue. The &lt;atom_names&gt; is a comma-delimited list of atom names. Omitting the &lt;atom_names&gt; means to reset the residue to the initial setting. When no arguments are given, the current settings are shown.

== anim ==
 anim forward {&lt;value&gt;}
Starts animation forward. If the &lt;value&gt; is given, just move frames forward by the specified amount.

 anim backward {&lt;value&gt;}
Starts animation backward. If the &lt;value&gt; is given, just move frames backward by the specified amount.

 anim stop
Stops animation.

== animframe ==
 animframe &lt;frame&gt; {&lt;file_ID&gt;}
Sets the frame of all animation files for the specified value. When &lt;file_ID&gt; is given, only the specified file is processed.

== animmode ==
 animmode once
Sets the behavior of animation for 'once'. When the frame reaches the last one, animation is stopped.

 animmode loop
Sets the behavior of animation for 'loop'. When the frame reaches the last one, animation is reset to the first frame and continues playing.

 animmode swing
Sets the behavior of animation for 'swing'. When the frame reaches the last one, the direction of animation is reversed.

== animrange ==
 animrange &lt;init_frame&gt;-&lt;term_frame&gt; {&lt;file_IDs&gt;}
Sets the range of all animation files. When is given, only the specified file is processed.

== animselect ==
 animselect {-a/-r} &lt;file_IDs&gt;
Selects the specified files and makes the others not selected. More than one file IDs can be specified by putting commas as the delimiter. When the option -a or -r is specified, only the selection status of the specified files are modified, selected or not selected, respectively, and the others remain unchanged.

== animspeed ==
 animspeed &lt;speed&gt;
Sets the animation speed. The argument should be an integer value from 1 to 20.

== animstep ==
 animstep &lt;step&gt; {&lt;file_ID&gt;}
Sets the step of all animation files for the specified value. When &lt;file_ID&gt; is given, only the specified file is processed.

== backbone ==
 backbone {on/true}
Turns on the selected backbone bonds.

 backbone off/false
Turns off the selected backbone bonds.

 backbone &lt;radius&gt;
Turns on the selected backbone bonds with the specified raidus (angstrom or Rasmol unit). The maximum parameter value is 2.0.

== background ==
 background &lt;color&gt;
Changes the background color. The color may be given as RGB values [r,g,b], or predefined color names.

== ball_and_stick ==
 ball_and_stick {on/true}
Turns on the ball and stick image of the selected atoms with ball radius 0.5 and stick radius 0.2 in angstrom.

 ball_and_stick off/false
Turns off the ball and stick image of the selected atoms.

 ball_and_stick &lt;ball_radius&gt; &lt;stick_radius&gt;
Turns on the ball and stick image of the selected atoms with the specified ball radius and stick radius (angstrom or Rasmol unit). The maximum parameter value is 3.0 and 2.0, respectively.

== cartoon ==
 cartoon {on/true}
Turns on the thick ribbons for the selected residues. When a chain does not have enough atoms to draw the ribbon model, a backbone will be shown instead.

 cartoon off/false
Turns off the thick ribbons for the selected residues.

 cartoon &lt;half_width&gt;
Turns on the thick ribbons for the selected residues with the specified half width (angstrom or Rasmol unit). The maximum parameter value is 4.0.

== center ==
 center {-r/-s} {&lt;atom_expression&gt;}
Sets the center of rotation and the center of the screen to the center of a group of atoms specified by the [[Atom Expression|atom expression]]. When the option -r or -s is specified, only the center of rotation or the center of the screen is modified, respectively.

 center {-r} [x, y, z]
Moves the center of rotation and the center of the screen from the current position by the specified amount. When the option -r is specified, only the center of rotation is modified.

 center {-r} {x, y, z}
Sets the center of rotation and the center of the screen to the specified coordinates. When the option -r is specified, only the center of rotation is modified.

 center -s [x, y]
Moves the center of the screen from the current position by the specified amount.

 center -s {x, y}
Sets the center of the screen to the specified coordinates.

== color ==
 color {atoms} &lt;color&gt;
Sets the color of the selected atoms. The color may be given as RGB values [r,g,b], predefined color names, or predefined color schemes; amino, chain, charge, cpk, group, shapely, structure, and temperature.

 color bonds/backbone/ribbons/hbonds/ssbonds &lt;color&gt;
Sets the color of the specified object. The color may be given as RGB values [r,g,b] or predefined color names. For hydrogen bonds, color scheme 'type' can be specified.

 color bonds/backbone/ribbons/hbonds/ssbonds none
Resets the color of the specified object.

== colorvertex ==
 colorvertex &lt;color&gt;
Sets the color of the selected vertices. The color may be given as RGB values [r,g,b] or predefined color names.

 colorvertex none
Resets the color of the selected vertices.

== cpk ==
 cpk
A synonym of the [[#spacefill|spacefill]] command.

== define ==
 define &lt;name&gt; &lt;atom_expression&gt;
Associates an arbitrary set of atoms specified by the [[Atom Expression|atom expression]] with a unique name.

== display ==
 display all
Displays the image of all files.

 display none
Turns off the image of all files.

 display {-a/-r} &lt;file_IDs&gt;
Displays the image of the specified files and turns off the others. More than one file IDs can be specified by putting commas as the delimiter. When the option -a or -r is specified, turns the image of the specified files on or off, respectively, and the others remain unchanged.

== displayatom ==
 displayatom {on/true}
Displays the selected atoms.

 displayatom off/false
Turns off the selected atoms.

== displayvertex ==
 displayvertex {on/true}
Displays the selected vertices.

 displayvertex off/false
Turns off the selected vertices.

== echo ==
 echo &lt;string&gt;
Echoes the specified message back to the message area.

== exit ==
 exit
Terminates the application.

== fit ==
 fit &lt;file1_ID&gt; &lt;file2_ID&gt;
Sets the transform matrix of file1 identical to that of file2. 

== fselect ==
 fselect all
Selects all files.

 fselect none
Selects no files.

 fselect {-a/-r} &lt;file_IDs&gt;
Selects the specified files and makes the others not selected. More than one file IDs can be specified by putting commas as the delimiter. When the option -a or -r is specified, only the selection status of the specified files are modified, selected or not selected, respectively, and the others remain unchanged.

== hbonds ==
 hbonds {on/true}
Turns on the selected hydrogen bonds.

 hbonds off/false
Turns off the selected hydrogen bonds.

 hbonds &lt;radius&gt;
Turns on the selected hydrogen bonds with the specified raidus (angstrom or Rasmol unit). The maximum parameter value is 2.0. 

== load ==
 load {pdbml} &lt;filename&gt; {fit &lt;file_ID&gt;}
Opens a PDBML file. URL can be used to open a remote file. On loading, the transform matrix can be set identical to that of the specified file.

 load pdb &lt;filename&gt; {fit &lt;file_ID&gt;}
Opens a PDB file. URL can be used to open a remote file. On loading, the transform matrix can be set identical to that of the specified file.

 load polygon &lt;filename&gt; {fit &lt;file_ID&gt;}
Opens a polygon file. URL can be used to open a remote file. On loading, the transform matrix can be set identical to that of the specified file.

 load polygon_cgo &lt;filename&gt; {fit &lt;file_ID&gt;}
Opens a polygon CGO file distributed at eF-site system. URL can be used to open a remote file. On loading, the transform matrix can be set identical to that of the specified file.

 load animation &lt;filename&gt; {fit &lt;file_ID&gt;}
Opens an animation file. URL can be used to open a remote file. On loading, the transform matrix can be set identical to that of the specified file.

 load ftp &lt;PDB_code&gt; {fit &lt;file_ID&gt;}
Retrieves a PDBML file from the PDBj FTP site and opens it. On loading, the transform matrix can be set identical to that of the specified file.

== pause ==
 pause
Stops the execution of a script file until any key is pressed to restart. 

== pdbj_describe ==
 pdbj_describe &lt;file_id&gt; {&lt;name&gt;} 
Shows the document for the jV_command in PDBMLplus specified by file ID and name. When the name is not specified, all available names are listed.

== pdbj_execute ==
 pdbj_execute &lt;file_id&gt; &lt;name&gt; 
Executes the jV_command in PDBMLplus specified by file ID and name.

== quit ==
 quit
A synonym of the [[#exit|exit]] command.

== refresh ==
 refresh
Redraws all images. 

== reset ==
=== default ===
 reset
Restores the original viewing transformation of all images, the center of rotation, and the view point. 

=== cartoon ===
 reset cartoon
Restores the thickness of the cartoon representation. 

=== line_width ===
 reset line_width
Restores the width of lines in polygon images. 

=== pickradius ===
 reset pickradius
Restores the mouse-pickable region of each atom. 

=== point_size ===
 reset point_size
Restores the size of points in polygon images. 

=== polyline_width ===
 reset polyline_width
Restores the width of polylines in polygon images. 

=== transparency ===
 reset transparency
Restores the transparency of polygon images.

 reset point_transparency
Restores the transparency of points in polygon images.

 reset line_transparency
Restores the transparency of lines in polygon images.

 reset triangle_transparency
Restores the transparency of triangles in polygon images.

 reset quad_transparency
Restores the transparency of quads in polygon images.

 reset polyline_transparency
Restores the transparency of polylines in polygon images. 

== ribbons ==
 ribbons {on/true}
Turns on the ribbon surfaces for the selected residues. When a chain does not have enough atoms to draw the ribbon model, a backbone will be shown instead.

 ribbons off/false
Turns off the ribbon surfaces for the selected residues.

 ribbons &lt;half_width&gt;
Turns on the ribbon surfaces for the selected residues with the specified half width (angstrom or Rasmol unit). The maximum parameter value is 4.0.

== rotate ==
 rotate x/y/z &lt;angle&gt;
Rotates images about the specified axis by the specified angle in degrees. 

== save ==
 save {pdb} &lt;filename&gt;
Saves the currently selected set of atoms in a PDB format file.

 save script &lt;filename&gt;
Creates a script file that reproduces the currently displayed image.

 save png &lt;filename&gt;
Creates a PNG image file of the currently displayed image.

 save jpeg &lt;filename&gt; {&lt;quality&gt;}
Creates a JPEG image file of the currently displayed image. The compression quality can be specified, 0 &lt; quality &lt;= 1, where 'quality = 1' means no compression. 

== script ==
 script &lt;filename&gt;
Opens and executes the specified script file. URL can be used to open a remote file. 

== select ==
 select
Selects all atoms. Whether hetero atoms and hydrogens are selected or not depends on the internal parameters, hetero and hydrogen, respectively.

 select all
Selects all atoms including hetero atoms and hydrogens.

 select none
Selects no atoms.

 select &lt;atom_expression&gt;
Selects a group of atoms specified by the [[Atom Expression|atom expression]].

== selectvertex ==
 selectvertex {all}
Selects all vertices.

 selectvertex none
Selects no vertices.

 selectvertex &lt;vertex_expression&gt;
Selects a group of vertices specified by the [[Vertex Expression|vertex expression]].

== set ==
=== ambient ===
 set ambient {&lt;value&gt;}
Sets the amount of ambient light. The value must be between 0 and 100. When the parameter is not specified, it is restored to the default value 33.

=== adjustview ===
 set adjustview on
The view point is automatically adjusted when a new file is loaded.

 set adjustview off
The view point is kept unchanged when a new file is loaded. 

=== background ===
 set background &lt;color&gt;
Changes the background color. The color may be given as RGB values [r,g,b], or predefined color names. 

=== bondmode ===
 set bondmode and
Specifies how to select an individual bonds. A bond is selected when both atoms connected by the bond are selected.

 set bondmode or
Specifies how to select an individual bonds. A bond is selected when either of the connected atoms is selected. 

=== cartoon ===
 set cartoon {&lt;value&gt;}
Specifies the thickness of the cartoon representation (angstrom or Rasmol unit). The maximum parameter value is 2.0. When the parameter is not specified, it is restored to the default value. 

=== cartoon_loop_tube ===
 set cartoon_loop_tube on
The loop region is drawn as tube in the cartoon representation.

 set cartoon_loop_tube off
The loop region is drawn as square pillar in the cartoon representation.

=== cartoon_round ===
 set cartoon_round on
Square pillar with round edge is drawn in the cartoon representation (except beta strands). 

 set cartoon_round off
Square pillar is drawn in the cartoon representation.

=== center ===
 set center &lt;atom_expression&gt;
Sets the default center of the selected files to the center of a group of atoms specified by the [[Atom Expression|atom expression]].

 set center [x, y, z]
Sets the default center of the selected files to the specified coordinates.

=== diffuse1 ===
 set diffuse1 {&lt;value&gt;}
Sets the amount of the first diffuse light. The value must be between 0 and 100. When the parameter is not specified, it is restored to the default value 50.

=== diffuse1_direction ===
 set diffuse1_direction {[x, y, z]}
Sets the direction of the first diffuse light. When the parameter is not specified, it is restored to the default value [-1, -1, -1].

=== diffuse2 ===
 set diffuse2 {&lt;value&gt;}
Sets the amount of the second diffuse light. The value must be between 0 and 100. When the parameter is not specified, it is restored to the default value 50.

=== diffuse2_direction ===
 set diffuse2_direction {[x, y, z]}
Sets the direction of the second diffuse light. When the parameter is not specified, it is restored to the default value [-1, -1, -1].

=== drawlevel ===
 set drawlevel &lt;value&gt;
Specifies precision of the rendering of spheres and cylinders. The value may be given as an integer (minimum 5) that stands for the number of straight line segments to represent an arc of 180 degrees. 

=== efsite_url ===
 set efsite_url &lt;URL&gt;
Sets the URL for eF-site.

=== ext_site_url ===
 set ext_site_url &lt;prefix&gt; &lt;URL&gt;
Sets the URL for an external database site.

=== hbonds ===
 set hbonds backbone
Hydrogen bonds are displayed between backbones.

 set hbonds sidechain
Hydrogen bonds are displayed between sidechains. 

=== hetero ===
 set hetero on
Sets the default behavior of the select command such that hetero atoms are selected.

 set hetero off
Sets the default behavior of the select command such that hetero atoms are not selected. 

=== hydrogen ===
 set hydrogen on
Sets the default behavior of the select command such that hydrogens are selected.

 set hydrogen off
Sets the default behavior of the select command such that hydrogens are not selected. 

=== imagesize ===
 set imagesize &lt;width&gt; &lt;height&gt;
Sets the size of the 3D-rendering panel in pixels. The size will be set within the screen size with the width being an even integer. 

=== line_width ===
 set line_width &lt;value&gt;
Sets the width of lines in polygon images. The &lt;value&gt; should be larger than 0. 

=== loadcenter ===
 set loadcenter on
When a file is opened, sets the default center of that file to the center of all files that have already opened.

 set loadcenter off
When a file is opened, sets the default center of that file according to its own coordiantes. 

=== pdbml_noatom_url ===
 set pdbml_noatom_url &lt;URL&gt;
Sets the URL for PDBML noatom files.

=== pdbml_extatom_url ===
 set pdbml_extatom_url &lt;URL&gt;
Sets the URL for PDBML extatom files.

=== pdbml_plus_url ===
 set pdbml_plus_url &lt;URL&gt;
Sets the URL for PDBMLplus files.

=== picking ===
 set picking off
Turns off the mouse picking.

 set picking ident
Sets the mouse picking behavior to show atom identification.

 set picking coord
Sets the mouse picking behavior to show atom coordinates with identification.

 set picking distance
Sets the mouse picking behavior to show the distance between atoms successively picked.

 set picking center
Sets the mouse picking behavior to specify the center of rotation and center of the screen.

 set picking select
Sets the mouse picking behavior to select the file that contains the atom picked. 

=== pickradius ===
 set pickradius &lt;value&gt;
Sets the mouse-pickable region of each atom to be the sphere centered to each atom with the specified radius (angstrom or Rasmol unit). 

=== point_size ===
 set point_size &lt;value&gt;
Sets the size of points in polygon images. The &lt;value&gt; should be larger than 0. 

=== polyline_width ===
 set polyline_width &lt;value&gt;
Sets the width of polylines in polygon images. The &lt;value&gt; should be larger than 0. 

=== projection ===
 set projection perspective
Sets the projection mode for a perspective projection.

 set projection parallel {&lt;size&gt;}
Sets the projection mode for a parallel projection. The size of image (fit to the height of the screen) can be specified (angstrom or Rasmol unit). 

=== ribbonback ===
 set ribbonback &lt;color&gt;
Sets the color of the back of ribbon models. The color may be given as RGB values [r,g,b] or predefined color names.

 set ribbonback none
Resets the color of the back of ribbon models.

=== specular ===
 set specular on/true
Enables the display of specular highlights on solid objects.

 set specular off/false
Disables the display of specular highlights on solid objects.

 set specular &lt;value&gt;
Enables the display of specular highlights on solid objects. The value between 0 and 100 specifies the specular color in gray scale with 0 and 100 being black and white, respectively. The default value is 50.0. 

=== specpower ===
 set specpower &lt;value&gt;
Sets the shininess of solid objects. The value between 0 and 100 specifies a material reflection coefficient with 0 being diffuse surfaces and 100 being shiny surfaces. 

=== ssbonds ===
 set ssbonds backbone
Disulfide bonds are displayed between backbones.

 set ssbonds sidechain
Disulfide bonds are displayed between sidechains. 

=== stereo ===
 set stereo
A synonym of the [[#stereo_2|stereo]] command.

=== transparency ===
 set transparency &lt;value&gt;
Sets the transparency of polygon images.

 set point_transparency &lt;value&gt;
Sets the transparency of points in polygon images.

 set line_transparency &lt;value&gt;
Sets the transparency of lines in polygon images.

 set triangle_transparency &lt;value&gt;
Sets the transparency of triangles in polygon images.

 set quad_transparency &lt;value&gt;
Sets the transparency of quads in polygon images.

 set polyline_transparency &lt;value&gt;
Sets the transparency of polylines in polygon images. 

=== viewpoint ===
 set viewpoint {x, y, z}
Sets the viewpoint to the specified coordinates. 

== show ==
 show godata
Displays gene ontology data of molecules.

 show imagesize
Displays the size of the 3D-rendering panel.

 show information
Displays a detail discription of molecules.

 show site {&lt;prefix&gt;:&lt;db&gt;:&lt;category&gt;}
Displays site information in an external database.

 show transform
Displays the transform matrix of molecules.

 show viewpoint
Displays the current viewpoint.

 show pdbj
Displays keywords available in [[Atom Expression#PDBj expression|PDBj expression]].

== slab ==
 slab {on/true}
Enables the z-clipping plane of molecules and polygons.

 slab off/false
Disables the z-clipping plane of molecules and polygons.

 slab &lt;ratio&gt;
Sets the position of the z-clipping plane of molecules and polygons. The parameter may be given as a number from 0 to 100. The values 0 and 100 represent that image as a whole is completely invisible and visible, respectively.

 slab -v &lt;value&gt;
Sets the position of the z-clipping plane of molecules and polygons by specifying the z coordinate value. 

== spacefill ==
 spacefill {on/true}
Turns on the ball image of the selected atoms.

 spacefill off/false
Turns off the ball image of the selected atoms.

 spacefill &lt;radius&gt;
Turns on the ball image of the selected atoms with the specified radius (angstrom or Rasmol unit). The maximum parameter value is 3.0.

 spacefill temperature
Turns on the ball image of the selected atoms using the temperature factor as radius. 

== ssbonds ==
 ssbonds {on/true}
Turns on the selected disulfide bonds.

 ssbonds off/false
Turns off the selected disulfide bonds.

 ssbonds &lt;radius&gt;
Turns on the selected disulfide bonds with the specified raidus (angstrom or Rasmol unit). The maximum parameter value is 2.0. 

== stereo ==
 stereo {on/true}
Enables stereo display. This command without arguments cycles three state; 'stereo off', 'stereo on' in cross-eyed mode and 'stereo on' in parallel-eyed mode.

 stereo off/false
Disables stereo display.

 stereo &lt;angle&gt;
Enables stereo display with the specified separation angle. Positive and negative values represent cross-eyed and parallel-eyed viewing, respectively.


== structure ==
 structure
Estimates the secondary structure using Kabsch and Sander's DSSP algorithm. 

== trace ==
 trace {on/true}
Turns on a tube representation for the selected residues. When a chain does not have enough atoms to draw the tube model, a backbone will be shown instead.

 trace off/false
Turns off a tube representation for the selected residues.

 trace &lt;radius&gt;
Turns on a tube representation for the selected residues with the specified radius (angstrom or Rasmol unit). The maximum parameter value is 2.0.

== translate ==
 translate x/y/z &lt;value&gt;
Moves images along the specified axis by the specified amount (angstrom). 

== wireframe ==
 wireframe {on/true}
Turns on the selected bonds.

 wireframe off/false
Turns off the selected bonds.

 wireframe &lt;radius&gt;
Turns on the selected bonds with the specified raidus (angstrom or Rasmol unit). The maximum parameter value is 2.0. 

== write ==
 write
A synonym of the [[#save|save]] command.

== zap ==
 zap {&lt;file_IDs&gt;}
Closes the specified files. More than one file IDs can be specified by putting commas as the delimiter. When the paraneter is absent, all files are closed. 

== zoom ==
 zoom {&lt;value&gt;}
Sets the magnification of the image as a whole. The value stands for the magnification as a percentage of the current scale. The minimum parameter value is 10.0.</text>
    <sha1>f622e32dceb4cd18b4ea590f9874cca12fb5c575</sha1>
  </revision>
</page>
<page arvcontinue="20120326072111|504">
  <title>Release note</title>
  <ns>0</ns>
  <id>17</id>
  <revision>
    <id>508</id>
    <parentid>497</parentid>
    <timestamp>2012-03-29T03:10:59Z</timestamp>
    <contributor>
      <username>IMSsato</username>
      <id>4</id>
    </contributor>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="4904" xml:space="preserve">Changes and improvements have been made as follows.

* version 3.1
** The following commands have been added; 'animrange', 'set adjustview', 'show godata', and 'show xps3'.
** The xPSSS expression has been added in order to select a group of atoms.
** Several public methods have been added to the applet so as to append molecule or polygon files after the applet started.
** The applet can send information about mouse-picked atoms to JavaScript.
* version 3.1.1
** Some problems in GUI menu [Options]-[Hetero Atoms] and [Hydrogens] have been fixed.
** Some problems in 'trace' command have been fixed.
* version 3.1.2
** eF-site ID has been changed to a new format.
* version 3.1.3
** Some problems in xps3 atom selection have been fixed.
* version 3.1.4
** Some problems in finalization process of openGL rendering have been fixed.
* version 3.1.5
** The output of 'show xps3' command has been modified.
** Some problems in 'save png/jpeg' command have been fixed.
* version 3.1.6
** Some problems in loading an empty polygon file have been fixed.
* version 3.1.7
** Some problems in initialization process of the applet have been fixed.
* version 3.2
** 'show site' command has been added.
* version 3.3 beta 1
** Availabe JOGL version is restricted to JSR-231 beta 5 only.
* version 3.3
** Both the previous JOGL (version 1.1.1) and JSR-231 are available.
** The following commands have been added; 'set viewpoint', 'show viewpoint', 'set imagesize', and 'show imagesize'.
* version 3.3.1
** Some problems in reading a pdbMLplus file have been fixed.
* version 3.4
** PDB format version 3 can be processed.
* version 3.5
** Discrimination of DNA and RNA linking nucleotides is based on [http://remediation.wwpdb.org/ccd.html Chemical Component Dictionary] for PDB format version 3.
** The default representation of the cartoon model has been changed. Commands 'set cartoon_loop_tube', 'set cartoon_round' and 'set ribbonback' have been added.
** The default parameters of lighting have been changed. Commands 'set ambient', 'set diffuse1', 'set diffuse1_direction', 'set diffuse2' and 'set diffuse1_direction' have been added.
** Commands 'set pdbml_noatom_url', 'set pdbml_extatom_url', 'set pdbml_plus_url', 'set efsite_url', 'set ext_site_url', 'show pdbml_url', 'show efsite_url' and 'show ext_site_url' have been added.
** The command-line option '-stdin' has been added to receive commands from stdin stream.
* version 3.6
** Users can specify the JavaScript function name used in Applet-to-JavaScript Communication.
** Applet parameter 'file_load_message' has been added.
* version 3.6.1
** Predefined set of residues has been modified.
** Old JOGL API is not supported.
* version 3.6.2
** Latest version of PDBML can be processed.
** Some problems in mouse control on Mac have been fixed.
* version 3.6.3
** Molecule file parsing has been modified to detect chain breaks properly by reading the 'label_asym_id' column in PDBML and the TER line in PDB flat file, respectively.
* version 3.6.4
** Some problems in GUI menu on Mac have been fixed.
* version 3.6.5
** The jV applet can invoke a JavaScript function when it started.
* version 3.7
** Commands 'pdbj_describe' and 'pdbj_execute' have been added.
** Keyword 'xps3' have been replaced by 'pdbj'.
* version 3.7.1
** Default PDBML URLs have been changed.
* version 3.7.2
** Some problems in creating png/jpeg image files have been fixed.
* version 3.8
** Command 'displayatom' has been added.
** The signed jV applet can save PNG/JPEG image files.
* version 3.8.1
** In commands 'cartoon', 'ribbons' and 'trace', a backbone will be drawn instead when a chain does not have enough atoms to draw those models.
** Recognition of amino acids is based on [http://remediation.wwpdb.org/ccd.html Chemical Component Dictionary].
* version 3.8.2
** Command 'ball_and_stick' has been added.
* version 3.8.3
** Binary distribution contains the JOGL library and pre-installation of JOGL is not necessary to use jV.
* version 4.0
** The program supports PDB format version 4.0.
** Atom expression has been extended to handle case-sensitive chain ID and label_asym_id in PDBML.
* version 4.1
** The program runs with new JOGL library (2.0-rc4 or later) which enables jV applets to run on Mac.
** From this release, the program requires JRE 1.6 or later.
** Command 'add_backbone' has been added.
** The program uses MODRES data and chem_comp/type data (PDBML only) to determine residue types.
* version 4.2
** The program reads polygon CGO (PyMOL-specific Compiled Graphics Objects) files distributed at eF-site system. Command 'load polygon_cgo' has been added.
** A parameter 'pdbid' and a method 'loadFTP' have been added to applet.
** When the program loads a PDBML noatom file whose directory is 'all-noatom' or 'XML-noatom', the coordinate file is retrieved from the corresponding directory; '../all-extatom' or '../XML-extatom', respectively.</text>
    <sha1>b194fcae5d06784dd080fd5142183910020930ce</sha1>
  </revision>
  <revision>
    <id>523</id>
    <parentid>508</parentid>
    <timestamp>2013-03-05T00:13:25Z</timestamp>
    <contributor>
      <username>Cudo29</username>
      <id>5</id>
    </contributor>
    <comment>Description about involved in ver. 4.2.1 was added.</comment>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="4974" xml:space="preserve">Changes and improvements have been made as follows.

* version 3.1
** The following commands have been added; 'animrange', 'set adjustview', 'show godata', and 'show xps3'.
** The xPSSS expression has been added in order to select a group of atoms.
** Several public methods have been added to the applet so as to append molecule or polygon files after the applet started.
** The applet can send information about mouse-picked atoms to JavaScript.
* version 3.1.1
** Some problems in GUI menu [Options]-[Hetero Atoms] and [Hydrogens] have been fixed.
** Some problems in 'trace' command have been fixed.
* version 3.1.2
** eF-site ID has been changed to a new format.
* version 3.1.3
** Some problems in xps3 atom selection have been fixed.
* version 3.1.4
** Some problems in finalization process of openGL rendering have been fixed.
* version 3.1.5
** The output of 'show xps3' command has been modified.
** Some problems in 'save png/jpeg' command have been fixed.
* version 3.1.6
** Some problems in loading an empty polygon file have been fixed.
* version 3.1.7
** Some problems in initialization process of the applet have been fixed.
* version 3.2
** 'show site' command has been added.
* version 3.3 beta 1
** Availabe JOGL version is restricted to JSR-231 beta 5 only.
* version 3.3
** Both the previous JOGL (version 1.1.1) and JSR-231 are available.
** The following commands have been added; 'set viewpoint', 'show viewpoint', 'set imagesize', and 'show imagesize'.
* version 3.3.1
** Some problems in reading a pdbMLplus file have been fixed.
* version 3.4
** PDB format version 3 can be processed.
* version 3.5
** Discrimination of DNA and RNA linking nucleotides is based on [http://remediation.wwpdb.org/ccd.html Chemical Component Dictionary] for PDB format version 3.
** The default representation of the cartoon model has been changed. Commands 'set cartoon_loop_tube', 'set cartoon_round' and 'set ribbonback' have been added.
** The default parameters of lighting have been changed. Commands 'set ambient', 'set diffuse1', 'set diffuse1_direction', 'set diffuse2' and 'set diffuse1_direction' have been added.
** Commands 'set pdbml_noatom_url', 'set pdbml_extatom_url', 'set pdbml_plus_url', 'set efsite_url', 'set ext_site_url', 'show pdbml_url', 'show efsite_url' and 'show ext_site_url' have been added.
** The command-line option '-stdin' has been added to receive commands from stdin stream.
* version 3.6
** Users can specify the JavaScript function name used in Applet-to-JavaScript Communication.
** Applet parameter 'file_load_message' has been added.
* version 3.6.1
** Predefined set of residues has been modified.
** Old JOGL API is not supported.
* version 3.6.2
** Latest version of PDBML can be processed.
** Some problems in mouse control on Mac have been fixed.
* version 3.6.3
** Molecule file parsing has been modified to detect chain breaks properly by reading the 'label_asym_id' column in PDBML and the TER line in PDB flat file, respectively.
* version 3.6.4
** Some problems in GUI menu on Mac have been fixed.
* version 3.6.5
** The jV applet can invoke a JavaScript function when it started.
* version 3.7
** Commands 'pdbj_describe' and 'pdbj_execute' have been added.
** Keyword 'xps3' have been replaced by 'pdbj'.
* version 3.7.1
** Default PDBML URLs have been changed.
* version 3.7.2
** Some problems in creating png/jpeg image files have been fixed.
* version 3.8
** Command 'displayatom' has been added.
** The signed jV applet can save PNG/JPEG image files.
* version 3.8.1
** In commands 'cartoon', 'ribbons' and 'trace', a backbone will be drawn instead when a chain does not have enough atoms to draw those models.
** Recognition of amino acids is based on [http://remediation.wwpdb.org/ccd.html Chemical Component Dictionary].
* version 3.8.2
** Command 'ball_and_stick' has been added.
* version 3.8.3
** Binary distribution contains the JOGL library and pre-installation of JOGL is not necessary to use jV.
* version 4.0
** The program supports PDB format version 4.0.
** Atom expression has been extended to handle case-sensitive chain ID and label_asym_id in PDBML.
* version 4.1
** The program runs with new JOGL library (2.0-rc4 or later) which enables jV applets to run on Mac.
** From this release, the program requires JRE 1.6 or later.
** Command 'add_backbone' has been added.
** The program uses MODRES data and chem_comp/type data (PDBML only) to determine residue types.
* version 4.2
** The program reads polygon CGO (PyMOL-specific Compiled Graphics Objects) files distributed at eF-site system. Command 'load polygon_cgo' has been added.
** A parameter 'pdbid' and a method 'loadFTP' have been added to applet.
** When the program loads a PDBML noatom file whose directory is 'all-noatom' or 'XML-noatom', the coordinate file is retrieved from the corresponding directory; '../all-extatom' or '../XML-extatom', respectively.
* version 4.2.1
** The program runs with new JOGL library (2.0-rc11).</text>
    <sha1>33f6211af05fcd63382444b0bb6364c078cb4629</sha1>
  </revision>
  <revision>
    <id>526</id>
    <parentid>523</parentid>
    <timestamp>2013-03-06T05:11:11Z</timestamp>
    <contributor>
      <username>IMSsato</username>
      <id>4</id>
    </contributor>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="5043" xml:space="preserve">Changes and improvements have been made as follows.

* version 3.1
** The following commands have been added; 'animrange', 'set adjustview', 'show godata', and 'show xps3'.
** The xPSSS expression has been added in order to select a group of atoms.
** Several public methods have been added to the applet so as to append molecule or polygon files after the applet started.
** The applet can send information about mouse-picked atoms to JavaScript.
* version 3.1.1
** Some problems in GUI menu [Options]-[Hetero Atoms] and [Hydrogens] have been fixed.
** Some problems in 'trace' command have been fixed.
* version 3.1.2
** eF-site ID has been changed to a new format.
* version 3.1.3
** Some problems in xps3 atom selection have been fixed.
* version 3.1.4
** Some problems in finalization process of openGL rendering have been fixed.
* version 3.1.5
** The output of 'show xps3' command has been modified.
** Some problems in 'save png/jpeg' command have been fixed.
* version 3.1.6
** Some problems in loading an empty polygon file have been fixed.
* version 3.1.7
** Some problems in initialization process of the applet have been fixed.
* version 3.2
** 'show site' command has been added.
* version 3.3 beta 1
** Availabe JOGL version is restricted to JSR-231 beta 5 only.
* version 3.3
** Both the previous JOGL (version 1.1.1) and JSR-231 are available.
** The following commands have been added; 'set viewpoint', 'show viewpoint', 'set imagesize', and 'show imagesize'.
* version 3.3.1
** Some problems in reading a pdbMLplus file have been fixed.
* version 3.4
** PDB format version 3 can be processed.
* version 3.5
** Discrimination of DNA and RNA linking nucleotides is based on [http://remediation.wwpdb.org/ccd.html Chemical Component Dictionary] for PDB format version 3.
** The default representation of the cartoon model has been changed. Commands 'set cartoon_loop_tube', 'set cartoon_round' and 'set ribbonback' have been added.
** The default parameters of lighting have been changed. Commands 'set ambient', 'set diffuse1', 'set diffuse1_direction', 'set diffuse2' and 'set diffuse1_direction' have been added.
** Commands 'set pdbml_noatom_url', 'set pdbml_extatom_url', 'set pdbml_plus_url', 'set efsite_url', 'set ext_site_url', 'show pdbml_url', 'show efsite_url' and 'show ext_site_url' have been added.
** The command-line option '-stdin' has been added to receive commands from stdin stream.
* version 3.6
** Users can specify the JavaScript function name used in Applet-to-JavaScript Communication.
** Applet parameter 'file_load_message' has been added.
* version 3.6.1
** Predefined set of residues has been modified.
** Old JOGL API is not supported.
* version 3.6.2
** Latest version of PDBML can be processed.
** Some problems in mouse control on Mac have been fixed.
* version 3.6.3
** Molecule file parsing has been modified to detect chain breaks properly by reading the 'label_asym_id' column in PDBML and the TER line in PDB flat file, respectively.
* version 3.6.4
** Some problems in GUI menu on Mac have been fixed.
* version 3.6.5
** The jV applet can invoke a JavaScript function when it started.
* version 3.7
** Commands 'pdbj_describe' and 'pdbj_execute' have been added.
** Keyword 'xps3' have been replaced by 'pdbj'.
* version 3.7.1
** Default PDBML URLs have been changed.
* version 3.7.2
** Some problems in creating png/jpeg image files have been fixed.
* version 3.8
** Command 'displayatom' has been added.
** The signed jV applet can save PNG/JPEG image files.
* version 3.8.1
** In commands 'cartoon', 'ribbons' and 'trace', a backbone will be drawn instead when a chain does not have enough atoms to draw those models.
** Recognition of amino acids is based on [http://remediation.wwpdb.org/ccd.html Chemical Component Dictionary].
* version 3.8.2
** Command 'ball_and_stick' has been added.
* version 3.8.3
** Binary distribution contains the JOGL library and pre-installation of JOGL is not necessary to use jV.
* version 4.0
** The program supports PDB format version 4.0.
** Atom expression has been extended to handle case-sensitive chain ID and label_asym_id in PDBML.
* version 4.1
** The program runs with new JOGL library (2.0-rc4 or later) which enables jV applets to run on Mac.
** From this release, the program requires JRE 1.6 or later.
** Command 'add_backbone' has been added.
** The program uses MODRES data and chem_comp/type data (PDBML only) to determine residue types.
* version 4.2
** The program reads polygon CGO (PyMOL-specific Compiled Graphics Objects) files distributed at eF-site system. Command 'load polygon_cgo' has been added.
** A parameter 'pdbid' and a method 'loadFTP' have been added to applet.
** When the program loads a PDBML noatom file whose directory is 'all-noatom' or 'XML-noatom', the coordinate file is retrieved from the corresponding directory; '../all-extatom' or '../XML-extatom', respectively.
* version 4.2.1
** The program runs with new JOGL library (2.0-rc11).
* version 4.3
** Anaglyph 3D rendering is added to 'stereo' command.</text>
    <sha1>36c4f7a7c10ec1bef5a0e8fad0bde6793ea723b8</sha1>
  </revision>
  <revision>
    <id>529</id>
    <parentid>526</parentid>
    <timestamp>2013-03-14T03:30:41Z</timestamp>
    <contributor>
      <username>IMSsato</username>
      <id>4</id>
    </contributor>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="5122" xml:space="preserve">Changes and improvements have been made as follows.

* version 3.1
** The following commands have been added; 'animrange', 'set adjustview', 'show godata', and 'show xps3'.
** The xPSSS expression has been added in order to select a group of atoms.
** Several public methods have been added to the applet so as to append molecule or polygon files after the applet started.
** The applet can send information about mouse-picked atoms to JavaScript.
* version 3.1.1
** Some problems in GUI menu [Options]-[Hetero Atoms] and [Hydrogens] have been fixed.
** Some problems in 'trace' command have been fixed.
* version 3.1.2
** eF-site ID has been changed to a new format.
* version 3.1.3
** Some problems in xps3 atom selection have been fixed.
* version 3.1.4
** Some problems in finalization process of openGL rendering have been fixed.
* version 3.1.5
** The output of 'show xps3' command has been modified.
** Some problems in 'save png/jpeg' command have been fixed.
* version 3.1.6
** Some problems in loading an empty polygon file have been fixed.
* version 3.1.7
** Some problems in initialization process of the applet have been fixed.
* version 3.2
** 'show site' command has been added.
* version 3.3 beta 1
** Availabe JOGL version is restricted to JSR-231 beta 5 only.
* version 3.3
** Both the previous JOGL (version 1.1.1) and JSR-231 are available.
** The following commands have been added; 'set viewpoint', 'show viewpoint', 'set imagesize', and 'show imagesize'.
* version 3.3.1
** Some problems in reading a pdbMLplus file have been fixed.
* version 3.4
** PDB format version 3 can be processed.
* version 3.5
** Discrimination of DNA and RNA linking nucleotides is based on [http://remediation.wwpdb.org/ccd.html Chemical Component Dictionary] for PDB format version 3.
** The default representation of the cartoon model has been changed. Commands 'set cartoon_loop_tube', 'set cartoon_round' and 'set ribbonback' have been added.
** The default parameters of lighting have been changed. Commands 'set ambient', 'set diffuse1', 'set diffuse1_direction', 'set diffuse2' and 'set diffuse1_direction' have been added.
** Commands 'set pdbml_noatom_url', 'set pdbml_extatom_url', 'set pdbml_plus_url', 'set efsite_url', 'set ext_site_url', 'show pdbml_url', 'show efsite_url' and 'show ext_site_url' have been added.
** The command-line option '-stdin' has been added to receive commands from stdin stream.
* version 3.6
** Users can specify the JavaScript function name used in Applet-to-JavaScript Communication.
** Applet parameter 'file_load_message' has been added.
* version 3.6.1
** Predefined set of residues has been modified.
** Old JOGL API is not supported.
* version 3.6.2
** Latest version of PDBML can be processed.
** Some problems in mouse control on Mac have been fixed.
* version 3.6.3
** Molecule file parsing has been modified to detect chain breaks properly by reading the 'label_asym_id' column in PDBML and the TER line in PDB flat file, respectively.
* version 3.6.4
** Some problems in GUI menu on Mac have been fixed.
* version 3.6.5
** The jV applet can invoke a JavaScript function when it started.
* version 3.7
** Commands 'pdbj_describe' and 'pdbj_execute' have been added.
** Keyword 'xps3' have been replaced by 'pdbj'.
* version 3.7.1
** Default PDBML URLs have been changed.
* version 3.7.2
** Some problems in creating png/jpeg image files have been fixed.
* version 3.8
** Command 'displayatom' has been added.
** The signed jV applet can save PNG/JPEG image files.
* version 3.8.1
** In commands 'cartoon', 'ribbons' and 'trace', a backbone will be drawn instead when a chain does not have enough atoms to draw those models.
** Recognition of amino acids is based on [http://remediation.wwpdb.org/ccd.html Chemical Component Dictionary].
* version 3.8.2
** Command 'ball_and_stick' has been added.
* version 3.8.3
** Binary distribution contains the JOGL library and pre-installation of JOGL is not necessary to use jV.
* version 4.0
** The program supports PDB format version 4.0.
** Atom expression has been extended to handle case-sensitive chain ID and label_asym_id in PDBML.
* version 4.1
** The program runs with new JOGL library (2.0-rc4 or later) which enables jV applets to run on Mac.
** From this release, the program requires JRE 1.6 or later.
** Command 'add_backbone' has been added.
** The program uses MODRES data and chem_comp/type data (PDBML only) to determine residue types.
* version 4.2
** The program reads polygon CGO (PyMOL-specific Compiled Graphics Objects) files distributed at eF-site system. Command 'load polygon_cgo' has been added.
** A parameter 'pdbid' and a method 'loadFTP' have been added to applet.
** When the program loads a PDBML noatom file whose directory is 'all-noatom' or 'XML-noatom', the coordinate file is retrieved from the corresponding directory; '../all-extatom' or '../XML-extatom', respectively.
* version 4.2.1
** The program runs with new JOGL library (2.0-rc11).
* version 4.3
** Anaglyph 3D rendering is added to 'stereo' command.
* version 4.3.1
** A workaround for a cache problem in JRE 1.7 has been added.</text>
    <sha1>2b64c6c0e37037ca234c9307d8f1afe98bd5aad2</sha1>
  </revision>
</page>
<page arvcontinue="20120326072111|504">
  <title>Main Page</title>
  <ns>0</ns>
  <id>1</id>
  <revision>
    <id>509</id>
    <parentid>503</parentid>
    <timestamp>2012-12-11T10:21:08Z</timestamp>
    <contributor>
      <username>IMSsato</username>
      <id>4</id>
    </contributor>
    <comment>/* Start up */</comment>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="6585" xml:space="preserve">&lt;big&gt;'''Welcome to jV wiki.'''&lt;/big&gt;

jV (formerly known as PDBjViewer) is a program to display molecular graphics of protein and nucleic acids. 
jV supports the following features:
* jV can read and display PDBML files, the canonical XML format for the Protein Data Bank.
* Of course, jV can read and display the traditional PDB format files, too.
* RasMol-like usability.
* jV can process more than one molecules.
* jV can display polygons specified by XML. ([http://www.pdbj.org/jv/polygonSchema XML Schema for polygons] is available.)
* Multiple polygons can be processed simultaneously, and be superimposed onto molecular images.
* Animation can be realized.
* jV runs on the Java Runtime Environment ([http://java.sun.com/javase/index.jsp JRE]) so that it can work as a stand-alone application as well as an applet.
* The graphics of jV is based on OpenGL ([http://jogamp.org/jogl/www/ JOGL]), thereby producing fairly beautiful pictures.


The program 'jV' has been developed by [http://www.hgc.jp/~kinosita/TOP.html Kengo Kinoshita] ([http://www.is.tohoku.ac.jp/index-e.html Graduate School of Information Sciences], [http://www.tohoku.ac.jp/english/ Tohoku University]) and [http://www.protein.osaka-u.ac.jp/rcsfp/pi/ Haruki Nakamura] ([http://www.protein.osaka-u.ac.jp/index_e.php Institute for Protein Research], [http://www.osaka-u.ac.jp/eng/index.html Osaka Univeristy]), with the support from [http://biosciencedbc.jp/ JST-NBDC] and [http://www.osaka-u.ac.jp/ Osaka University].
      

&lt;gallery&gt;
File:Spacefill.jpg
File:Cartoon.jpg
File:Surface.jpg
File:edmap.jpg
&lt;/gallery&gt;


== Start up ==
You can start up jV (4.2.1) with Java Web Start technology immediately from here.
* [http://ef-site.hgc.jp/eF-site/servlet/stable/jV.jnlp stable JOGL version] (recommended)
* [http://ef-site.hgc.jp/eF-site/servlet/current/jV.jnlp recent JOGL version]
The current jV requires JRE 1.6 or later.
The previous version, jV version 4.0, can run with JRE 1.4 and 1.5.
* [http://ef-site.hgc.jp/jV/stable/jV_4_0.jnlp jV 4.0]

== Basic Usage ==
You can execute basic operations such as rotation and translation with mouse action. Major actions are described in the following table:
{| style="margin:auto;border:1px solid gray"
! rowspan="2" style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap;font-weight:bold" |Action
! colspan="2" style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap;font-weight:bold" |Mouse Operation
|-
! style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap;font-weight:bold" |Windows, Linux
! style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap;font-weight:bold" |Mac OS X
|-
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |rotate around X (horizontal) axis&lt;br /&gt;rotate around Y (vertical) axis
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |left drag
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |drag
|-
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |translate along X axis (holizontally)&lt;br /&gt;translate along Y axis (vertically)
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |right drag
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |Command + drag
|-
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |translate along Z axis (zoom in/out)
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |Shift + left drag
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |Shift + drag
|}

Operations such as changing display models and colors and saving the image, can be executed with a menu. The location of the menu is at the top of the application window in Windows and at the top of screen in Mac as the stand-alone application. As an applet usage, a popup menu appears by clicking the right mouse button on the display screen, or clicking with a "Command" button in case of Mac.

{| style="margin:auto;border:0"
|-
| [[File:Jv_menu_win.png|The location of menu in jV stand-alone version in Windows.|250px]]
| [[File:Jv_menu_mac.png|The location of menu in jV stand-alone version in Mac.|250px]]
| [[File:popupmenu_en.png|The location of menu in applet version.|250px]]
|-
| style="text-align:center" |Stand-alone (Windows)
| style="text-align:center" |Stand-alone (Mac)
| style="text-align:center" |Applet
|}

Basic menu operations are following (see also [[GUI]] for details):

{| style="margin:auto;border:1px solid gray;border-collapse:collapse"
! style="padding:0 0.5em;border:1px solid gray" | Operations
! style="padding:0 0.5em;border:1px solid gray" | Menu location
|-
| style="padding:0 0.5em;border:1px solid gray" | Save a static image
| style="padding:0 0.5em;border:1px solid gray" | [File]-[Save]-[PNG/JPEG]
|-
| style="padding:0 0.5em;border:1px solid gray" | Change the expression format
| style="padding:0 0.5em;border:1px solid gray" | [File]-[Display]-[Wireframe/Backbone/Sticks/Spacefill/Ball&amp;amp;Stick/Ribbons/Cartoon]
|-
| style="padding:0 0.5em;border:1px solid gray" | Change the color
| style="padding:0 0.5em;border:1px solid gray" | [File]-[Colors]-[Monochrome/CPK/Shapely/Group/Chain/Temperature/Structure/Charge/Amino]
|}

To execute more complicated operation such as diplaying some piece of the molecule or changing some part of molecule in another style, use command line operation.

See also [[#Other resources]] for details:


== Download ==
You can also download the program and start it up locally.
In this case, installing JOGL is required in advance (see [[Installation_of_jV3 | Installation]] page).
The following links take you to the download pages. (latest version is 4.2@2012/3/26)
* [http://ef-site.hgc.jp/eF-site/servlet/DownloadViewerBinary binary (4.2)] 
* [http://ef-site.hgc.jp/eF-site/servlet/Registration source code (4.2)] (registration will be required)

== Other resources ==
* [http://ef-site.hgc.jp/eF-site/jV/jV_manual.html Manual] (html in English)
* [[How_to_use]] (in this site in English)
* [http://www.pdbj.org/jv/manual/index_ja.html Manual] (html in Japanese)
* [http://www.pdbj.org/jv/manual/jV_manual.pdf Manual] (pdf in English, for ver. 3.3)
* [http://ef-site.hgc.jp/eF-site/jV/jV3_User'sGuide.pdf User's guide] (for ver. 3.8.3 in English)</text>
    <sha1>1965319320a5da8336770df839700161b05eca33</sha1>
  </revision>
  <revision>
    <id>510</id>
    <parentid>509</parentid>
    <timestamp>2012-12-11T10:21:35Z</timestamp>
    <contributor>
      <username>IMSsato</username>
      <id>4</id>
    </contributor>
    <comment>/* Download */</comment>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="6592" xml:space="preserve">&lt;big&gt;'''Welcome to jV wiki.'''&lt;/big&gt;

jV (formerly known as PDBjViewer) is a program to display molecular graphics of protein and nucleic acids. 
jV supports the following features:
* jV can read and display PDBML files, the canonical XML format for the Protein Data Bank.
* Of course, jV can read and display the traditional PDB format files, too.
* RasMol-like usability.
* jV can process more than one molecules.
* jV can display polygons specified by XML. ([http://www.pdbj.org/jv/polygonSchema XML Schema for polygons] is available.)
* Multiple polygons can be processed simultaneously, and be superimposed onto molecular images.
* Animation can be realized.
* jV runs on the Java Runtime Environment ([http://java.sun.com/javase/index.jsp JRE]) so that it can work as a stand-alone application as well as an applet.
* The graphics of jV is based on OpenGL ([http://jogamp.org/jogl/www/ JOGL]), thereby producing fairly beautiful pictures.


The program 'jV' has been developed by [http://www.hgc.jp/~kinosita/TOP.html Kengo Kinoshita] ([http://www.is.tohoku.ac.jp/index-e.html Graduate School of Information Sciences], [http://www.tohoku.ac.jp/english/ Tohoku University]) and [http://www.protein.osaka-u.ac.jp/rcsfp/pi/ Haruki Nakamura] ([http://www.protein.osaka-u.ac.jp/index_e.php Institute for Protein Research], [http://www.osaka-u.ac.jp/eng/index.html Osaka Univeristy]), with the support from [http://biosciencedbc.jp/ JST-NBDC] and [http://www.osaka-u.ac.jp/ Osaka University].
      

&lt;gallery&gt;
File:Spacefill.jpg
File:Cartoon.jpg
File:Surface.jpg
File:edmap.jpg
&lt;/gallery&gt;


== Start up ==
You can start up jV (4.2.1) with Java Web Start technology immediately from here.
* [http://ef-site.hgc.jp/eF-site/servlet/stable/jV.jnlp stable JOGL version] (recommended)
* [http://ef-site.hgc.jp/eF-site/servlet/current/jV.jnlp recent JOGL version]
The current jV requires JRE 1.6 or later.
The previous version, jV version 4.0, can run with JRE 1.4 and 1.5.
* [http://ef-site.hgc.jp/jV/stable/jV_4_0.jnlp jV 4.0]

== Basic Usage ==
You can execute basic operations such as rotation and translation with mouse action. Major actions are described in the following table:
{| style="margin:auto;border:1px solid gray"
! rowspan="2" style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap;font-weight:bold" |Action
! colspan="2" style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap;font-weight:bold" |Mouse Operation
|-
! style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap;font-weight:bold" |Windows, Linux
! style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap;font-weight:bold" |Mac OS X
|-
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |rotate around X (horizontal) axis&lt;br /&gt;rotate around Y (vertical) axis
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |left drag
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |drag
|-
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |translate along X axis (holizontally)&lt;br /&gt;translate along Y axis (vertically)
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |right drag
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |Command + drag
|-
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |translate along Z axis (zoom in/out)
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |Shift + left drag
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |Shift + drag
|}

Operations such as changing display models and colors and saving the image, can be executed with a menu. The location of the menu is at the top of the application window in Windows and at the top of screen in Mac as the stand-alone application. As an applet usage, a popup menu appears by clicking the right mouse button on the display screen, or clicking with a "Command" button in case of Mac.

{| style="margin:auto;border:0"
|-
| [[File:Jv_menu_win.png|The location of menu in jV stand-alone version in Windows.|250px]]
| [[File:Jv_menu_mac.png|The location of menu in jV stand-alone version in Mac.|250px]]
| [[File:popupmenu_en.png|The location of menu in applet version.|250px]]
|-
| style="text-align:center" |Stand-alone (Windows)
| style="text-align:center" |Stand-alone (Mac)
| style="text-align:center" |Applet
|}

Basic menu operations are following (see also [[GUI]] for details):

{| style="margin:auto;border:1px solid gray;border-collapse:collapse"
! style="padding:0 0.5em;border:1px solid gray" | Operations
! style="padding:0 0.5em;border:1px solid gray" | Menu location
|-
| style="padding:0 0.5em;border:1px solid gray" | Save a static image
| style="padding:0 0.5em;border:1px solid gray" | [File]-[Save]-[PNG/JPEG]
|-
| style="padding:0 0.5em;border:1px solid gray" | Change the expression format
| style="padding:0 0.5em;border:1px solid gray" | [File]-[Display]-[Wireframe/Backbone/Sticks/Spacefill/Ball&amp;amp;Stick/Ribbons/Cartoon]
|-
| style="padding:0 0.5em;border:1px solid gray" | Change the color
| style="padding:0 0.5em;border:1px solid gray" | [File]-[Colors]-[Monochrome/CPK/Shapely/Group/Chain/Temperature/Structure/Charge/Amino]
|}

To execute more complicated operation such as diplaying some piece of the molecule or changing some part of molecule in another style, use command line operation.

See also [[#Other resources]] for details:


== Download ==
You can also download the program and start it up locally.
In this case, installing JOGL is required in advance (see [[Installation_of_jV3 | Installation]] page).
The following links take you to the download pages. (latest version is 4.2.1@2012/12/11)
* [http://ef-site.hgc.jp/eF-site/servlet/DownloadViewerBinary binary (4.2.1)] 
* [http://ef-site.hgc.jp/eF-site/servlet/Registration source code (4.2.1)] (registration will be required)

== Other resources ==
* [http://ef-site.hgc.jp/eF-site/jV/jV_manual.html Manual] (html in English)
* [[How_to_use]] (in this site in English)
* [http://www.pdbj.org/jv/manual/index_ja.html Manual] (html in Japanese)
* [http://www.pdbj.org/jv/manual/jV_manual.pdf Manual] (pdf in English, for ver. 3.3)
* [http://ef-site.hgc.jp/eF-site/jV/jV3_User'sGuide.pdf User's guide] (for ver. 3.8.3 in English)</text>
    <sha1>2e7e2a31f8ec5a85b9e3692a150e24c030437922</sha1>
  </revision>
  <revision>
    <id>524</id>
    <parentid>510</parentid>
    <timestamp>2013-03-06T01:06:59Z</timestamp>
    <contributor>
      <username>IMSsato</username>
      <id>4</id>
    </contributor>
    <comment>/* Start up */</comment>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="6590" xml:space="preserve">&lt;big&gt;'''Welcome to jV wiki.'''&lt;/big&gt;

jV (formerly known as PDBjViewer) is a program to display molecular graphics of protein and nucleic acids. 
jV supports the following features:
* jV can read and display PDBML files, the canonical XML format for the Protein Data Bank.
* Of course, jV can read and display the traditional PDB format files, too.
* RasMol-like usability.
* jV can process more than one molecules.
* jV can display polygons specified by XML. ([http://www.pdbj.org/jv/polygonSchema XML Schema for polygons] is available.)
* Multiple polygons can be processed simultaneously, and be superimposed onto molecular images.
* Animation can be realized.
* jV runs on the Java Runtime Environment ([http://java.sun.com/javase/index.jsp JRE]) so that it can work as a stand-alone application as well as an applet.
* The graphics of jV is based on OpenGL ([http://jogamp.org/jogl/www/ JOGL]), thereby producing fairly beautiful pictures.


The program 'jV' has been developed by [http://www.hgc.jp/~kinosita/TOP.html Kengo Kinoshita] ([http://www.is.tohoku.ac.jp/index-e.html Graduate School of Information Sciences], [http://www.tohoku.ac.jp/english/ Tohoku University]) and [http://www.protein.osaka-u.ac.jp/rcsfp/pi/ Haruki Nakamura] ([http://www.protein.osaka-u.ac.jp/index_e.php Institute for Protein Research], [http://www.osaka-u.ac.jp/eng/index.html Osaka Univeristy]), with the support from [http://biosciencedbc.jp/ JST-NBDC] and [http://www.osaka-u.ac.jp/ Osaka University].
      

&lt;gallery&gt;
File:Spacefill.jpg
File:Cartoon.jpg
File:Surface.jpg
File:edmap.jpg
&lt;/gallery&gt;


== Start up ==
You can start up jV (4.3) with Java Web Start technology immediately from here.
* [http://ef-site.hgc.jp/eF-site/servlet/stable/jV.jnlp stable JOGL version] (recommended)
* [http://ef-site.hgc.jp/eF-site/servlet/current/jV.jnlp recent JOGL version]
The current jV requires JRE 1.6 or later.
The previous version, jV version 4.0, can run with JRE 1.4 and 1.5.
* [http://ef-site.hgc.jp/jV/stable/jV_4_0.jnlp jV 4.0]

== Basic Usage ==
You can execute basic operations such as rotation and translation with mouse action. Major actions are described in the following table:
{| style="margin:auto;border:1px solid gray"
! rowspan="2" style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap;font-weight:bold" |Action
! colspan="2" style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap;font-weight:bold" |Mouse Operation
|-
! style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap;font-weight:bold" |Windows, Linux
! style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap;font-weight:bold" |Mac OS X
|-
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |rotate around X (horizontal) axis&lt;br /&gt;rotate around Y (vertical) axis
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |left drag
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |drag
|-
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |translate along X axis (holizontally)&lt;br /&gt;translate along Y axis (vertically)
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |right drag
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |Command + drag
|-
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |translate along Z axis (zoom in/out)
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |Shift + left drag
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |Shift + drag
|}

Operations such as changing display models and colors and saving the image, can be executed with a menu. The location of the menu is at the top of the application window in Windows and at the top of screen in Mac as the stand-alone application. As an applet usage, a popup menu appears by clicking the right mouse button on the display screen, or clicking with a "Command" button in case of Mac.

{| style="margin:auto;border:0"
|-
| [[File:Jv_menu_win.png|The location of menu in jV stand-alone version in Windows.|250px]]
| [[File:Jv_menu_mac.png|The location of menu in jV stand-alone version in Mac.|250px]]
| [[File:popupmenu_en.png|The location of menu in applet version.|250px]]
|-
| style="text-align:center" |Stand-alone (Windows)
| style="text-align:center" |Stand-alone (Mac)
| style="text-align:center" |Applet
|}

Basic menu operations are following (see also [[GUI]] for details):

{| style="margin:auto;border:1px solid gray;border-collapse:collapse"
! style="padding:0 0.5em;border:1px solid gray" | Operations
! style="padding:0 0.5em;border:1px solid gray" | Menu location
|-
| style="padding:0 0.5em;border:1px solid gray" | Save a static image
| style="padding:0 0.5em;border:1px solid gray" | [File]-[Save]-[PNG/JPEG]
|-
| style="padding:0 0.5em;border:1px solid gray" | Change the expression format
| style="padding:0 0.5em;border:1px solid gray" | [File]-[Display]-[Wireframe/Backbone/Sticks/Spacefill/Ball&amp;amp;Stick/Ribbons/Cartoon]
|-
| style="padding:0 0.5em;border:1px solid gray" | Change the color
| style="padding:0 0.5em;border:1px solid gray" | [File]-[Colors]-[Monochrome/CPK/Shapely/Group/Chain/Temperature/Structure/Charge/Amino]
|}

To execute more complicated operation such as diplaying some piece of the molecule or changing some part of molecule in another style, use command line operation.

See also [[#Other resources]] for details:


== Download ==
You can also download the program and start it up locally.
In this case, installing JOGL is required in advance (see [[Installation_of_jV3 | Installation]] page).
The following links take you to the download pages. (latest version is 4.2.1@2012/12/11)
* [http://ef-site.hgc.jp/eF-site/servlet/DownloadViewerBinary binary (4.2.1)] 
* [http://ef-site.hgc.jp/eF-site/servlet/Registration source code (4.2.1)] (registration will be required)

== Other resources ==
* [http://ef-site.hgc.jp/eF-site/jV/jV_manual.html Manual] (html in English)
* [[How_to_use]] (in this site in English)
* [http://www.pdbj.org/jv/manual/index_ja.html Manual] (html in Japanese)
* [http://www.pdbj.org/jv/manual/jV_manual.pdf Manual] (pdf in English, for ver. 3.3)
* [http://ef-site.hgc.jp/eF-site/jV/jV3_User'sGuide.pdf User's guide] (for ver. 3.8.3 in English)</text>
    <sha1>8a4cc438eb3f13d503572f990bd39e16a029510c</sha1>
  </revision>
  <revision>
    <id>525</id>
    <parentid>524</parentid>
    <timestamp>2013-03-06T01:07:26Z</timestamp>
    <contributor>
      <username>IMSsato</username>
      <id>4</id>
    </contributor>
    <comment>/* Download */</comment>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="6582" xml:space="preserve">&lt;big&gt;'''Welcome to jV wiki.'''&lt;/big&gt;

jV (formerly known as PDBjViewer) is a program to display molecular graphics of protein and nucleic acids. 
jV supports the following features:
* jV can read and display PDBML files, the canonical XML format for the Protein Data Bank.
* Of course, jV can read and display the traditional PDB format files, too.
* RasMol-like usability.
* jV can process more than one molecules.
* jV can display polygons specified by XML. ([http://www.pdbj.org/jv/polygonSchema XML Schema for polygons] is available.)
* Multiple polygons can be processed simultaneously, and be superimposed onto molecular images.
* Animation can be realized.
* jV runs on the Java Runtime Environment ([http://java.sun.com/javase/index.jsp JRE]) so that it can work as a stand-alone application as well as an applet.
* The graphics of jV is based on OpenGL ([http://jogamp.org/jogl/www/ JOGL]), thereby producing fairly beautiful pictures.


The program 'jV' has been developed by [http://www.hgc.jp/~kinosita/TOP.html Kengo Kinoshita] ([http://www.is.tohoku.ac.jp/index-e.html Graduate School of Information Sciences], [http://www.tohoku.ac.jp/english/ Tohoku University]) and [http://www.protein.osaka-u.ac.jp/rcsfp/pi/ Haruki Nakamura] ([http://www.protein.osaka-u.ac.jp/index_e.php Institute for Protein Research], [http://www.osaka-u.ac.jp/eng/index.html Osaka Univeristy]), with the support from [http://biosciencedbc.jp/ JST-NBDC] and [http://www.osaka-u.ac.jp/ Osaka University].
      

&lt;gallery&gt;
File:Spacefill.jpg
File:Cartoon.jpg
File:Surface.jpg
File:edmap.jpg
&lt;/gallery&gt;


== Start up ==
You can start up jV (4.3) with Java Web Start technology immediately from here.
* [http://ef-site.hgc.jp/eF-site/servlet/stable/jV.jnlp stable JOGL version] (recommended)
* [http://ef-site.hgc.jp/eF-site/servlet/current/jV.jnlp recent JOGL version]
The current jV requires JRE 1.6 or later.
The previous version, jV version 4.0, can run with JRE 1.4 and 1.5.
* [http://ef-site.hgc.jp/jV/stable/jV_4_0.jnlp jV 4.0]

== Basic Usage ==
You can execute basic operations such as rotation and translation with mouse action. Major actions are described in the following table:
{| style="margin:auto;border:1px solid gray"
! rowspan="2" style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap;font-weight:bold" |Action
! colspan="2" style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap;font-weight:bold" |Mouse Operation
|-
! style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap;font-weight:bold" |Windows, Linux
! style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap;font-weight:bold" |Mac OS X
|-
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |rotate around X (horizontal) axis&lt;br /&gt;rotate around Y (vertical) axis
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |left drag
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |drag
|-
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |translate along X axis (holizontally)&lt;br /&gt;translate along Y axis (vertically)
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |right drag
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |Command + drag
|-
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |translate along Z axis (zoom in/out)
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |Shift + left drag
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |Shift + drag
|}

Operations such as changing display models and colors and saving the image, can be executed with a menu. The location of the menu is at the top of the application window in Windows and at the top of screen in Mac as the stand-alone application. As an applet usage, a popup menu appears by clicking the right mouse button on the display screen, or clicking with a "Command" button in case of Mac.

{| style="margin:auto;border:0"
|-
| [[File:Jv_menu_win.png|The location of menu in jV stand-alone version in Windows.|250px]]
| [[File:Jv_menu_mac.png|The location of menu in jV stand-alone version in Mac.|250px]]
| [[File:popupmenu_en.png|The location of menu in applet version.|250px]]
|-
| style="text-align:center" |Stand-alone (Windows)
| style="text-align:center" |Stand-alone (Mac)
| style="text-align:center" |Applet
|}

Basic menu operations are following (see also [[GUI]] for details):

{| style="margin:auto;border:1px solid gray;border-collapse:collapse"
! style="padding:0 0.5em;border:1px solid gray" | Operations
! style="padding:0 0.5em;border:1px solid gray" | Menu location
|-
| style="padding:0 0.5em;border:1px solid gray" | Save a static image
| style="padding:0 0.5em;border:1px solid gray" | [File]-[Save]-[PNG/JPEG]
|-
| style="padding:0 0.5em;border:1px solid gray" | Change the expression format
| style="padding:0 0.5em;border:1px solid gray" | [File]-[Display]-[Wireframe/Backbone/Sticks/Spacefill/Ball&amp;amp;Stick/Ribbons/Cartoon]
|-
| style="padding:0 0.5em;border:1px solid gray" | Change the color
| style="padding:0 0.5em;border:1px solid gray" | [File]-[Colors]-[Monochrome/CPK/Shapely/Group/Chain/Temperature/Structure/Charge/Amino]
|}

To execute more complicated operation such as diplaying some piece of the molecule or changing some part of molecule in another style, use command line operation.

See also [[#Other resources]] for details:


== Download ==
You can also download the program and start it up locally.
In this case, installing JOGL is required in advance (see [[Installation_of_jV3 | Installation]] page).
The following links take you to the download pages. (latest version is 4.3@2013/3/6)
* [http://ef-site.hgc.jp/eF-site/servlet/DownloadViewerBinary binary (4.3)] 
* [http://ef-site.hgc.jp/eF-site/servlet/Registration source code (4.3)] (registration will be required)

== Other resources ==
* [http://ef-site.hgc.jp/eF-site/jV/jV_manual.html Manual] (html in English)
* [[How_to_use]] (in this site in English)
* [http://www.pdbj.org/jv/manual/index_ja.html Manual] (html in Japanese)
* [http://www.pdbj.org/jv/manual/jV_manual.pdf Manual] (pdf in English, for ver. 3.3)
* [http://ef-site.hgc.jp/eF-site/jV/jV3_User'sGuide.pdf User's guide] (for ver. 3.8.3 in English)</text>
    <sha1>69ba93407c963556b4a2119dea4b47bb7f6a849f</sha1>
  </revision>
  <revision>
    <id>527</id>
    <parentid>525</parentid>
    <timestamp>2013-03-14T03:28:56Z</timestamp>
    <contributor>
      <username>IMSsato</username>
      <id>4</id>
    </contributor>
    <comment>/* Start up */</comment>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="6584" xml:space="preserve">&lt;big&gt;'''Welcome to jV wiki.'''&lt;/big&gt;

jV (formerly known as PDBjViewer) is a program to display molecular graphics of protein and nucleic acids. 
jV supports the following features:
* jV can read and display PDBML files, the canonical XML format for the Protein Data Bank.
* Of course, jV can read and display the traditional PDB format files, too.
* RasMol-like usability.
* jV can process more than one molecules.
* jV can display polygons specified by XML. ([http://www.pdbj.org/jv/polygonSchema XML Schema for polygons] is available.)
* Multiple polygons can be processed simultaneously, and be superimposed onto molecular images.
* Animation can be realized.
* jV runs on the Java Runtime Environment ([http://java.sun.com/javase/index.jsp JRE]) so that it can work as a stand-alone application as well as an applet.
* The graphics of jV is based on OpenGL ([http://jogamp.org/jogl/www/ JOGL]), thereby producing fairly beautiful pictures.


The program 'jV' has been developed by [http://www.hgc.jp/~kinosita/TOP.html Kengo Kinoshita] ([http://www.is.tohoku.ac.jp/index-e.html Graduate School of Information Sciences], [http://www.tohoku.ac.jp/english/ Tohoku University]) and [http://www.protein.osaka-u.ac.jp/rcsfp/pi/ Haruki Nakamura] ([http://www.protein.osaka-u.ac.jp/index_e.php Institute for Protein Research], [http://www.osaka-u.ac.jp/eng/index.html Osaka Univeristy]), with the support from [http://biosciencedbc.jp/ JST-NBDC] and [http://www.osaka-u.ac.jp/ Osaka University].
      

&lt;gallery&gt;
File:Spacefill.jpg
File:Cartoon.jpg
File:Surface.jpg
File:edmap.jpg
&lt;/gallery&gt;


== Start up ==
You can start up jV (4.3.1) with Java Web Start technology immediately from here.
* [http://ef-site.hgc.jp/eF-site/servlet/stable/jV.jnlp stable JOGL version] (recommended)
* [http://ef-site.hgc.jp/eF-site/servlet/current/jV.jnlp recent JOGL version]
The current jV requires JRE 1.6 or later.
The previous version, jV version 4.0, can run with JRE 1.4 and 1.5.
* [http://ef-site.hgc.jp/jV/stable/jV_4_0.jnlp jV 4.0]

== Basic Usage ==
You can execute basic operations such as rotation and translation with mouse action. Major actions are described in the following table:
{| style="margin:auto;border:1px solid gray"
! rowspan="2" style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap;font-weight:bold" |Action
! colspan="2" style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap;font-weight:bold" |Mouse Operation
|-
! style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap;font-weight:bold" |Windows, Linux
! style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap;font-weight:bold" |Mac OS X
|-
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |rotate around X (horizontal) axis&lt;br /&gt;rotate around Y (vertical) axis
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |left drag
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |drag
|-
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |translate along X axis (holizontally)&lt;br /&gt;translate along Y axis (vertically)
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |right drag
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |Command + drag
|-
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |translate along Z axis (zoom in/out)
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |Shift + left drag
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |Shift + drag
|}

Operations such as changing display models and colors and saving the image, can be executed with a menu. The location of the menu is at the top of the application window in Windows and at the top of screen in Mac as the stand-alone application. As an applet usage, a popup menu appears by clicking the right mouse button on the display screen, or clicking with a "Command" button in case of Mac.

{| style="margin:auto;border:0"
|-
| [[File:Jv_menu_win.png|The location of menu in jV stand-alone version in Windows.|250px]]
| [[File:Jv_menu_mac.png|The location of menu in jV stand-alone version in Mac.|250px]]
| [[File:popupmenu_en.png|The location of menu in applet version.|250px]]
|-
| style="text-align:center" |Stand-alone (Windows)
| style="text-align:center" |Stand-alone (Mac)
| style="text-align:center" |Applet
|}

Basic menu operations are following (see also [[GUI]] for details):

{| style="margin:auto;border:1px solid gray;border-collapse:collapse"
! style="padding:0 0.5em;border:1px solid gray" | Operations
! style="padding:0 0.5em;border:1px solid gray" | Menu location
|-
| style="padding:0 0.5em;border:1px solid gray" | Save a static image
| style="padding:0 0.5em;border:1px solid gray" | [File]-[Save]-[PNG/JPEG]
|-
| style="padding:0 0.5em;border:1px solid gray" | Change the expression format
| style="padding:0 0.5em;border:1px solid gray" | [File]-[Display]-[Wireframe/Backbone/Sticks/Spacefill/Ball&amp;amp;Stick/Ribbons/Cartoon]
|-
| style="padding:0 0.5em;border:1px solid gray" | Change the color
| style="padding:0 0.5em;border:1px solid gray" | [File]-[Colors]-[Monochrome/CPK/Shapely/Group/Chain/Temperature/Structure/Charge/Amino]
|}

To execute more complicated operation such as diplaying some piece of the molecule or changing some part of molecule in another style, use command line operation.

See also [[#Other resources]] for details:


== Download ==
You can also download the program and start it up locally.
In this case, installing JOGL is required in advance (see [[Installation_of_jV3 | Installation]] page).
The following links take you to the download pages. (latest version is 4.3@2013/3/6)
* [http://ef-site.hgc.jp/eF-site/servlet/DownloadViewerBinary binary (4.3)] 
* [http://ef-site.hgc.jp/eF-site/servlet/Registration source code (4.3)] (registration will be required)

== Other resources ==
* [http://ef-site.hgc.jp/eF-site/jV/jV_manual.html Manual] (html in English)
* [[How_to_use]] (in this site in English)
* [http://www.pdbj.org/jv/manual/index_ja.html Manual] (html in Japanese)
* [http://www.pdbj.org/jv/manual/jV_manual.pdf Manual] (pdf in English, for ver. 3.3)
* [http://ef-site.hgc.jp/eF-site/jV/jV3_User'sGuide.pdf User's guide] (for ver. 3.8.3 in English)</text>
    <sha1>54b94a829ea374a8c74764f35802021e4f8abfda</sha1>
  </revision>
  <revision>
    <id>528</id>
    <parentid>527</parentid>
    <timestamp>2013-03-14T03:29:15Z</timestamp>
    <contributor>
      <username>IMSsato</username>
      <id>4</id>
    </contributor>
    <comment>/* Download */</comment>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="6591" xml:space="preserve">&lt;big&gt;'''Welcome to jV wiki.'''&lt;/big&gt;

jV (formerly known as PDBjViewer) is a program to display molecular graphics of protein and nucleic acids. 
jV supports the following features:
* jV can read and display PDBML files, the canonical XML format for the Protein Data Bank.
* Of course, jV can read and display the traditional PDB format files, too.
* RasMol-like usability.
* jV can process more than one molecules.
* jV can display polygons specified by XML. ([http://www.pdbj.org/jv/polygonSchema XML Schema for polygons] is available.)
* Multiple polygons can be processed simultaneously, and be superimposed onto molecular images.
* Animation can be realized.
* jV runs on the Java Runtime Environment ([http://java.sun.com/javase/index.jsp JRE]) so that it can work as a stand-alone application as well as an applet.
* The graphics of jV is based on OpenGL ([http://jogamp.org/jogl/www/ JOGL]), thereby producing fairly beautiful pictures.


The program 'jV' has been developed by [http://www.hgc.jp/~kinosita/TOP.html Kengo Kinoshita] ([http://www.is.tohoku.ac.jp/index-e.html Graduate School of Information Sciences], [http://www.tohoku.ac.jp/english/ Tohoku University]) and [http://www.protein.osaka-u.ac.jp/rcsfp/pi/ Haruki Nakamura] ([http://www.protein.osaka-u.ac.jp/index_e.php Institute for Protein Research], [http://www.osaka-u.ac.jp/eng/index.html Osaka Univeristy]), with the support from [http://biosciencedbc.jp/ JST-NBDC] and [http://www.osaka-u.ac.jp/ Osaka University].
      

&lt;gallery&gt;
File:Spacefill.jpg
File:Cartoon.jpg
File:Surface.jpg
File:edmap.jpg
&lt;/gallery&gt;


== Start up ==
You can start up jV (4.3.1) with Java Web Start technology immediately from here.
* [http://ef-site.hgc.jp/eF-site/servlet/stable/jV.jnlp stable JOGL version] (recommended)
* [http://ef-site.hgc.jp/eF-site/servlet/current/jV.jnlp recent JOGL version]
The current jV requires JRE 1.6 or later.
The previous version, jV version 4.0, can run with JRE 1.4 and 1.5.
* [http://ef-site.hgc.jp/jV/stable/jV_4_0.jnlp jV 4.0]

== Basic Usage ==
You can execute basic operations such as rotation and translation with mouse action. Major actions are described in the following table:
{| style="margin:auto;border:1px solid gray"
! rowspan="2" style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap;font-weight:bold" |Action
! colspan="2" style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap;font-weight:bold" |Mouse Operation
|-
! style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap;font-weight:bold" |Windows, Linux
! style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap;font-weight:bold" |Mac OS X
|-
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |rotate around X (horizontal) axis&lt;br /&gt;rotate around Y (vertical) axis
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |left drag
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |drag
|-
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |translate along X axis (holizontally)&lt;br /&gt;translate along Y axis (vertically)
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |right drag
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |Command + drag
|-
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |translate along Z axis (zoom in/out)
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |Shift + left drag
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |Shift + drag
|}

Operations such as changing display models and colors and saving the image, can be executed with a menu. The location of the menu is at the top of the application window in Windows and at the top of screen in Mac as the stand-alone application. As an applet usage, a popup menu appears by clicking the right mouse button on the display screen, or clicking with a "Command" button in case of Mac.

{| style="margin:auto;border:0"
|-
| [[File:Jv_menu_win.png|The location of menu in jV stand-alone version in Windows.|250px]]
| [[File:Jv_menu_mac.png|The location of menu in jV stand-alone version in Mac.|250px]]
| [[File:popupmenu_en.png|The location of menu in applet version.|250px]]
|-
| style="text-align:center" |Stand-alone (Windows)
| style="text-align:center" |Stand-alone (Mac)
| style="text-align:center" |Applet
|}

Basic menu operations are following (see also [[GUI]] for details):

{| style="margin:auto;border:1px solid gray;border-collapse:collapse"
! style="padding:0 0.5em;border:1px solid gray" | Operations
! style="padding:0 0.5em;border:1px solid gray" | Menu location
|-
| style="padding:0 0.5em;border:1px solid gray" | Save a static image
| style="padding:0 0.5em;border:1px solid gray" | [File]-[Save]-[PNG/JPEG]
|-
| style="padding:0 0.5em;border:1px solid gray" | Change the expression format
| style="padding:0 0.5em;border:1px solid gray" | [File]-[Display]-[Wireframe/Backbone/Sticks/Spacefill/Ball&amp;amp;Stick/Ribbons/Cartoon]
|-
| style="padding:0 0.5em;border:1px solid gray" | Change the color
| style="padding:0 0.5em;border:1px solid gray" | [File]-[Colors]-[Monochrome/CPK/Shapely/Group/Chain/Temperature/Structure/Charge/Amino]
|}

To execute more complicated operation such as diplaying some piece of the molecule or changing some part of molecule in another style, use command line operation.

See also [[#Other resources]] for details:


== Download ==
You can also download the program and start it up locally.
In this case, installing JOGL is required in advance (see [[Installation_of_jV3 | Installation]] page).
The following links take you to the download pages. (latest version is 4.3.1@2013/3/14)
* [http://ef-site.hgc.jp/eF-site/servlet/DownloadViewerBinary binary (4.3.1)] 
* [http://ef-site.hgc.jp/eF-site/servlet/Registration source code (4.3.1)] (registration will be required)

== Other resources ==
* [http://ef-site.hgc.jp/eF-site/jV/jV_manual.html Manual] (html in English)
* [[How_to_use]] (in this site in English)
* [http://www.pdbj.org/jv/manual/index_ja.html Manual] (html in Japanese)
* [http://www.pdbj.org/jv/manual/jV_manual.pdf Manual] (pdf in English, for ver. 3.3)
* [http://ef-site.hgc.jp/eF-site/jV/jV3_User'sGuide.pdf User's guide] (for ver. 3.8.3 in English)</text>
    <sha1>1639320e7568d22b20ae430f20fde559695153d0</sha1>
  </revision>
  <revision>
    <id>542</id>
    <parentid>528</parentid>
    <timestamp>2013-05-28T06:14:28Z</timestamp>
    <contributor>
      <username>IMSsato</username>
      <id>4</id>
    </contributor>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="6620" xml:space="preserve">&lt;big&gt;'''Welcome to jV wiki.'''&lt;/big&gt;

jV (formerly known as PDBjViewer) is a program to display molecular graphics of protein and nucleic acids. 
jV supports the following features:
* jV can read and display PDBML files, the canonical XML format for the Protein Data Bank.
* Of course, jV can read and display the traditional PDB format files, too.
* RasMol-like usability.
* jV can process more than one molecules.
* jV can display polygons specified by XML. ([http://www.pdbj.org/jv/polygonSchema XML Schema for polygons] is available.)
* Multiple polygons can be processed simultaneously, and be superimposed onto molecular images.
* Animation can be realized.
* jV runs on the Java Runtime Environment ([http://www.oracle.com/technetwork/java/javase/overview/index.html JRE]) so that it can work as a stand-alone application as well as an applet.
* The graphics of jV is based on OpenGL ([http://jogamp.org/jogl/www/ JOGL]), thereby producing fairly beautiful pictures.


The program 'jV' has been developed by [http://www.hgc.jp/~kinosita/TOP.html Kengo Kinoshita] ([http://www.is.tohoku.ac.jp/index-e.html Graduate School of Information Sciences], [http://www.tohoku.ac.jp/english/ Tohoku University]) and [http://www.protein.osaka-u.ac.jp/rcsfp/pi/ Haruki Nakamura] ([http://www.protein.osaka-u.ac.jp/index_e.php Institute for Protein Research], [http://www.osaka-u.ac.jp/eng/index.html Osaka Univeristy]), with the support from [http://biosciencedbc.jp/ JST-NBDC] and [http://www.osaka-u.ac.jp/ Osaka University].
      

&lt;gallery&gt;
File:Spacefill.jpg
File:Cartoon.jpg
File:Surface.jpg
File:edmap.jpg
&lt;/gallery&gt;


== Start up ==
You can start up jV (4.3.1) with Java Web Start technology immediately from here.
* [http://ef-site.hgc.jp/eF-site/servlet/stable/jV.jnlp stable JOGL version] (recommended)
* [http://ef-site.hgc.jp/eF-site/servlet/current/jV.jnlp recent JOGL version]
The current jV requires JRE 1.6 or later.
The previous version, jV version 4.0, can run with JRE 1.4 and 1.5.
* [http://ef-site.hgc.jp/jV/stable/jV_4_0.jnlp jV 4.0]

== Basic Usage ==
You can execute basic operations such as rotation and translation with mouse action. Major actions are described in the following table:
{| style="margin:auto;border:1px solid gray"
! rowspan="2" style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap;font-weight:bold" |Action
! colspan="2" style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap;font-weight:bold" |Mouse Operation
|-
! style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap;font-weight:bold" |Windows, Linux
! style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap;font-weight:bold" |Mac OS X
|-
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |rotate around X (horizontal) axis&lt;br /&gt;rotate around Y (vertical) axis
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |left drag
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |drag
|-
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |translate along X axis (holizontally)&lt;br /&gt;translate along Y axis (vertically)
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |right drag
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |Command + drag
|-
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |translate along Z axis (zoom in/out)
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |Shift + left drag
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |Shift + drag
|}

Operations such as changing display models and colors and saving the image, can be executed with a menu. The location of the menu is at the top of the application window in Windows and at the top of screen in Mac as the stand-alone application. As an applet usage, a popup menu appears by clicking the right mouse button on the display screen, or clicking with a "Command" button in case of Mac.

{| style="margin:auto;border:0"
|-
| [[File:Jv_menu_win.png|The location of menu in jV stand-alone version in Windows.|250px]]
| [[File:Jv_menu_mac.png|The location of menu in jV stand-alone version in Mac.|250px]]
| [[File:popupmenu_en.png|The location of menu in applet version.|250px]]
|-
| style="text-align:center" |Stand-alone (Windows)
| style="text-align:center" |Stand-alone (Mac)
| style="text-align:center" |Applet
|}

Basic menu operations are following (see also [[GUI]] for details):

{| style="margin:auto;border:1px solid gray;border-collapse:collapse"
! style="padding:0 0.5em;border:1px solid gray" | Operations
! style="padding:0 0.5em;border:1px solid gray" | Menu location
|-
| style="padding:0 0.5em;border:1px solid gray" | Save a static image
| style="padding:0 0.5em;border:1px solid gray" | [File]-[Save]-[PNG/JPEG]
|-
| style="padding:0 0.5em;border:1px solid gray" | Change the expression format
| style="padding:0 0.5em;border:1px solid gray" | [File]-[Display]-[Wireframe/Backbone/Sticks/Spacefill/Ball&amp;amp;Stick/Ribbons/Cartoon]
|-
| style="padding:0 0.5em;border:1px solid gray" | Change the color
| style="padding:0 0.5em;border:1px solid gray" | [File]-[Colors]-[Monochrome/CPK/Shapely/Group/Chain/Temperature/Structure/Charge/Amino]
|}

To execute more complicated operation such as diplaying some piece of the molecule or changing some part of molecule in another style, use command line operation.

See also [[#Other resources]] for details:


== Download ==
You can also download the program and start it up locally.
In this case, installing JOGL is required in advance (see [[Installation_of_jV3 | Installation]] page).
The following links take you to the download pages. (latest version is 4.3.1@2013/3/14)
* [http://ef-site.hgc.jp/eF-site/servlet/DownloadViewerBinary binary (4.3.1)] 
* [http://ef-site.hgc.jp/eF-site/servlet/Registration source code (4.3.1)] (registration will be required)

== Other resources ==
* [http://ef-site.hgc.jp/eF-site/jV/jV_manual.html Manual] (html in English)
* [[How_to_use]] (in this site in English)
* [http://www.pdbj.org/jv/manual/index_ja.html Manual] (html in Japanese)
* [http://www.pdbj.org/jv/manual/jV_manual.pdf Manual] (pdf in English, for ver. 3.3)
* [http://ef-site.hgc.jp/eF-site/jV/jV3_User'sGuide.pdf User's guide] (for ver. 3.8.3 in English)</text>
    <sha1>3bff0a9fb07c818c3607b83bdfaa016a935662ba</sha1>
  </revision>
  <revision>
    <id>553</id>
    <parentid>542</parentid>
    <timestamp>2014-04-16T02:49:53Z</timestamp>
    <contributor>
      <username>IMSsato</username>
      <id>4</id>
    </contributor>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="6709" xml:space="preserve">&lt;big&gt;'''Welcome to jV wiki.'''&lt;/big&gt;

jV (formerly known as PDBjViewer) is a program to display molecular graphics of protein and nucleic acids. 
jV supports the following features:
* jV can read and display PDBML files, the canonical XML format for the Protein Data Bank.
* Of course, jV can read and display the traditional PDB format files, too.
* RasMol-like usability.
* jV can process more than one molecules.
* jV can display polygons specified by XML. ([http://www.pdbj.org/jv/polygonSchema XML Schema for polygons] is available.)
* Multiple polygons can be processed simultaneously, and be superimposed onto molecular images.
* Animation can be realized.
* jV runs on the Java Runtime Environment ([http://www.oracle.com/technetwork/java/javase/overview/index.html JRE]) so that it can work as a stand-alone application as well as an applet.
* The graphics of jV is based on OpenGL ([http://jogamp.org/jogl/www/ JOGL]), thereby producing fairly beautiful pictures.


The program 'jV' has been developed by [http://www.hgc.jp/~kinosita/TOP.html Kengo Kinoshita] ([http://www.is.tohoku.ac.jp/index-e.html Graduate School of Information Sciences], [http://www.tohoku.ac.jp/english/ Tohoku University]) and [http://www.protein.osaka-u.ac.jp/rcsfp/pi/ Haruki Nakamura] ([http://www.protein.osaka-u.ac.jp/index_e.php Institute for Protein Research], [http://www.osaka-u.ac.jp/eng/index.html Osaka Univeristy]), with the support from [http://biosciencedbc.jp/ JST-NBDC] and [http://www.protein.osaka-u.ac.jp/index_e.php Institute for Protein Research IPR], [http://www.osaka-u.ac.jp/eng/index.html Osaka Univeristy].
      

&lt;gallery&gt;
File:Spacefill.jpg
File:Cartoon.jpg
File:Surface.jpg
File:edmap.jpg
&lt;/gallery&gt;


== Start up ==
You can start up jV (4.4) with Java Web Start technology immediately from here.
* [http://ef-site.hgc.jp/eF-site/servlet/stable/jV.jnlp stable JOGL version] (recommended)
* [http://ef-site.hgc.jp/eF-site/servlet/current/jV.jnlp recent JOGL version]
The current jV requires JRE 1.6 or later.
The previous version, jV version 4.0, can run with JRE 1.4 and 1.5.
* [http://ef-site.hgc.jp/jV/stable/jV_4_0.jnlp jV 4.0]

== Basic Usage ==
You can execute basic operations such as rotation and translation with mouse action. Major actions are described in the following table:
{| style="margin:auto;border:1px solid gray"
! rowspan="2" style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap;font-weight:bold" |Action
! colspan="2" style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap;font-weight:bold" |Mouse Operation
|-
! style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap;font-weight:bold" |Windows, Linux
! style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap;font-weight:bold" |Mac OS X
|-
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |rotate around X (horizontal) axis&lt;br /&gt;rotate around Y (vertical) axis
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |left drag
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |drag
|-
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |translate along X axis (holizontally)&lt;br /&gt;translate along Y axis (vertically)
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |right drag
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |Command + drag
|-
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |translate along Z axis (zoom in/out)
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |Shift + left drag
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |Shift + drag
|}

Operations such as changing display models and colors and saving the image, can be executed with a menu. The location of the menu is at the top of the application window in Windows and at the top of screen in Mac as the stand-alone application. As an applet usage, a popup menu appears by clicking the right mouse button on the display screen, or clicking with a "Command" button in case of Mac.

{| style="margin:auto;border:0"
|-
| [[File:Jv_menu_win.png|The location of menu in jV stand-alone version in Windows.|250px]]
| [[File:Jv_menu_mac.png|The location of menu in jV stand-alone version in Mac.|250px]]
| [[File:popupmenu_en.png|The location of menu in applet version.|250px]]
|-
| style="text-align:center" |Stand-alone (Windows)
| style="text-align:center" |Stand-alone (Mac)
| style="text-align:center" |Applet
|}

Basic menu operations are following (see also [[GUI]] for details):

{| style="margin:auto;border:1px solid gray;border-collapse:collapse"
! style="padding:0 0.5em;border:1px solid gray" | Operations
! style="padding:0 0.5em;border:1px solid gray" | Menu location
|-
| style="padding:0 0.5em;border:1px solid gray" | Save a static image
| style="padding:0 0.5em;border:1px solid gray" | [File]-[Save]-[PNG/JPEG]
|-
| style="padding:0 0.5em;border:1px solid gray" | Change the expression format
| style="padding:0 0.5em;border:1px solid gray" | [File]-[Display]-[Wireframe/Backbone/Sticks/Spacefill/Ball&amp;amp;Stick/Ribbons/Cartoon]
|-
| style="padding:0 0.5em;border:1px solid gray" | Change the color
| style="padding:0 0.5em;border:1px solid gray" | [File]-[Colors]-[Monochrome/CPK/Shapely/Group/Chain/Temperature/Structure/Charge/Amino]
|}

To execute more complicated operation such as diplaying some piece of the molecule or changing some part of molecule in another style, use command line operation.

See also [[#Other resources]] for details:


== Download ==
You can also download the program and start it up locally.
In this case, installing JOGL is required in advance (see [[Installation_of_jV3 | Installation]] page).
The following links take you to the download pages. (latest version is 4.4@2014/4/16)
* [http://ef-site.hgc.jp/eF-site/servlet/DownloadViewerBinary binary (4.4)] 
* [http://ef-site.hgc.jp/eF-site/servlet/Registration source code (4.4)] (registration will be required)

== Other resources ==
* [http://ef-site.hgc.jp/eF-site/jV/jV_manual.html Manual] (html in English)
* [[How_to_use]] (in this site in English)
* [http://www.pdbj.org/jv/manual/index_ja.html Manual] (html in Japanese)
* [http://www.pdbj.org/jv/manual/jV_manual.pdf Manual] (pdf in English, for ver. 3.3)
* [http://ef-site.hgc.jp/eF-site/jV/jV3_User'sGuide.pdf User's guide] (for ver. 3.8.3 in English)</text>
    <sha1>e61f0e9ff6dbc440013fb7d3cf9119583b46efd5</sha1>
  </revision>
</page>
<page arvcontinue="20120326072111|504">
  <title>Trouble shooting</title>
  <ns>0</ns>
  <id>48</id>
  <revision>
    <id>511</id>
    <parentid>494</parentid>
    <timestamp>2013-01-17T08:26:37Z</timestamp>
    <contributor>
      <username>Cudo29</username>
      <id>5</id>
    </contributor>
    <comment>/* The jV applet can't be displayed on Mac OS 10.7 or later when the java is updated to 1.6.0_37 */ Added.</comment>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="9027" xml:space="preserve">{| style="left"
 |__TOC__
 |}

== Certificate error on applet ==

When you use JRE6 Update15 (1.6.0_15) or JRE6 Update16 (1.6.0_16) on Windows or Linux,
jV applet and applet-launcher fail to start up with the following error.

 Error:java.io.IOException:Cannot find certificates for JNLP AppletLauncher class

Please use JRE6 Update17 (1.6.0_17) or later.

== JOGL library conflict ==

If you cannot start jV via Java Web Start or view jV applets due to a failure of locating the JOGL library, try the followings.

===clear cached files===

On JRE of version 1.6.0_15 and 1.6.0_16, previously cached JOGL files cause a problem
even if newer files are placed on the server.
JRE of version 1.6.0_17 or later is recommended.
On Mac OS X Snow Leopard, however, the latest JRE is of version 1.6.0_15 at the moment.
The following steps show how to clear cached files.

;1) Open the Java Preferences window
:Double-click the [Java Preferences] icon, then the Java Preferences window appears. The place of [Java Preferences] depends on the version of Mac OS as following:
:{|style="border:1px solid gray;border-collapse:collapse"
!style="border:1px solid gray;padding:0 0.5em;background-color:lightyellow"|Max OS X version
!style="border:1px solid gray;padding:0 0.5em;background-color:lightyellow"|place
|-
|style="border:1px solid gray;padding:0 0.5em"|10.4
|style="border:1px solid gray;padding:0 0.5em"|[Applications]-[Utilities]-[Java]-[J2SE 5.0]
|-
|style="border:1px solid gray;padding:0 0.5em"|10.5 (before installing Java for Mac OS X 10.5 Update 4)
|style="border:1px solid gray;padding:0 0.5em"|[Applications]-[Utilities]-[Java]
|-
|style="border:1px solid gray;padding:0 0.5em"|10.5 (after installing Java for Mac OS X 10.5 Update 4 or later)
|style="border:1px solid gray;padding:0 0.5em"|[Applications]-[Utilities]
|-
|style="border:1px solid gray;padding:0 0.5em"|10.6
|style="border:1px solid gray;padding:0 0.5em"|[Applications]-[Utilities]
|}
:The contents of the [Java Preferences] differ for the version of Mac OS. In case 10.4, use the [General] tab, which is default displayed. In case 10.5 or later, click to display [Network] tab.
:{|style="border:1px solid gray;border-collapse:collapse"
!style="border:1px solid gray;padding:0 0.5em;background-color:lightyellow"|Max OS X 10.4
!style="border:1px solid gray;padding:0 0.5em;background-color:lightyellow"|Max OS X 10.5 or later
|-
|style="border:1px solid gray;padding:0.5ex 0.5em;text-align:center;vertical-align:top"|[[File:Javapref_tiger.png|400px]]
|style="border:1px solid gray;padding:0.5ex 0.5em;text-align:center;vertical-align:top"|[[File:Java_prefs1.png|400px]]&lt;br/&gt;&amp;darr;&lt;br/&gt;[[File:Java_prefs2.png|400px]]
|}

;2) Press 'Delete Files...' button
:The [Delete Temporary Files] window, which asks which items are to remove, will be opened.

:[[File:Javacache_del_en.png]]

;3) Leave all the checkboxs on and click 'OK' button.

;4) In some case, restoring the Java environment to the default may be also required. 
:To do it, click "Restore Defaults" button in the Java Preferences (the following figure is the case of Mac OS X 10.6).
:[[File:Javapref_general_10_6.png]]

===remove local JOGL library===

Locally-installed JOGL libraries of different version cause conflicts with Java Web Start technology.
JOGL library files are different between operating systems.

'''Mac OS X'''

Open the [Macintosh HD]-[Library]-[Java]-[Extensions] folder.
If some of the following files

* jogl.jar
* gluegen-rt.jar
* libjogl.jnilib
* libjogl_awt.jnilib
* libjogl_cg.jnilib
* libgluegen-rt.jnilib

exist in the folder, remove them.
Here, this operation requires root privilege.

'''Windows'''

Files that should be removed are as follows.

* &lt;JRE&gt;\lib\ext\jogl.jar
* &lt;JRE&gt;\lib\ext\gluegen-rt.jar
* &lt;JRE&gt;\bin\jogl.dll
* &lt;JRE&gt;\bin\jogl_cg.dll
* &lt;JRE&gt;\bin\jogl_awt.dll
* &lt;JRE&gt;\bin\gluegen-rt.dll

Here, &lt;JRE&gt; denotes the folder that JRE has been installed; typically &lt;JRE&gt;=C:\Program Files\Java\jre6.

'''Linux'''

Files that should be removed are as follows.

* &lt;JRE&gt;/lib/ext/jogl.jar
* &lt;JRE&gt;/lib/ext/gluegen-rt.jar
* &lt;JRE&gt;/lib/&lt;arch&gt;/libjogl.so
* &lt;JRE&gt;/lib/&lt;arch&gt;/libjogl_cg.so
* &lt;JRE&gt;/lib/&lt;arch&gt;/libjogl_awt.so
* &lt;JRE&gt;/lib/&lt;arch&gt;/libjogl_drihack.so
* &lt;JRE&gt;/lib/&lt;arch&gt;/libgluegen-rt.so

Here, &lt;JRE&gt; denotes the directory that JRE has been installed; typically &lt;JRE&gt;=/usr/java/jdk1.6.0_17/jre,
and &lt;arch&gt; the processor architecture such as &lt;arch&gt;=i386.

== jV applet with Internet Explorer ==

When visiting a web page that contains a jV applet with Internet Explorer, there sometimes occurs trouble in working with native JOGL libraries especially on Windows Vista. Please use Firefox web browser in that case.

== Class not found error on applet ==

When you use JRE6 Update21 (1.6.0_21) with the next-generation Java Plug-in enabled on Windows or Linux, 
the following error occurs for the combination of jV applet and applet-launcher.

 Error: Class not found: org.pdbj.viewer.gui.ViewerApplet

You can avoid this problem by disabling the next-generation Java Plug-in.
[http://www.java.com/en/download/help/new_plugin.xml Here] is how to do that for Windows users.
On Linux platform, users can manually replace the symbolic link to new plug-in &lt;tt&gt;libnpjp2.so&lt;/tt&gt;
with the symbolic link to classic plug-in &lt;tt&gt;libjavaplugin_oji.so&lt;/tt&gt;
(see [http://www.oracle.com/technetwork/java/javase/manual-plugin-install-linux-136395.html this page] for help).
If you are using firefox 3.6 or later, however, you need to downgrade JRE to 1.6.0_20
because firefox of those versions run applets only with the new Java Plug-in.
To get JRE 1.6.0_20, see [https://cds.sun.com/is-bin/INTERSHOP.enfinity/WFS/CDS-CDS_Developer-Site/en_US/-/USD/ViewProductDetail-Start?ProductRef=jre-6u20-oth-JPR@CDS-CDS_Developer this page].


== The jV applet can't be displayed on Mac + Firefox/Safari/Google Chrome ==
The Mac OS and browser described below can't display jV applets.
To display them, please downgrade the browser or use another browser such as [http://www.opera.com/ Opera], [http://caminobrowser.org/ Camino], or [http://sourceforge.jp/projects/shiira/ Shiira].
We are sorry for the inconvenient.
;OS
:Mac OS X 10.5 update 4 or later
;Browser
* Firefox 6.0 or later
* Safari 5.1 or later
* Google Chrome
;Reason
:You can specify which Java Plug-in is to use at the Java Preferences. If you select 'In their own process' to use new Java Plug-in, and select 'Within the browser process' to use classic Java Plug-in. But none the less, Firefox 6.0 or later, Safari 5.1 or later and Google Chrome force to use new Java Plug-in. Currently the new Java Plug-in for Mac doesn't support hardware-accelerated technologies like JOGL and Java3D[http://developer.apple.com/library/mac/#releasenotes/CrossPlatform/JavaSnowLeopardUpdate2LeopardUpdate7RN/NewandNoteworthy/NewandNoteworthy.html#//apple_ref/doc/uid/TP40009967-CH4-SW1], so the jV applet under these environment can't be displayed.

* The Windows and Linux users don't affect this problem.
* The Firefox 5.0 or older can display jV applets even if on Mac OS.
* The Safari 5.0 or older can display jV applets even if on Mac OS.

'''Resolved''': jV version 4.1 runs on Mac + latest Firefox/Safari/Google Chrome .

== The jV applet can't be displayed on Mac with JRE 1.6.0_29 ==
The Mac OS with JRE6 Update29 (1.6.0_29) cannot display jV applets on any browser at the moment.
In JRE 1.6.0_29, the classic Java Plug-in has been removed and only new Java Plug-in is available. 
However, the current version of JOGL library does not work with the new Java Plug-in.
The issue will be resolved by the next release of JOGL library.
We are sorry for the inconvenience.

'''Resolved''': jV version 4.1 runs on Mac with JRE 1.6.0_29.


== The jV applet can't be displayed on Mac OS 10.7 or later when the java is updated to 1.6.0_37 ==

When you update your java to 1.6.0_37 on Mac OS 10.7 or later, following change will be adopted[http://support.apple.com/kb/HT5493]:

# All the java plug-ins for every web browser provided from Apple Inc. will be removed.
# The "Java Preferences" application will be removed.

You have to install JDK, not JRE manually, and then change a symbolic link to run jnlp 'javaws' as following[http://stackoverflow.com/questions/13405242/java-web-start-in-10-8-2-with-native-apple-java-1-6-cant-find-jre]:

 &lt;span style="color:gray"&gt;mac:~ user$ &lt;/span&gt;which javaws
 &lt;span style="color:blue"&gt;/usr/bin/javaws&lt;/span&gt;
 &lt;span style="color:gray"&gt;mac:~ user$ &lt;/span&gt;ls -l /usr/bin/javaws
 &lt;span style="color:blue"&gt;lrwxr-xr-x  1 root  wheel  76 12  3 14:48 /usr/bin/javaws
    -&gt; /System/Library/Frameworks/JavaVM.framework/Versions/Current/Commands/javaws&lt;/span&gt;
 &lt;span style="color:gray"&gt;mac:~ user$ &lt;/span&gt;ln -sf /System/Library/Frameworks/JavaVM.framework/Commands/javaws /usr/bin/javaws
 &lt;span style="color:gray"&gt;mac:~ user$ &lt;/span&gt;ls -l /usr/bin/javaws
 &lt;span style="color:blue"&gt;lrwxr-xr-x  1 root  wheel  59 12  4 10:19 /usr/bin/javaws
    -&gt; /System/Library/Frameworks/JavaVM.framework/Commands/javaws&lt;/span&gt;</text>
    <sha1>a3034c9fa5bd8ddbb965f65fd58455fd5f56caa2</sha1>
  </revision>
  <revision>
    <id>522</id>
    <parentid>511</parentid>
    <timestamp>2013-02-25T05:48:30Z</timestamp>
    <contributor>
      <username>IMSsato</username>
      <id>4</id>
    </contributor>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="9420" xml:space="preserve">{| style="left"
 |__TOC__
 |}

== Latest environment is recommended ==

Using latest version of Java and jV is recommended to avoid problems.
Following issues are known for older versions of them.

* jV applet fails to start on JRE 1.6.0_15 and 1.6.0_16 by a certificate error.
* Java's file-cache functionality causes a problem on JRE 1.6.0_15 and 1.6.0_16.
* jV applet fails to start on JRE 1.6.0_21 because of a conflict with next-generation Java Plug-in.
* jV of versions eariler than 4.1 do not run as an applet on recent Mac OS.

== The jV applet can't be displayed on Mac OS 10.7 or later when the java is updated to 1.6.0_37 ==

When you update your java to 1.6.0_37 on Mac OS 10.7 or later, following change will be adopted[http://support.apple.com/kb/HT5493]:

# All the java plug-ins for every web browser provided from Apple Inc. will be removed.
# The "Java Preferences" application will be removed.

You have to install JDK, not JRE manually, and then change a symbolic link to run jnlp 'javaws' as following[http://stackoverflow.com/questions/13405242/java-web-start-in-10-8-2-with-native-apple-java-1-6-cant-find-jre]:

 &lt;span style="color:gray"&gt;mac:~ user$ &lt;/span&gt;which javaws
 &lt;span style="color:blue"&gt;/usr/bin/javaws&lt;/span&gt;
 &lt;span style="color:gray"&gt;mac:~ user$ &lt;/span&gt;ls -l /usr/bin/javaws
 &lt;span style="color:blue"&gt;lrwxr-xr-x  1 root  wheel  76 12  3 14:48 /usr/bin/javaws
    -&gt; /System/Library/Frameworks/JavaVM.framework/Versions/Current/Commands/javaws&lt;/span&gt;
 &lt;span style="color:gray"&gt;mac:~ user$ &lt;/span&gt;ln -sf /System/Library/Frameworks/JavaVM.framework/Commands/javaws /usr/bin/javaws
 &lt;span style="color:gray"&gt;mac:~ user$ &lt;/span&gt;ls -l /usr/bin/javaws
 &lt;span style="color:blue"&gt;lrwxr-xr-x  1 root  wheel  59 12  4 10:19 /usr/bin/javaws
    -&gt; /System/Library/Frameworks/JavaVM.framework/Commands/javaws&lt;/span&gt;

== JOGL library conflict ==

If you cannot start jV via Java Web Start or view jV applets due to a failure of locating the JOGL library, try the followings.

===clear cached files===

Previously cached JOGL files may be the cause of a problem
(on JRE 1.6.0_15 and 1.6.0_16, cached JOGL files conflict with newer files placed on the server).
The following steps show how to clear cached files. 

;1) Open the Java Preferences window
:Double-click the [Java Preferences] icon, then the Java Preferences window appears. The place of [Java Preferences] depends on the version of Mac OS as following:
:{|style="border:1px solid gray;border-collapse:collapse"
!style="border:1px solid gray;padding:0 0.5em;background-color:lightyellow"|Max OS X version
!style="border:1px solid gray;padding:0 0.5em;background-color:lightyellow"|place
|-
|style="border:1px solid gray;padding:0 0.5em"|10.4
|style="border:1px solid gray;padding:0 0.5em"|[Applications]-[Utilities]-[Java]-[J2SE 5.0]
|-
|style="border:1px solid gray;padding:0 0.5em"|10.5 (before installing Java for Mac OS X 10.5 Update 4)
|style="border:1px solid gray;padding:0 0.5em"|[Applications]-[Utilities]-[Java]
|-
|style="border:1px solid gray;padding:0 0.5em"|10.5 (after installing Java for Mac OS X 10.5 Update 4 or later)
|style="border:1px solid gray;padding:0 0.5em"|[Applications]-[Utilities]
|-
|style="border:1px solid gray;padding:0 0.5em"|10.6
|style="border:1px solid gray;padding:0 0.5em"|[Applications]-[Utilities]
|}
:The contents of the [Java Preferences] differ for the version of Mac OS. In case 10.4, use the [General] tab, which is default displayed. In case 10.5 or later, click to display [Network] tab.
:{|style="border:1px solid gray;border-collapse:collapse"
!style="border:1px solid gray;padding:0 0.5em;background-color:lightyellow"|Max OS X 10.4
!style="border:1px solid gray;padding:0 0.5em;background-color:lightyellow"|Max OS X 10.5 or later
|-
|style="border:1px solid gray;padding:0.5ex 0.5em;text-align:center;vertical-align:top"|[[File:Javapref_tiger.png|400px]]
|style="border:1px solid gray;padding:0.5ex 0.5em;text-align:center;vertical-align:top"|[[File:Java_prefs1.png|400px]]&lt;br/&gt;&amp;darr;&lt;br/&gt;[[File:Java_prefs2.png|400px]]
|}

;2) Press 'Delete Files...' button
:The [Delete Temporary Files] window, which asks which items are to remove, will be opened.

:[[File:Javacache_del_en.png]]

;3) Leave all the checkboxs on and click 'OK' button.

;4) In some case, restoring the Java environment to the default may be also required. 
:To do it, click "Restore Defaults" button in the Java Preferences (the following figure is the case of Mac OS X 10.6).
:[[File:Javapref_general_10_6.png]]

===remove local JOGL library===

Locally-installed JOGL libraries of different version cause conflicts with Java Web Start technology.
JOGL library files are different between operating systems.

'''Mac OS X'''

Open the [Macintosh HD]-[Library]-[Java]-[Extensions] folder.
If some of the following files

* jogl.jar
* gluegen-rt.jar
* libjogl.jnilib
* libjogl_awt.jnilib
* libjogl_cg.jnilib
* libgluegen-rt.jnilib

exist in the folder, remove them.
Here, this operation requires root privilege.

'''Windows'''

Files that should be removed are as follows.

* &lt;JRE&gt;\lib\ext\jogl.jar
* &lt;JRE&gt;\lib\ext\gluegen-rt.jar
* &lt;JRE&gt;\bin\jogl.dll
* &lt;JRE&gt;\bin\jogl_cg.dll
* &lt;JRE&gt;\bin\jogl_awt.dll
* &lt;JRE&gt;\bin\gluegen-rt.dll

Here, &lt;JRE&gt; denotes the folder that JRE has been installed; typically &lt;JRE&gt;=C:\Program Files\Java\jre6.

'''Linux'''

Files that should be removed are as follows.

* &lt;JRE&gt;/lib/ext/jogl.jar
* &lt;JRE&gt;/lib/ext/gluegen-rt.jar
* &lt;JRE&gt;/lib/&lt;arch&gt;/libjogl.so
* &lt;JRE&gt;/lib/&lt;arch&gt;/libjogl_cg.so
* &lt;JRE&gt;/lib/&lt;arch&gt;/libjogl_awt.so
* &lt;JRE&gt;/lib/&lt;arch&gt;/libjogl_drihack.so
* &lt;JRE&gt;/lib/&lt;arch&gt;/libgluegen-rt.so

Here, &lt;JRE&gt; denotes the directory that JRE has been installed; typically &lt;JRE&gt;=/usr/java/jdk1.6.0_17/jre,
and &lt;arch&gt; the processor architecture such as &lt;arch&gt;=i386.

== Certificate error on applet ==

When you use JRE6 Update15 (1.6.0_15) or JRE6 Update16 (1.6.0_16) on Windows or Linux,
jV applet and applet-launcher fail to start up with the following error.

 Error:java.io.IOException:Cannot find certificates for JNLP AppletLauncher class

Please use JRE6 Update17 (1.6.0_17) or later.

== jV applet with Internet Explorer ==

When visiting a web page that contains a jV applet with Internet Explorer, there sometimes occurs trouble in working with native JOGL libraries especially on Windows Vista. Please use Firefox web browser in that case.

== Class not found error on applet ==

When you use JRE6 Update21 (1.6.0_21) with the next-generation Java Plug-in enabled on Windows or Linux, 
the following error occurs for the combination of jV applet and applet-launcher.

 Error: Class not found: org.pdbj.viewer.gui.ViewerApplet

You can avoid this problem by disabling the next-generation Java Plug-in.
[http://www.java.com/en/download/help/new_plugin.xml Here] is how to do that for Windows users.
On Linux platform, users can manually replace the symbolic link to new plug-in &lt;tt&gt;libnpjp2.so&lt;/tt&gt;
with the symbolic link to classic plug-in &lt;tt&gt;libjavaplugin_oji.so&lt;/tt&gt;
(see [http://www.oracle.com/technetwork/java/javase/manual-plugin-install-linux-136395.html this page] for help).
If you are using firefox 3.6 or later, however, you need to downgrade JRE to 1.6.0_20
because firefox of those versions run applets only with the new Java Plug-in.
To get JRE 1.6.0_20, see [https://cds.sun.com/is-bin/INTERSHOP.enfinity/WFS/CDS-CDS_Developer-Site/en_US/-/USD/ViewProductDetail-Start?ProductRef=jre-6u20-oth-JPR@CDS-CDS_Developer this page].


== The jV applet can't be displayed on Mac + Firefox/Safari/Google Chrome ==
The Mac OS and browser described below can't display jV applets.
To display them, please downgrade the browser or use another browser such as [http://www.opera.com/ Opera], [http://caminobrowser.org/ Camino], or [http://sourceforge.jp/projects/shiira/ Shiira].
We are sorry for the inconvenient.
;OS
:Mac OS X 10.5 update 4 or later
;Browser
* Firefox 6.0 or later
* Safari 5.1 or later
* Google Chrome
;Reason
:You can specify which Java Plug-in is to use at the Java Preferences. If you select 'In their own process' to use new Java Plug-in, and select 'Within the browser process' to use classic Java Plug-in. But none the less, Firefox 6.0 or later, Safari 5.1 or later and Google Chrome force to use new Java Plug-in. Currently the new Java Plug-in for Mac doesn't support hardware-accelerated technologies like JOGL and Java3D[http://developer.apple.com/library/mac/#releasenotes/CrossPlatform/JavaSnowLeopardUpdate2LeopardUpdate7RN/NewandNoteworthy/NewandNoteworthy.html#//apple_ref/doc/uid/TP40009967-CH4-SW1], so the jV applet under these environment can't be displayed.

* The Windows and Linux users don't affect this problem.
* The Firefox 5.0 or older can display jV applets even if on Mac OS.
* The Safari 5.0 or older can display jV applets even if on Mac OS.

'''Resolved''': jV version 4.1 runs on Mac + latest Firefox/Safari/Google Chrome .

== The jV applet can't be displayed on Mac with JRE 1.6.0_29 ==
The Mac OS with JRE6 Update29 (1.6.0_29) cannot display jV applets on any browser at the moment.
In JRE 1.6.0_29, the classic Java Plug-in has been removed and only new Java Plug-in is available. 
However, the current version of JOGL library does not work with the new Java Plug-in.
The issue will be resolved by the next release of JOGL library.
We are sorry for the inconvenience.

'''Resolved''': jV version 4.1 runs on Mac with JRE 1.6.0_29.</text>
    <sha1>a00873cb655e4fc14c306253e18fcb4585e0437e</sha1>
  </revision>
  <revision>
    <id>530</id>
    <parentid>522</parentid>
    <timestamp>2013-03-18T03:02:29Z</timestamp>
    <contributor>
      <username>IMSsato</username>
      <id>4</id>
    </contributor>
    <comment>/* JOGL library conflict */</comment>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="10073" xml:space="preserve">{| style="left"
 |__TOC__
 |}

== Latest environment is recommended ==

Using latest version of Java and jV is recommended to avoid problems.
Following issues are known for older versions of them.

* jV applet fails to start on JRE 1.6.0_15 and 1.6.0_16 by a certificate error.
* Java's file-cache functionality causes a problem on JRE 1.6.0_15 and 1.6.0_16.
* jV applet fails to start on JRE 1.6.0_21 because of a conflict with next-generation Java Plug-in.
* jV of versions eariler than 4.1 do not run as an applet on recent Mac OS.

== The jV applet can't be displayed on Mac OS 10.7 or later when the java is updated to 1.6.0_37 ==

When you update your java to 1.6.0_37 on Mac OS 10.7 or later, following change will be adopted[http://support.apple.com/kb/HT5493]:

# All the java plug-ins for every web browser provided from Apple Inc. will be removed.
# The "Java Preferences" application will be removed.

You have to install JDK, not JRE manually, and then change a symbolic link to run jnlp 'javaws' as following[http://stackoverflow.com/questions/13405242/java-web-start-in-10-8-2-with-native-apple-java-1-6-cant-find-jre]:

 &lt;span style="color:gray"&gt;mac:~ user$ &lt;/span&gt;which javaws
 &lt;span style="color:blue"&gt;/usr/bin/javaws&lt;/span&gt;
 &lt;span style="color:gray"&gt;mac:~ user$ &lt;/span&gt;ls -l /usr/bin/javaws
 &lt;span style="color:blue"&gt;lrwxr-xr-x  1 root  wheel  76 12  3 14:48 /usr/bin/javaws
    -&gt; /System/Library/Frameworks/JavaVM.framework/Versions/Current/Commands/javaws&lt;/span&gt;
 &lt;span style="color:gray"&gt;mac:~ user$ &lt;/span&gt;ln -sf /System/Library/Frameworks/JavaVM.framework/Commands/javaws /usr/bin/javaws
 &lt;span style="color:gray"&gt;mac:~ user$ &lt;/span&gt;ls -l /usr/bin/javaws
 &lt;span style="color:blue"&gt;lrwxr-xr-x  1 root  wheel  59 12  4 10:19 /usr/bin/javaws
    -&gt; /System/Library/Frameworks/JavaVM.framework/Commands/javaws&lt;/span&gt;

== JOGL library conflict ==

If you cannot start jV via Java Web Start or view jV applets due to a failure of locating the JOGL library, try the followings.

===clear cached files===

Previously cached JOGL files may be the cause of a problem
(on JRE 1.6.0_15 and 1.6.0_16, cached JOGL files conflict with newer files placed on the server).
The following steps show how to clear cached files. 

;1) Open Java Control Panel
:In Windows, double-click the [Java] icon located at Control Panel. In Mac OS, click the [Java] icon in System Preferences.

;2) Open Java Cache Viewer
:On the Java Control Panel, select [General] tab and click [View...] button at the section of Temporary Internet Files, then Java Cache Viewer window appears.

;3) Remove cache files
:In Java Cache Viewer, you can switch categories with [Show:] pull-down list. Remove all cache files in [Applications] and [Resources] categories.

In old versions of Mac OS, Java Preferences utility is offered instead of Java Control Panel.
In such cases, use Java Preferences as follows.
;1) Open the Java Preferences window
:Double-click the [Java Preferences] icon, then the Java Preferences window appears. The place of [Java Preferences] depends on the version of Mac OS as following:
:{|style="border:1px solid gray;border-collapse:collapse"
!style="border:1px solid gray;padding:0 0.5em;background-color:lightyellow"|Max OS X version
!style="border:1px solid gray;padding:0 0.5em;background-color:lightyellow"|place
|-
|style="border:1px solid gray;padding:0 0.5em"|10.4
|style="border:1px solid gray;padding:0 0.5em"|[Applications]-[Utilities]-[Java]-[J2SE 5.0]
|-
|style="border:1px solid gray;padding:0 0.5em"|10.5 (before installing Java for Mac OS X 10.5 Update 4)
|style="border:1px solid gray;padding:0 0.5em"|[Applications]-[Utilities]-[Java]
|-
|style="border:1px solid gray;padding:0 0.5em"|10.5 (after installing Java for Mac OS X 10.5 Update 4 or later)
|style="border:1px solid gray;padding:0 0.5em"|[Applications]-[Utilities]
|-
|style="border:1px solid gray;padding:0 0.5em"|10.6
|style="border:1px solid gray;padding:0 0.5em"|[Applications]-[Utilities]
|}
:The contents of the [Java Preferences] differ for the version of Mac OS. In case 10.4, use the [General] tab, which is default displayed. In case 10.5 or later, click to display [Network] tab.
:{|style="border:1px solid gray;border-collapse:collapse"
!style="border:1px solid gray;padding:0 0.5em;background-color:lightyellow"|Max OS X 10.4
!style="border:1px solid gray;padding:0 0.5em;background-color:lightyellow"|Max OS X 10.5 or later
|-
|style="border:1px solid gray;padding:0.5ex 0.5em;text-align:center;vertical-align:top"|[[File:Javapref_tiger.png|400px]]
|style="border:1px solid gray;padding:0.5ex 0.5em;text-align:center;vertical-align:top"|[[File:Java_prefs1.png|400px]]&lt;br/&gt;&amp;darr;&lt;br/&gt;[[File:Java_prefs2.png|400px]]
|}

;2) Press 'Delete Files...' button
:The [Delete Temporary Files] window, which asks which items are to remove, will be opened.

:[[File:Javacache_del_en.png]]

;3) Leave all the checkboxs on and click 'OK' button.

;4) In some case, restoring the Java environment to the default may be also required. 
:To do it, click "Restore Defaults" button in the Java Preferences (the following figure is the case of Mac OS X 10.6).
:[[File:Javapref_general_10_6.png]]

===remove local JOGL library===

Locally-installed JOGL libraries of different version cause conflicts with Java Web Start technology.
JOGL library files are different between operating systems.

'''Mac OS X'''

Open the [Macintosh HD]-[Library]-[Java]-[Extensions] folder.
If some of the following files

* jogl.jar
* gluegen-rt.jar
* libjogl.jnilib
* libjogl_awt.jnilib
* libjogl_cg.jnilib
* libgluegen-rt.jnilib

exist in the folder, remove them.
Here, this operation requires root privilege.

'''Windows'''

Files that should be removed are as follows.

* &lt;JRE&gt;\lib\ext\jogl.jar
* &lt;JRE&gt;\lib\ext\gluegen-rt.jar
* &lt;JRE&gt;\bin\jogl.dll
* &lt;JRE&gt;\bin\jogl_cg.dll
* &lt;JRE&gt;\bin\jogl_awt.dll
* &lt;JRE&gt;\bin\gluegen-rt.dll

Here, &lt;JRE&gt; denotes the folder that JRE has been installed; typically &lt;JRE&gt;=C:\Program Files\Java\jre6.

'''Linux'''

Files that should be removed are as follows.

* &lt;JRE&gt;/lib/ext/jogl.jar
* &lt;JRE&gt;/lib/ext/gluegen-rt.jar
* &lt;JRE&gt;/lib/&lt;arch&gt;/libjogl.so
* &lt;JRE&gt;/lib/&lt;arch&gt;/libjogl_cg.so
* &lt;JRE&gt;/lib/&lt;arch&gt;/libjogl_awt.so
* &lt;JRE&gt;/lib/&lt;arch&gt;/libjogl_drihack.so
* &lt;JRE&gt;/lib/&lt;arch&gt;/libgluegen-rt.so

Here, &lt;JRE&gt; denotes the directory that JRE has been installed; typically &lt;JRE&gt;=/usr/java/jdk1.6.0_17/jre,
and &lt;arch&gt; the processor architecture such as &lt;arch&gt;=i386.

== Certificate error on applet ==

When you use JRE6 Update15 (1.6.0_15) or JRE6 Update16 (1.6.0_16) on Windows or Linux,
jV applet and applet-launcher fail to start up with the following error.

 Error:java.io.IOException:Cannot find certificates for JNLP AppletLauncher class

Please use JRE6 Update17 (1.6.0_17) or later.

== jV applet with Internet Explorer ==

When visiting a web page that contains a jV applet with Internet Explorer, there sometimes occurs trouble in working with native JOGL libraries especially on Windows Vista. Please use Firefox web browser in that case.

== Class not found error on applet ==

When you use JRE6 Update21 (1.6.0_21) with the next-generation Java Plug-in enabled on Windows or Linux, 
the following error occurs for the combination of jV applet and applet-launcher.

 Error: Class not found: org.pdbj.viewer.gui.ViewerApplet

You can avoid this problem by disabling the next-generation Java Plug-in.
[http://www.java.com/en/download/help/new_plugin.xml Here] is how to do that for Windows users.
On Linux platform, users can manually replace the symbolic link to new plug-in &lt;tt&gt;libnpjp2.so&lt;/tt&gt;
with the symbolic link to classic plug-in &lt;tt&gt;libjavaplugin_oji.so&lt;/tt&gt;
(see [http://www.oracle.com/technetwork/java/javase/manual-plugin-install-linux-136395.html this page] for help).
If you are using firefox 3.6 or later, however, you need to downgrade JRE to 1.6.0_20
because firefox of those versions run applets only with the new Java Plug-in.
To get JRE 1.6.0_20, see [https://cds.sun.com/is-bin/INTERSHOP.enfinity/WFS/CDS-CDS_Developer-Site/en_US/-/USD/ViewProductDetail-Start?ProductRef=jre-6u20-oth-JPR@CDS-CDS_Developer this page].


== The jV applet can't be displayed on Mac + Firefox/Safari/Google Chrome ==
The Mac OS and browser described below can't display jV applets.
To display them, please downgrade the browser or use another browser such as [http://www.opera.com/ Opera], [http://caminobrowser.org/ Camino], or [http://sourceforge.jp/projects/shiira/ Shiira].
We are sorry for the inconvenient.
;OS
:Mac OS X 10.5 update 4 or later
;Browser
* Firefox 6.0 or later
* Safari 5.1 or later
* Google Chrome
;Reason
:You can specify which Java Plug-in is to use at the Java Preferences. If you select 'In their own process' to use new Java Plug-in, and select 'Within the browser process' to use classic Java Plug-in. But none the less, Firefox 6.0 or later, Safari 5.1 or later and Google Chrome force to use new Java Plug-in. Currently the new Java Plug-in for Mac doesn't support hardware-accelerated technologies like JOGL and Java3D[http://developer.apple.com/library/mac/#releasenotes/CrossPlatform/JavaSnowLeopardUpdate2LeopardUpdate7RN/NewandNoteworthy/NewandNoteworthy.html#//apple_ref/doc/uid/TP40009967-CH4-SW1], so the jV applet under these environment can't be displayed.

* The Windows and Linux users don't affect this problem.
* The Firefox 5.0 or older can display jV applets even if on Mac OS.
* The Safari 5.0 or older can display jV applets even if on Mac OS.

'''Resolved''': jV version 4.1 runs on Mac + latest Firefox/Safari/Google Chrome .

== The jV applet can't be displayed on Mac with JRE 1.6.0_29 ==
The Mac OS with JRE6 Update29 (1.6.0_29) cannot display jV applets on any browser at the moment.
In JRE 1.6.0_29, the classic Java Plug-in has been removed and only new Java Plug-in is available. 
However, the current version of JOGL library does not work with the new Java Plug-in.
The issue will be resolved by the next release of JOGL library.
We are sorry for the inconvenience.

'''Resolved''': jV version 4.1 runs on Mac with JRE 1.6.0_29.</text>
    <sha1>b7d011738111044ee49301226a859f91aa6459fe</sha1>
  </revision>
  <revision>
    <id>531</id>
    <parentid>530</parentid>
    <timestamp>2013-03-18T03:08:06Z</timestamp>
    <contributor>
      <username>IMSsato</username>
      <id>4</id>
    </contributor>
    <comment>/* The jV applet can't be displayed on Mac OS 10.7 or later when the java is updated to 1.6.0_37 */</comment>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="9432" xml:space="preserve">{| style="left"
 |__TOC__
 |}

== Latest environment is recommended ==

Using latest version of Java and jV is recommended to avoid problems.
Following issues are known for older versions of them.

* jV applet fails to start on JRE 1.6.0_15 and 1.6.0_16 by a certificate error.
* Java's file-cache functionality causes a problem on JRE 1.6.0_15 and 1.6.0_16.
* jV applet fails to start on JRE 1.6.0_21 because of a conflict with next-generation Java Plug-in.
* jV of versions eariler than 4.1 do not run as an applet on recent Mac OS.

== JRE 1.7 is required on Mac OS 10.7 or later ==

Apple-provided Java SE 6 does not support Java applets now.
The following changes were made at Java 1.6.0_37[http://support.apple.com/kb/HT5493]:

# All the java plug-ins for every web browser provided from Apple Inc. will be removed.
# The "Java Preferences" application will be removed.

If you access a web page containing a Java applet and click on the region labeled "Missing plug-in",
you can go to a download page of JRE 1.7.
When JRE 1.7 is installed, you can use Java applets.
It is reported, however, that Java Web Start fails to invoke with JRE 1.7 in some cases,
and the issue is not resolved yet.

== JOGL library conflict ==

If you cannot start jV via Java Web Start or view jV applets due to a failure of locating the JOGL library, try the followings.

===clear cached files===

Previously cached JOGL files may be the cause of a problem
(on JRE 1.6.0_15 and 1.6.0_16, cached JOGL files conflict with newer files placed on the server).
The following steps show how to clear cached files. 

;1) Open Java Control Panel
:In Windows, double-click the [Java] icon located at Control Panel. In Mac OS, click the [Java] icon in System Preferences.

;2) Open Java Cache Viewer
:On the Java Control Panel, select [General] tab and click [View...] button at the section of Temporary Internet Files, then Java Cache Viewer window appears.

;3) Remove cache files
:In Java Cache Viewer, you can switch categories with [Show:] pull-down list. Remove all cache files in [Applications] and [Resources] categories.

In old versions of Mac OS, Java Preferences utility is offered instead of Java Control Panel.
In such cases, use Java Preferences as follows.
;1) Open the Java Preferences window
:Double-click the [Java Preferences] icon, then the Java Preferences window appears. The place of [Java Preferences] depends on the version of Mac OS as following:
:{|style="border:1px solid gray;border-collapse:collapse"
!style="border:1px solid gray;padding:0 0.5em;background-color:lightyellow"|Max OS X version
!style="border:1px solid gray;padding:0 0.5em;background-color:lightyellow"|place
|-
|style="border:1px solid gray;padding:0 0.5em"|10.4
|style="border:1px solid gray;padding:0 0.5em"|[Applications]-[Utilities]-[Java]-[J2SE 5.0]
|-
|style="border:1px solid gray;padding:0 0.5em"|10.5 (before installing Java for Mac OS X 10.5 Update 4)
|style="border:1px solid gray;padding:0 0.5em"|[Applications]-[Utilities]-[Java]
|-
|style="border:1px solid gray;padding:0 0.5em"|10.5 (after installing Java for Mac OS X 10.5 Update 4 or later)
|style="border:1px solid gray;padding:0 0.5em"|[Applications]-[Utilities]
|-
|style="border:1px solid gray;padding:0 0.5em"|10.6
|style="border:1px solid gray;padding:0 0.5em"|[Applications]-[Utilities]
|}
:The contents of the [Java Preferences] differ for the version of Mac OS. In case 10.4, use the [General] tab, which is default displayed. In case 10.5 or later, click to display [Network] tab.
:{|style="border:1px solid gray;border-collapse:collapse"
!style="border:1px solid gray;padding:0 0.5em;background-color:lightyellow"|Max OS X 10.4
!style="border:1px solid gray;padding:0 0.5em;background-color:lightyellow"|Max OS X 10.5 or later
|-
|style="border:1px solid gray;padding:0.5ex 0.5em;text-align:center;vertical-align:top"|[[File:Javapref_tiger.png|400px]]
|style="border:1px solid gray;padding:0.5ex 0.5em;text-align:center;vertical-align:top"|[[File:Java_prefs1.png|400px]]&lt;br/&gt;&amp;darr;&lt;br/&gt;[[File:Java_prefs2.png|400px]]
|}

;2) Press 'Delete Files...' button
:The [Delete Temporary Files] window, which asks which items are to remove, will be opened.

:[[File:Javacache_del_en.png]]

;3) Leave all the checkboxs on and click 'OK' button.

;4) In some case, restoring the Java environment to the default may be also required. 
:To do it, click "Restore Defaults" button in the Java Preferences (the following figure is the case of Mac OS X 10.6).
:[[File:Javapref_general_10_6.png]]

===remove local JOGL library===

Locally-installed JOGL libraries of different version cause conflicts with Java Web Start technology.
JOGL library files are different between operating systems.

'''Mac OS X'''

Open the [Macintosh HD]-[Library]-[Java]-[Extensions] folder.
If some of the following files

* jogl.jar
* gluegen-rt.jar
* libjogl.jnilib
* libjogl_awt.jnilib
* libjogl_cg.jnilib
* libgluegen-rt.jnilib

exist in the folder, remove them.
Here, this operation requires root privilege.

'''Windows'''

Files that should be removed are as follows.

* &lt;JRE&gt;\lib\ext\jogl.jar
* &lt;JRE&gt;\lib\ext\gluegen-rt.jar
* &lt;JRE&gt;\bin\jogl.dll
* &lt;JRE&gt;\bin\jogl_cg.dll
* &lt;JRE&gt;\bin\jogl_awt.dll
* &lt;JRE&gt;\bin\gluegen-rt.dll

Here, &lt;JRE&gt; denotes the folder that JRE has been installed; typically &lt;JRE&gt;=C:\Program Files\Java\jre6.

'''Linux'''

Files that should be removed are as follows.

* &lt;JRE&gt;/lib/ext/jogl.jar
* &lt;JRE&gt;/lib/ext/gluegen-rt.jar
* &lt;JRE&gt;/lib/&lt;arch&gt;/libjogl.so
* &lt;JRE&gt;/lib/&lt;arch&gt;/libjogl_cg.so
* &lt;JRE&gt;/lib/&lt;arch&gt;/libjogl_awt.so
* &lt;JRE&gt;/lib/&lt;arch&gt;/libjogl_drihack.so
* &lt;JRE&gt;/lib/&lt;arch&gt;/libgluegen-rt.so

Here, &lt;JRE&gt; denotes the directory that JRE has been installed; typically &lt;JRE&gt;=/usr/java/jdk1.6.0_17/jre,
and &lt;arch&gt; the processor architecture such as &lt;arch&gt;=i386.

== Certificate error on applet ==

When you use JRE6 Update15 (1.6.0_15) or JRE6 Update16 (1.6.0_16) on Windows or Linux,
jV applet and applet-launcher fail to start up with the following error.

 Error:java.io.IOException:Cannot find certificates for JNLP AppletLauncher class

Please use JRE6 Update17 (1.6.0_17) or later.

== jV applet with Internet Explorer ==

When visiting a web page that contains a jV applet with Internet Explorer, there sometimes occurs trouble in working with native JOGL libraries especially on Windows Vista. Please use Firefox web browser in that case.

== Class not found error on applet ==

When you use JRE6 Update21 (1.6.0_21) with the next-generation Java Plug-in enabled on Windows or Linux, 
the following error occurs for the combination of jV applet and applet-launcher.

 Error: Class not found: org.pdbj.viewer.gui.ViewerApplet

You can avoid this problem by disabling the next-generation Java Plug-in.
[http://www.java.com/en/download/help/new_plugin.xml Here] is how to do that for Windows users.
On Linux platform, users can manually replace the symbolic link to new plug-in &lt;tt&gt;libnpjp2.so&lt;/tt&gt;
with the symbolic link to classic plug-in &lt;tt&gt;libjavaplugin_oji.so&lt;/tt&gt;
(see [http://www.oracle.com/technetwork/java/javase/manual-plugin-install-linux-136395.html this page] for help).
If you are using firefox 3.6 or later, however, you need to downgrade JRE to 1.6.0_20
because firefox of those versions run applets only with the new Java Plug-in.
To get JRE 1.6.0_20, see [https://cds.sun.com/is-bin/INTERSHOP.enfinity/WFS/CDS-CDS_Developer-Site/en_US/-/USD/ViewProductDetail-Start?ProductRef=jre-6u20-oth-JPR@CDS-CDS_Developer this page].


== The jV applet can't be displayed on Mac + Firefox/Safari/Google Chrome ==
The Mac OS and browser described below can't display jV applets.
To display them, please downgrade the browser or use another browser such as [http://www.opera.com/ Opera], [http://caminobrowser.org/ Camino], or [http://sourceforge.jp/projects/shiira/ Shiira].
We are sorry for the inconvenient.
;OS
:Mac OS X 10.5 update 4 or later
;Browser
* Firefox 6.0 or later
* Safari 5.1 or later
* Google Chrome
;Reason
:You can specify which Java Plug-in is to use at the Java Preferences. If you select 'In their own process' to use new Java Plug-in, and select 'Within the browser process' to use classic Java Plug-in. But none the less, Firefox 6.0 or later, Safari 5.1 or later and Google Chrome force to use new Java Plug-in. Currently the new Java Plug-in for Mac doesn't support hardware-accelerated technologies like JOGL and Java3D[http://developer.apple.com/library/mac/#releasenotes/CrossPlatform/JavaSnowLeopardUpdate2LeopardUpdate7RN/NewandNoteworthy/NewandNoteworthy.html#//apple_ref/doc/uid/TP40009967-CH4-SW1], so the jV applet under these environment can't be displayed.

* The Windows and Linux users don't affect this problem.
* The Firefox 5.0 or older can display jV applets even if on Mac OS.
* The Safari 5.0 or older can display jV applets even if on Mac OS.

'''Resolved''': jV version 4.1 runs on Mac + latest Firefox/Safari/Google Chrome .

== The jV applet can't be displayed on Mac with JRE 1.6.0_29 ==
The Mac OS with JRE6 Update29 (1.6.0_29) cannot display jV applets on any browser at the moment.
In JRE 1.6.0_29, the classic Java Plug-in has been removed and only new Java Plug-in is available. 
However, the current version of JOGL library does not work with the new Java Plug-in.
The issue will be resolved by the next release of JOGL library.
We are sorry for the inconvenience.

'''Resolved''': jV version 4.1 runs on Mac with JRE 1.6.0_29.</text>
    <sha1>170baaf0e72768942952df74986efbd27b9d901d</sha1>
  </revision>
  <revision>
    <id>532</id>
    <parentid>531</parentid>
    <timestamp>2013-03-18T03:23:07Z</timestamp>
    <contributor>
      <username>IMSsato</username>
      <id>4</id>
    </contributor>
    <comment>/* JRE 1.7 is required on Mac OS 10.7 or later */</comment>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="9431" xml:space="preserve">{| style="left"
 |__TOC__
 |}

== Latest environment is recommended ==

Using latest version of Java and jV is recommended to avoid problems.
Following issues are known for older versions of them.

* jV applet fails to start on JRE 1.6.0_15 and 1.6.0_16 by a certificate error.
* Java's file-cache functionality causes a problem on JRE 1.6.0_15 and 1.6.0_16.
* jV applet fails to start on JRE 1.6.0_21 because of a conflict with next-generation Java Plug-in.
* jV of versions eariler than 4.1 do not run as an applet on recent Mac OS.

== JRE 1.7 is required on Mac OS 10.7 or later ==

Apple-provided Java SE 6 does not support Java applets now.
The following changes were made at Java 1.6.0_37[http://support.apple.com/kb/HT5493]:

# All the java plug-ins for every web browser provided from Apple Inc. will be removed.
# The "Java Preferences" application will be removed.

If you access a web page containing a Java applet and click on the region labeled "Missing plug-in",
you can go to a download page of JRE 1.7.
When JRE 1.7 is installed, you can use Java applets.
It is reported, however, that Java Web Start fails to start with JRE 1.7 in some cases,
and the issue is not resolved yet.

== JOGL library conflict ==

If you cannot start jV via Java Web Start or view jV applets due to a failure of locating the JOGL library, try the followings.

===clear cached files===

Previously cached JOGL files may be the cause of a problem
(on JRE 1.6.0_15 and 1.6.0_16, cached JOGL files conflict with newer files placed on the server).
The following steps show how to clear cached files. 

;1) Open Java Control Panel
:In Windows, double-click the [Java] icon located at Control Panel. In Mac OS, click the [Java] icon in System Preferences.

;2) Open Java Cache Viewer
:On the Java Control Panel, select [General] tab and click [View...] button at the section of Temporary Internet Files, then Java Cache Viewer window appears.

;3) Remove cache files
:In Java Cache Viewer, you can switch categories with [Show:] pull-down list. Remove all cache files in [Applications] and [Resources] categories.

In old versions of Mac OS, Java Preferences utility is offered instead of Java Control Panel.
In such cases, use Java Preferences as follows.
;1) Open the Java Preferences window
:Double-click the [Java Preferences] icon, then the Java Preferences window appears. The place of [Java Preferences] depends on the version of Mac OS as following:
:{|style="border:1px solid gray;border-collapse:collapse"
!style="border:1px solid gray;padding:0 0.5em;background-color:lightyellow"|Max OS X version
!style="border:1px solid gray;padding:0 0.5em;background-color:lightyellow"|place
|-
|style="border:1px solid gray;padding:0 0.5em"|10.4
|style="border:1px solid gray;padding:0 0.5em"|[Applications]-[Utilities]-[Java]-[J2SE 5.0]
|-
|style="border:1px solid gray;padding:0 0.5em"|10.5 (before installing Java for Mac OS X 10.5 Update 4)
|style="border:1px solid gray;padding:0 0.5em"|[Applications]-[Utilities]-[Java]
|-
|style="border:1px solid gray;padding:0 0.5em"|10.5 (after installing Java for Mac OS X 10.5 Update 4 or later)
|style="border:1px solid gray;padding:0 0.5em"|[Applications]-[Utilities]
|-
|style="border:1px solid gray;padding:0 0.5em"|10.6
|style="border:1px solid gray;padding:0 0.5em"|[Applications]-[Utilities]
|}
:The contents of the [Java Preferences] differ for the version of Mac OS. In case 10.4, use the [General] tab, which is default displayed. In case 10.5 or later, click to display [Network] tab.
:{|style="border:1px solid gray;border-collapse:collapse"
!style="border:1px solid gray;padding:0 0.5em;background-color:lightyellow"|Max OS X 10.4
!style="border:1px solid gray;padding:0 0.5em;background-color:lightyellow"|Max OS X 10.5 or later
|-
|style="border:1px solid gray;padding:0.5ex 0.5em;text-align:center;vertical-align:top"|[[File:Javapref_tiger.png|400px]]
|style="border:1px solid gray;padding:0.5ex 0.5em;text-align:center;vertical-align:top"|[[File:Java_prefs1.png|400px]]&lt;br/&gt;&amp;darr;&lt;br/&gt;[[File:Java_prefs2.png|400px]]
|}

;2) Press 'Delete Files...' button
:The [Delete Temporary Files] window, which asks which items are to remove, will be opened.

:[[File:Javacache_del_en.png]]

;3) Leave all the checkboxs on and click 'OK' button.

;4) In some case, restoring the Java environment to the default may be also required. 
:To do it, click "Restore Defaults" button in the Java Preferences (the following figure is the case of Mac OS X 10.6).
:[[File:Javapref_general_10_6.png]]

===remove local JOGL library===

Locally-installed JOGL libraries of different version cause conflicts with Java Web Start technology.
JOGL library files are different between operating systems.

'''Mac OS X'''

Open the [Macintosh HD]-[Library]-[Java]-[Extensions] folder.
If some of the following files

* jogl.jar
* gluegen-rt.jar
* libjogl.jnilib
* libjogl_awt.jnilib
* libjogl_cg.jnilib
* libgluegen-rt.jnilib

exist in the folder, remove them.
Here, this operation requires root privilege.

'''Windows'''

Files that should be removed are as follows.

* &lt;JRE&gt;\lib\ext\jogl.jar
* &lt;JRE&gt;\lib\ext\gluegen-rt.jar
* &lt;JRE&gt;\bin\jogl.dll
* &lt;JRE&gt;\bin\jogl_cg.dll
* &lt;JRE&gt;\bin\jogl_awt.dll
* &lt;JRE&gt;\bin\gluegen-rt.dll

Here, &lt;JRE&gt; denotes the folder that JRE has been installed; typically &lt;JRE&gt;=C:\Program Files\Java\jre6.

'''Linux'''

Files that should be removed are as follows.

* &lt;JRE&gt;/lib/ext/jogl.jar
* &lt;JRE&gt;/lib/ext/gluegen-rt.jar
* &lt;JRE&gt;/lib/&lt;arch&gt;/libjogl.so
* &lt;JRE&gt;/lib/&lt;arch&gt;/libjogl_cg.so
* &lt;JRE&gt;/lib/&lt;arch&gt;/libjogl_awt.so
* &lt;JRE&gt;/lib/&lt;arch&gt;/libjogl_drihack.so
* &lt;JRE&gt;/lib/&lt;arch&gt;/libgluegen-rt.so

Here, &lt;JRE&gt; denotes the directory that JRE has been installed; typically &lt;JRE&gt;=/usr/java/jdk1.6.0_17/jre,
and &lt;arch&gt; the processor architecture such as &lt;arch&gt;=i386.

== Certificate error on applet ==

When you use JRE6 Update15 (1.6.0_15) or JRE6 Update16 (1.6.0_16) on Windows or Linux,
jV applet and applet-launcher fail to start up with the following error.

 Error:java.io.IOException:Cannot find certificates for JNLP AppletLauncher class

Please use JRE6 Update17 (1.6.0_17) or later.

== jV applet with Internet Explorer ==

When visiting a web page that contains a jV applet with Internet Explorer, there sometimes occurs trouble in working with native JOGL libraries especially on Windows Vista. Please use Firefox web browser in that case.

== Class not found error on applet ==

When you use JRE6 Update21 (1.6.0_21) with the next-generation Java Plug-in enabled on Windows or Linux, 
the following error occurs for the combination of jV applet and applet-launcher.

 Error: Class not found: org.pdbj.viewer.gui.ViewerApplet

You can avoid this problem by disabling the next-generation Java Plug-in.
[http://www.java.com/en/download/help/new_plugin.xml Here] is how to do that for Windows users.
On Linux platform, users can manually replace the symbolic link to new plug-in &lt;tt&gt;libnpjp2.so&lt;/tt&gt;
with the symbolic link to classic plug-in &lt;tt&gt;libjavaplugin_oji.so&lt;/tt&gt;
(see [http://www.oracle.com/technetwork/java/javase/manual-plugin-install-linux-136395.html this page] for help).
If you are using firefox 3.6 or later, however, you need to downgrade JRE to 1.6.0_20
because firefox of those versions run applets only with the new Java Plug-in.
To get JRE 1.6.0_20, see [https://cds.sun.com/is-bin/INTERSHOP.enfinity/WFS/CDS-CDS_Developer-Site/en_US/-/USD/ViewProductDetail-Start?ProductRef=jre-6u20-oth-JPR@CDS-CDS_Developer this page].


== The jV applet can't be displayed on Mac + Firefox/Safari/Google Chrome ==
The Mac OS and browser described below can't display jV applets.
To display them, please downgrade the browser or use another browser such as [http://www.opera.com/ Opera], [http://caminobrowser.org/ Camino], or [http://sourceforge.jp/projects/shiira/ Shiira].
We are sorry for the inconvenient.
;OS
:Mac OS X 10.5 update 4 or later
;Browser
* Firefox 6.0 or later
* Safari 5.1 or later
* Google Chrome
;Reason
:You can specify which Java Plug-in is to use at the Java Preferences. If you select 'In their own process' to use new Java Plug-in, and select 'Within the browser process' to use classic Java Plug-in. But none the less, Firefox 6.0 or later, Safari 5.1 or later and Google Chrome force to use new Java Plug-in. Currently the new Java Plug-in for Mac doesn't support hardware-accelerated technologies like JOGL and Java3D[http://developer.apple.com/library/mac/#releasenotes/CrossPlatform/JavaSnowLeopardUpdate2LeopardUpdate7RN/NewandNoteworthy/NewandNoteworthy.html#//apple_ref/doc/uid/TP40009967-CH4-SW1], so the jV applet under these environment can't be displayed.

* The Windows and Linux users don't affect this problem.
* The Firefox 5.0 or older can display jV applets even if on Mac OS.
* The Safari 5.0 or older can display jV applets even if on Mac OS.

'''Resolved''': jV version 4.1 runs on Mac + latest Firefox/Safari/Google Chrome .

== The jV applet can't be displayed on Mac with JRE 1.6.0_29 ==
The Mac OS with JRE6 Update29 (1.6.0_29) cannot display jV applets on any browser at the moment.
In JRE 1.6.0_29, the classic Java Plug-in has been removed and only new Java Plug-in is available. 
However, the current version of JOGL library does not work with the new Java Plug-in.
The issue will be resolved by the next release of JOGL library.
We are sorry for the inconvenience.

'''Resolved''': jV version 4.1 runs on Mac with JRE 1.6.0_29.</text>
    <sha1>9117fc32b334ed85b80c8367c7b1b9042c4222ae</sha1>
  </revision>
  <revision>
    <id>533</id>
    <parentid>532</parentid>
    <timestamp>2013-03-18T05:49:57Z</timestamp>
    <contributor>
      <username>IMSsato</username>
      <id>4</id>
    </contributor>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="5797" xml:space="preserve">{| style="left"
 |__TOC__
 |}

== Latest environment is recommended ==

Using latest version of Java and jV is recommended to avoid problems.
Following issues are known for older versions of them.

* jV applet fails to start on JRE 1.6.0_15 and 1.6.0_16 by a certificate error.
* Java's file-cache functionality causes a problem on JRE 1.6.0_15 and 1.6.0_16.
* jV applet fails to start on JRE 1.6.0_21 because of a conflict with next-generation Java Plug-in.
* jV of versions eariler than 4.1 do not run as an applet on recent Mac OS.

== JRE 1.7 is required on Mac OS 10.7 or later ==

Apple-provided Java SE 6 does not support Java applets now.
The following changes were made at Java 1.6.0_37[http://support.apple.com/kb/HT5493]:

# All the java plug-ins for every web browser provided from Apple Inc. will be removed.
# The "Java Preferences" application will be removed.

If you access a web page containing a Java applet and click on the region labeled "Missing plug-in",
you can go to a download page of JRE 1.7.
When JRE 1.7 is installed, you can use Java applets.
It is reported, however, that Java Web Start fails to start with JRE 1.7 in some cases,
and the issue is not resolved yet.

== JOGL library conflict ==

If you cannot start jV via Java Web Start or view jV applets due to a failure of locating the JOGL library, try the followings.

===clear cached files===

Previously cached JOGL files may be the cause of a problem
(on JRE 1.6.0_15 and 1.6.0_16, cached JOGL files conflict with newer files placed on the server).
The following steps show how to clear cached files. 

;1) Open Java Control Panel
:In Windows, double-click the [Java] icon located at Control Panel. In Mac OS, click the [Java] icon in System Preferences.

;2) Open Java Cache Viewer
:On the Java Control Panel, select [General] tab and click [View...] button at the section of Temporary Internet Files, then Java Cache Viewer window appears.

;3) Remove cache files
:In Java Cache Viewer, you can switch categories with [Show:] pull-down list. Remove all cache files in [Applications] and [Resources] categories.

In old versions of Mac OS, Java Preferences utility is offered instead of Java Control Panel.
In such cases, use Java Preferences as follows.
;1) Open the Java Preferences window
:Double-click the [Java Preferences] icon, then the Java Preferences window appears. The place of [Java Preferences] depends on the version of Mac OS as following:
:{|style="border:1px solid gray;border-collapse:collapse"
!style="border:1px solid gray;padding:0 0.5em;background-color:lightyellow"|Max OS X version
!style="border:1px solid gray;padding:0 0.5em;background-color:lightyellow"|place
|-
|style="border:1px solid gray;padding:0 0.5em"|10.4
|style="border:1px solid gray;padding:0 0.5em"|[Applications]-[Utilities]-[Java]-[J2SE 5.0]
|-
|style="border:1px solid gray;padding:0 0.5em"|10.5 (before installing Java for Mac OS X 10.5 Update 4)
|style="border:1px solid gray;padding:0 0.5em"|[Applications]-[Utilities]-[Java]
|-
|style="border:1px solid gray;padding:0 0.5em"|10.5 (after installing Java for Mac OS X 10.5 Update 4 or later)
|style="border:1px solid gray;padding:0 0.5em"|[Applications]-[Utilities]
|-
|style="border:1px solid gray;padding:0 0.5em"|10.6
|style="border:1px solid gray;padding:0 0.5em"|[Applications]-[Utilities]
|}
:The contents of the [Java Preferences] differ for the version of Mac OS. In case 10.4, use the [General] tab, which is default displayed. In case 10.5 or later, click to display [Network] tab.
:{|style="border:1px solid gray;border-collapse:collapse"
!style="border:1px solid gray;padding:0 0.5em;background-color:lightyellow"|Max OS X 10.4
!style="border:1px solid gray;padding:0 0.5em;background-color:lightyellow"|Max OS X 10.5 or later
|-
|style="border:1px solid gray;padding:0.5ex 0.5em;text-align:center;vertical-align:top"|[[File:Javapref_tiger.png|400px]]
|style="border:1px solid gray;padding:0.5ex 0.5em;text-align:center;vertical-align:top"|[[File:Java_prefs1.png|400px]]&lt;br/&gt;&amp;darr;&lt;br/&gt;[[File:Java_prefs2.png|400px]]
|}

;2) Press 'Delete Files...' button
:The [Delete Temporary Files] window, which asks which items are to remove, will be opened.

:[[File:Javacache_del_en.png]]

;3) Leave all the checkboxs on and click 'OK' button.

;4) In some case, restoring the Java environment to the default may be also required. 
:To do it, click "Restore Defaults" button in the Java Preferences (the following figure is the case of Mac OS X 10.6).
:[[File:Javapref_general_10_6.png]]

===remove local JOGL library===

Locally-installed JOGL libraries of different version cause conflicts with Java Web Start technology.
JOGL library files are different between operating systems.

'''Mac OS X'''

Open the [Macintosh HD]-[Library]-[Java]-[Extensions] folder.
If some of the following files

* jogl.jar
* gluegen-rt.jar
* libjogl.jnilib
* libjogl_awt.jnilib
* libjogl_cg.jnilib
* libgluegen-rt.jnilib

exist in the folder, remove them.
Here, this operation requires root privilege.

'''Windows'''

Files that should be removed are as follows.

* &lt;JRE&gt;\lib\ext\jogl.jar
* &lt;JRE&gt;\lib\ext\gluegen-rt.jar
* &lt;JRE&gt;\bin\jogl.dll
* &lt;JRE&gt;\bin\jogl_cg.dll
* &lt;JRE&gt;\bin\jogl_awt.dll
* &lt;JRE&gt;\bin\gluegen-rt.dll

Here, &lt;JRE&gt; denotes the folder that JRE has been installed; typically &lt;JRE&gt;=C:\Program Files\Java\jre6.

'''Linux'''

Files that should be removed are as follows.

* &lt;JRE&gt;/lib/ext/jogl.jar
* &lt;JRE&gt;/lib/ext/gluegen-rt.jar
* &lt;JRE&gt;/lib/&lt;arch&gt;/libjogl.so
* &lt;JRE&gt;/lib/&lt;arch&gt;/libjogl_cg.so
* &lt;JRE&gt;/lib/&lt;arch&gt;/libjogl_awt.so
* &lt;JRE&gt;/lib/&lt;arch&gt;/libjogl_drihack.so
* &lt;JRE&gt;/lib/&lt;arch&gt;/libgluegen-rt.so

Here, &lt;JRE&gt; denotes the directory that JRE has been installed; typically &lt;JRE&gt;=/usr/java/jdk1.6.0_17/jre,
and &lt;arch&gt; the processor architecture such as &lt;arch&gt;=i386.</text>
    <sha1>a310b6d5dba637bd36605177faeef5a10d34d4c0</sha1>
  </revision>
  <revision>
    <id>534</id>
    <parentid>533</parentid>
    <timestamp>2013-03-18T05:58:20Z</timestamp>
    <contributor>
      <username>IMSsato</username>
      <id>4</id>
    </contributor>
    <comment>/* remove local JOGL library */</comment>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="5957" xml:space="preserve">{| style="left"
 |__TOC__
 |}

== Latest environment is recommended ==

Using latest version of Java and jV is recommended to avoid problems.
Following issues are known for older versions of them.

* jV applet fails to start on JRE 1.6.0_15 and 1.6.0_16 by a certificate error.
* Java's file-cache functionality causes a problem on JRE 1.6.0_15 and 1.6.0_16.
* jV applet fails to start on JRE 1.6.0_21 because of a conflict with next-generation Java Plug-in.
* jV of versions eariler than 4.1 do not run as an applet on recent Mac OS.

== JRE 1.7 is required on Mac OS 10.7 or later ==

Apple-provided Java SE 6 does not support Java applets now.
The following changes were made at Java 1.6.0_37[http://support.apple.com/kb/HT5493]:

# All the java plug-ins for every web browser provided from Apple Inc. will be removed.
# The "Java Preferences" application will be removed.

If you access a web page containing a Java applet and click on the region labeled "Missing plug-in",
you can go to a download page of JRE 1.7.
When JRE 1.7 is installed, you can use Java applets.
It is reported, however, that Java Web Start fails to start with JRE 1.7 in some cases,
and the issue is not resolved yet.

== JOGL library conflict ==

If you cannot start jV via Java Web Start or view jV applets due to a failure of locating the JOGL library, try the followings.

===clear cached files===

Previously cached JOGL files may be the cause of a problem
(on JRE 1.6.0_15 and 1.6.0_16, cached JOGL files conflict with newer files placed on the server).
The following steps show how to clear cached files. 

;1) Open Java Control Panel
:In Windows, double-click the [Java] icon located at Control Panel. In Mac OS, click the [Java] icon in System Preferences.

;2) Open Java Cache Viewer
:On the Java Control Panel, select [General] tab and click [View...] button at the section of Temporary Internet Files, then Java Cache Viewer window appears.

;3) Remove cache files
:In Java Cache Viewer, you can switch categories with [Show:] pull-down list. Remove all cache files in [Applications] and [Resources] categories.

In old versions of Mac OS, Java Preferences utility is offered instead of Java Control Panel.
In such cases, use Java Preferences as follows.
;1) Open the Java Preferences window
:Double-click the [Java Preferences] icon, then the Java Preferences window appears. The place of [Java Preferences] depends on the version of Mac OS as following:
:{|style="border:1px solid gray;border-collapse:collapse"
!style="border:1px solid gray;padding:0 0.5em;background-color:lightyellow"|Max OS X version
!style="border:1px solid gray;padding:0 0.5em;background-color:lightyellow"|place
|-
|style="border:1px solid gray;padding:0 0.5em"|10.4
|style="border:1px solid gray;padding:0 0.5em"|[Applications]-[Utilities]-[Java]-[J2SE 5.0]
|-
|style="border:1px solid gray;padding:0 0.5em"|10.5 (before installing Java for Mac OS X 10.5 Update 4)
|style="border:1px solid gray;padding:0 0.5em"|[Applications]-[Utilities]-[Java]
|-
|style="border:1px solid gray;padding:0 0.5em"|10.5 (after installing Java for Mac OS X 10.5 Update 4 or later)
|style="border:1px solid gray;padding:0 0.5em"|[Applications]-[Utilities]
|-
|style="border:1px solid gray;padding:0 0.5em"|10.6
|style="border:1px solid gray;padding:0 0.5em"|[Applications]-[Utilities]
|}
:The contents of the [Java Preferences] differ for the version of Mac OS. In case 10.4, use the [General] tab, which is default displayed. In case 10.5 or later, click to display [Network] tab.
:{|style="border:1px solid gray;border-collapse:collapse"
!style="border:1px solid gray;padding:0 0.5em;background-color:lightyellow"|Max OS X 10.4
!style="border:1px solid gray;padding:0 0.5em;background-color:lightyellow"|Max OS X 10.5 or later
|-
|style="border:1px solid gray;padding:0.5ex 0.5em;text-align:center;vertical-align:top"|[[File:Javapref_tiger.png|400px]]
|style="border:1px solid gray;padding:0.5ex 0.5em;text-align:center;vertical-align:top"|[[File:Java_prefs1.png|400px]]&lt;br/&gt;&amp;darr;&lt;br/&gt;[[File:Java_prefs2.png|400px]]
|}

;2) Press 'Delete Files...' button
:The [Delete Temporary Files] window, which asks which items are to remove, will be opened.

:[[File:Javacache_del_en.png]]

;3) Leave all the checkboxs on and click 'OK' button.

;4) In some case, restoring the Java environment to the default may be also required. 
:To do it, click "Restore Defaults" button in the Java Preferences (the following figure is the case of Mac OS X 10.6).
:[[File:Javapref_general_10_6.png]]

===remove local JOGL library===

Older versions of jV asked users to install JOGL libraries locally;
however, manual installation of JOGL is not necessary for recent jV.
Locally-installed JOGL libraries of different version cause conflicts with
recent distributions of jV and should be removed.
JOGL library files are different between operating systems.

'''Mac OS X'''

Open the [Macintosh HD]-[Library]-[Java]-[Extensions] folder.
If some of the following files

* jogl.jar
* gluegen-rt.jar
* libjogl.jnilib
* libjogl_awt.jnilib
* libjogl_cg.jnilib
* libgluegen-rt.jnilib

exist in the folder, remove them.
Here, this operation requires root privilege.

'''Windows'''

Files that should be removed are as follows.

* &lt;JRE&gt;\lib\ext\jogl.jar
* &lt;JRE&gt;\lib\ext\gluegen-rt.jar
* &lt;JRE&gt;\bin\jogl.dll
* &lt;JRE&gt;\bin\jogl_cg.dll
* &lt;JRE&gt;\bin\jogl_awt.dll
* &lt;JRE&gt;\bin\gluegen-rt.dll

Here, &lt;JRE&gt; denotes the folder that JRE has been installed; typically &lt;JRE&gt;=C:\Program Files\Java\jre6.

'''Linux'''

Files that should be removed are as follows.

* &lt;JRE&gt;/lib/ext/jogl.jar
* &lt;JRE&gt;/lib/ext/gluegen-rt.jar
* &lt;JRE&gt;/lib/&lt;arch&gt;/libjogl.so
* &lt;JRE&gt;/lib/&lt;arch&gt;/libjogl_cg.so
* &lt;JRE&gt;/lib/&lt;arch&gt;/libjogl_awt.so
* &lt;JRE&gt;/lib/&lt;arch&gt;/libjogl_drihack.so
* &lt;JRE&gt;/lib/&lt;arch&gt;/libgluegen-rt.so

Here, &lt;JRE&gt; denotes the directory that JRE has been installed; typically &lt;JRE&gt;=/usr/java/jdk1.6.0_17/jre,
and &lt;arch&gt; the processor architecture such as &lt;arch&gt;=i386.</text>
    <sha1>70cf3012ac0b3d59e11a9cf4361cfd086ab979d3</sha1>
  </revision>
  <revision>
    <id>535</id>
    <parentid>534</parentid>
    <timestamp>2013-03-18T05:59:42Z</timestamp>
    <contributor>
      <username>IMSsato</username>
      <id>4</id>
    </contributor>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="5959" xml:space="preserve">{| style="left"
 |__TOC__
 |}

== Latest environment is recommended ==

Using latest version of Java and jV is recommended to avoid problems.
Following issues are known for older versions of them.

* jV applet fails to start on JRE 1.6.0_15 and 1.6.0_16 by a certificate error.
* Java's file-cache functionality causes a problem on JRE 1.6.0_15 and 1.6.0_16.
* jV applet fails to start on JRE 1.6.0_21 because of a conflict with next-generation Java Plug-in.
* jV of versions eariler than 4.1 do not run as an applet on recent Mac OS.

=== JRE 1.7 is required on Mac OS 10.7 or later ===

Apple-provided Java SE 6 does not support Java applets now.
The following changes were made at Java 1.6.0_37[http://support.apple.com/kb/HT5493]:

# All the java plug-ins for every web browser provided from Apple Inc. will be removed.
# The "Java Preferences" application will be removed.

If you access a web page containing a Java applet and click on the region labeled "Missing plug-in",
you can go to a download page of JRE 1.7.
When JRE 1.7 is installed, you can use Java applets.
It is reported, however, that Java Web Start fails to start with JRE 1.7 in some cases,
and the issue is not resolved yet.

== JOGL library conflict ==

If you cannot start jV via Java Web Start or view jV applets due to a failure of locating the JOGL library, try the followings.

===clear cached files===

Previously cached JOGL files may be the cause of a problem
(on JRE 1.6.0_15 and 1.6.0_16, cached JOGL files conflict with newer files placed on the server).
The following steps show how to clear cached files. 

;1) Open Java Control Panel
:In Windows, double-click the [Java] icon located at Control Panel. In Mac OS, click the [Java] icon in System Preferences.

;2) Open Java Cache Viewer
:On the Java Control Panel, select [General] tab and click [View...] button at the section of Temporary Internet Files, then Java Cache Viewer window appears.

;3) Remove cache files
:In Java Cache Viewer, you can switch categories with [Show:] pull-down list. Remove all cache files in [Applications] and [Resources] categories.

In old versions of Mac OS, Java Preferences utility is offered instead of Java Control Panel.
In such cases, use Java Preferences as follows.
;1) Open the Java Preferences window
:Double-click the [Java Preferences] icon, then the Java Preferences window appears. The place of [Java Preferences] depends on the version of Mac OS as following:
:{|style="border:1px solid gray;border-collapse:collapse"
!style="border:1px solid gray;padding:0 0.5em;background-color:lightyellow"|Max OS X version
!style="border:1px solid gray;padding:0 0.5em;background-color:lightyellow"|place
|-
|style="border:1px solid gray;padding:0 0.5em"|10.4
|style="border:1px solid gray;padding:0 0.5em"|[Applications]-[Utilities]-[Java]-[J2SE 5.0]
|-
|style="border:1px solid gray;padding:0 0.5em"|10.5 (before installing Java for Mac OS X 10.5 Update 4)
|style="border:1px solid gray;padding:0 0.5em"|[Applications]-[Utilities]-[Java]
|-
|style="border:1px solid gray;padding:0 0.5em"|10.5 (after installing Java for Mac OS X 10.5 Update 4 or later)
|style="border:1px solid gray;padding:0 0.5em"|[Applications]-[Utilities]
|-
|style="border:1px solid gray;padding:0 0.5em"|10.6
|style="border:1px solid gray;padding:0 0.5em"|[Applications]-[Utilities]
|}
:The contents of the [Java Preferences] differ for the version of Mac OS. In case 10.4, use the [General] tab, which is default displayed. In case 10.5 or later, click to display [Network] tab.
:{|style="border:1px solid gray;border-collapse:collapse"
!style="border:1px solid gray;padding:0 0.5em;background-color:lightyellow"|Max OS X 10.4
!style="border:1px solid gray;padding:0 0.5em;background-color:lightyellow"|Max OS X 10.5 or later
|-
|style="border:1px solid gray;padding:0.5ex 0.5em;text-align:center;vertical-align:top"|[[File:Javapref_tiger.png|400px]]
|style="border:1px solid gray;padding:0.5ex 0.5em;text-align:center;vertical-align:top"|[[File:Java_prefs1.png|400px]]&lt;br/&gt;&amp;darr;&lt;br/&gt;[[File:Java_prefs2.png|400px]]
|}

;2) Press 'Delete Files...' button
:The [Delete Temporary Files] window, which asks which items are to remove, will be opened.

:[[File:Javacache_del_en.png]]

;3) Leave all the checkboxs on and click 'OK' button.

;4) In some case, restoring the Java environment to the default may be also required. 
:To do it, click "Restore Defaults" button in the Java Preferences (the following figure is the case of Mac OS X 10.6).
:[[File:Javapref_general_10_6.png]]

===remove local JOGL library===

Older versions of jV asked users to install JOGL libraries locally;
however, manual installation of JOGL is not necessary for recent jV.
Locally-installed JOGL libraries of different version cause conflicts with
recent distributions of jV and should be removed.
JOGL library files are different between operating systems.

'''Mac OS X'''

Open the [Macintosh HD]-[Library]-[Java]-[Extensions] folder.
If some of the following files

* jogl.jar
* gluegen-rt.jar
* libjogl.jnilib
* libjogl_awt.jnilib
* libjogl_cg.jnilib
* libgluegen-rt.jnilib

exist in the folder, remove them.
Here, this operation requires root privilege.

'''Windows'''

Files that should be removed are as follows.

* &lt;JRE&gt;\lib\ext\jogl.jar
* &lt;JRE&gt;\lib\ext\gluegen-rt.jar
* &lt;JRE&gt;\bin\jogl.dll
* &lt;JRE&gt;\bin\jogl_cg.dll
* &lt;JRE&gt;\bin\jogl_awt.dll
* &lt;JRE&gt;\bin\gluegen-rt.dll

Here, &lt;JRE&gt; denotes the folder that JRE has been installed; typically &lt;JRE&gt;=C:\Program Files\Java\jre6.

'''Linux'''

Files that should be removed are as follows.

* &lt;JRE&gt;/lib/ext/jogl.jar
* &lt;JRE&gt;/lib/ext/gluegen-rt.jar
* &lt;JRE&gt;/lib/&lt;arch&gt;/libjogl.so
* &lt;JRE&gt;/lib/&lt;arch&gt;/libjogl_cg.so
* &lt;JRE&gt;/lib/&lt;arch&gt;/libjogl_awt.so
* &lt;JRE&gt;/lib/&lt;arch&gt;/libjogl_drihack.so
* &lt;JRE&gt;/lib/&lt;arch&gt;/libgluegen-rt.so

Here, &lt;JRE&gt; denotes the directory that JRE has been installed; typically &lt;JRE&gt;=/usr/java/jdk1.6.0_17/jre,
and &lt;arch&gt; the processor architecture such as &lt;arch&gt;=i386.</text>
    <sha1>ccbaa8a05467baf11d4493c62b67e6a48a577c0c</sha1>
  </revision>
  <revision>
    <id>536</id>
    <parentid>535</parentid>
    <timestamp>2013-03-18T06:01:47Z</timestamp>
    <contributor>
      <username>IMSsato</username>
      <id>4</id>
    </contributor>
    <comment>/* JOGL library conflict */</comment>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="5964" xml:space="preserve">{| style="left"
 |__TOC__
 |}

== Latest environment is recommended ==

Using latest version of Java and jV is recommended to avoid problems.
Following issues are known for older versions of them.

* jV applet fails to start on JRE 1.6.0_15 and 1.6.0_16 by a certificate error.
* Java's file-cache functionality causes a problem on JRE 1.6.0_15 and 1.6.0_16.
* jV applet fails to start on JRE 1.6.0_21 because of a conflict with next-generation Java Plug-in.
* jV of versions eariler than 4.1 do not run as an applet on recent Mac OS.

=== JRE 1.7 is required on Mac OS 10.7 or later ===

Apple-provided Java SE 6 does not support Java applets now.
The following changes were made at Java 1.6.0_37[http://support.apple.com/kb/HT5493]:

# All the java plug-ins for every web browser provided from Apple Inc. will be removed.
# The "Java Preferences" application will be removed.

If you access a web page containing a Java applet and click on the region labeled "Missing plug-in",
you can go to a download page of JRE 1.7.
When JRE 1.7 is installed, you can use Java applets.
It is reported, however, that Java Web Start fails to start with JRE 1.7 in some cases,
and the issue is not resolved yet.

== JOGL library conflict ==

If you cannot start jV as a standalone program or view jV applets due to a failure of locating the JOGL library, try the followings.

===clear cached files===

Previously cached JOGL files may be the cause of a problem
(on JRE 1.6.0_15 and 1.6.0_16, cached JOGL files conflict with newer files placed on the server).
The following steps show how to clear cached files. 

;1) Open Java Control Panel
:In Windows, double-click the [Java] icon located at Control Panel. In Mac OS, click the [Java] icon in System Preferences.

;2) Open Java Cache Viewer
:On the Java Control Panel, select [General] tab and click [View...] button at the section of Temporary Internet Files, then Java Cache Viewer window appears.

;3) Remove cache files
:In Java Cache Viewer, you can switch categories with [Show:] pull-down list. Remove all cache files in [Applications] and [Resources] categories.

In old versions of Mac OS, Java Preferences utility is offered instead of Java Control Panel.
In such cases, use Java Preferences as follows.
;1) Open the Java Preferences window
:Double-click the [Java Preferences] icon, then the Java Preferences window appears. The place of [Java Preferences] depends on the version of Mac OS as following:
:{|style="border:1px solid gray;border-collapse:collapse"
!style="border:1px solid gray;padding:0 0.5em;background-color:lightyellow"|Max OS X version
!style="border:1px solid gray;padding:0 0.5em;background-color:lightyellow"|place
|-
|style="border:1px solid gray;padding:0 0.5em"|10.4
|style="border:1px solid gray;padding:0 0.5em"|[Applications]-[Utilities]-[Java]-[J2SE 5.0]
|-
|style="border:1px solid gray;padding:0 0.5em"|10.5 (before installing Java for Mac OS X 10.5 Update 4)
|style="border:1px solid gray;padding:0 0.5em"|[Applications]-[Utilities]-[Java]
|-
|style="border:1px solid gray;padding:0 0.5em"|10.5 (after installing Java for Mac OS X 10.5 Update 4 or later)
|style="border:1px solid gray;padding:0 0.5em"|[Applications]-[Utilities]
|-
|style="border:1px solid gray;padding:0 0.5em"|10.6
|style="border:1px solid gray;padding:0 0.5em"|[Applications]-[Utilities]
|}
:The contents of the [Java Preferences] differ for the version of Mac OS. In case 10.4, use the [General] tab, which is default displayed. In case 10.5 or later, click to display [Network] tab.
:{|style="border:1px solid gray;border-collapse:collapse"
!style="border:1px solid gray;padding:0 0.5em;background-color:lightyellow"|Max OS X 10.4
!style="border:1px solid gray;padding:0 0.5em;background-color:lightyellow"|Max OS X 10.5 or later
|-
|style="border:1px solid gray;padding:0.5ex 0.5em;text-align:center;vertical-align:top"|[[File:Javapref_tiger.png|400px]]
|style="border:1px solid gray;padding:0.5ex 0.5em;text-align:center;vertical-align:top"|[[File:Java_prefs1.png|400px]]&lt;br/&gt;&amp;darr;&lt;br/&gt;[[File:Java_prefs2.png|400px]]
|}

;2) Press 'Delete Files...' button
:The [Delete Temporary Files] window, which asks which items are to remove, will be opened.

:[[File:Javacache_del_en.png]]

;3) Leave all the checkboxs on and click 'OK' button.

;4) In some case, restoring the Java environment to the default may be also required. 
:To do it, click "Restore Defaults" button in the Java Preferences (the following figure is the case of Mac OS X 10.6).
:[[File:Javapref_general_10_6.png]]

===remove local JOGL library===

Older versions of jV asked users to install JOGL libraries locally;
however, manual installation of JOGL is not necessary for recent jV.
Locally-installed JOGL libraries of different version cause conflicts with
recent distributions of jV and should be removed.
JOGL library files are different between operating systems.

'''Mac OS X'''

Open the [Macintosh HD]-[Library]-[Java]-[Extensions] folder.
If some of the following files

* jogl.jar
* gluegen-rt.jar
* libjogl.jnilib
* libjogl_awt.jnilib
* libjogl_cg.jnilib
* libgluegen-rt.jnilib

exist in the folder, remove them.
Here, this operation requires root privilege.

'''Windows'''

Files that should be removed are as follows.

* &lt;JRE&gt;\lib\ext\jogl.jar
* &lt;JRE&gt;\lib\ext\gluegen-rt.jar
* &lt;JRE&gt;\bin\jogl.dll
* &lt;JRE&gt;\bin\jogl_cg.dll
* &lt;JRE&gt;\bin\jogl_awt.dll
* &lt;JRE&gt;\bin\gluegen-rt.dll

Here, &lt;JRE&gt; denotes the folder that JRE has been installed; typically &lt;JRE&gt;=C:\Program Files\Java\jre6.

'''Linux'''

Files that should be removed are as follows.

* &lt;JRE&gt;/lib/ext/jogl.jar
* &lt;JRE&gt;/lib/ext/gluegen-rt.jar
* &lt;JRE&gt;/lib/&lt;arch&gt;/libjogl.so
* &lt;JRE&gt;/lib/&lt;arch&gt;/libjogl_cg.so
* &lt;JRE&gt;/lib/&lt;arch&gt;/libjogl_awt.so
* &lt;JRE&gt;/lib/&lt;arch&gt;/libjogl_drihack.so
* &lt;JRE&gt;/lib/&lt;arch&gt;/libgluegen-rt.so

Here, &lt;JRE&gt; denotes the directory that JRE has been installed; typically &lt;JRE&gt;=/usr/java/jdk1.6.0_17/jre,
and &lt;arch&gt; the processor architecture such as &lt;arch&gt;=i386.</text>
    <sha1>4a1b1e005f68386e7b9d05d8dbb072714ce6dbfd</sha1>
  </revision>
  <revision>
    <id>537</id>
    <parentid>536</parentid>
    <timestamp>2013-03-18T06:04:40Z</timestamp>
    <contributor>
      <username>IMSsato</username>
      <id>4</id>
    </contributor>
    <comment>/* JOGL library conflict */</comment>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="5333" xml:space="preserve">{| style="left"
 |__TOC__
 |}

== Latest environment is recommended ==

Using latest version of Java and jV is recommended to avoid problems.
Following issues are known for older versions of them.

* jV applet fails to start on JRE 1.6.0_15 and 1.6.0_16 by a certificate error.
* Java's file-cache functionality causes a problem on JRE 1.6.0_15 and 1.6.0_16.
* jV applet fails to start on JRE 1.6.0_21 because of a conflict with next-generation Java Plug-in.
* jV of versions eariler than 4.1 do not run as an applet on recent Mac OS.

=== JRE 1.7 is required on Mac OS 10.7 or later ===

Apple-provided Java SE 6 does not support Java applets now.
The following changes were made at Java 1.6.0_37[http://support.apple.com/kb/HT5493]:

# All the java plug-ins for every web browser provided from Apple Inc. will be removed.
# The "Java Preferences" application will be removed.

If you access a web page containing a Java applet and click on the region labeled "Missing plug-in",
you can go to a download page of JRE 1.7.
When JRE 1.7 is installed, you can use Java applets.
It is reported, however, that Java Web Start fails to start with JRE 1.7 in some cases,
and the issue is not resolved yet.

== JOGL library conflict ==

If you cannot start jV as a standalone program or view jV applets due to a failure of locating the JOGL library, try the followings.

===clear cached files===

Previously cached JOGL files may be the cause of a problem
(on JRE 1.6.0_15 and 1.6.0_16, cached JOGL files conflict with newer files placed on the server).
The following steps show how to clear cached files. 

;1) Open Java Control Panel
:In Windows, double-click the [Java] icon located at Control Panel. In Mac OS, click the [Java] icon in System Preferences.

;2) Open Java Cache Viewer
:On the Java Control Panel, select [General] tab and click [View...] button at the section of Temporary Internet Files, then Java Cache Viewer window appears.

;3) Remove cache files
:In Java Cache Viewer, you can switch categories with [Show:] pull-down list. Remove all cache files in [Applications] and [Resources] categories.

In old versions of Mac OS, Java Preferences utility is offered instead of Java Control Panel.
In such cases, use Java Preferences as follows.
;1) Open the Java Preferences window
:Double-click the [Java Preferences] icon, then the Java Preferences window appears. The place of [Java Preferences] depends on the version of Mac OS as following:
:{|style="border:1px solid gray;border-collapse:collapse"
!style="border:1px solid gray;padding:0 0.5em;background-color:lightyellow"|Max OS X version
!style="border:1px solid gray;padding:0 0.5em;background-color:lightyellow"|place
|-
|style="border:1px solid gray;padding:0 0.5em"|10.4
|style="border:1px solid gray;padding:0 0.5em"|[Applications]-[Utilities]-[Java]-[J2SE 5.0]
|-
|style="border:1px solid gray;padding:0 0.5em"|10.5 (before installing Java for Mac OS X 10.5 Update 4)
|style="border:1px solid gray;padding:0 0.5em"|[Applications]-[Utilities]-[Java]
|-
|style="border:1px solid gray;padding:0 0.5em"|10.5 (after installing Java for Mac OS X 10.5 Update 4 or later)
|style="border:1px solid gray;padding:0 0.5em"|[Applications]-[Utilities]
|-
|style="border:1px solid gray;padding:0 0.5em"|10.6
|style="border:1px solid gray;padding:0 0.5em"|[Applications]-[Utilities]
|}
:The contents of the [Java Preferences] differ for the version of Mac OS. In case 10.4, use the [General] tab, which is default displayed. In case 10.5 or later, click to display [Network] tab.

;2) Press 'Delete Files...' button
:The [Delete Temporary Files] window, which asks which items are to remove, will be opened.

:[[File:Javacache_del_en.png]]

;3) Leave all the checkboxs on and click 'OK' button.

;4) In some case, restoring the Java environment to the default may be also required. 
:To do it, click "Restore Defaults" button in the [General] tab.

===remove local JOGL library===

Older versions of jV asked users to install JOGL libraries locally;
however, manual installation of JOGL is not necessary for recent jV.
Locally-installed JOGL libraries of different version cause conflicts with
recent distributions of jV and should be removed.
JOGL library files are different between operating systems.

'''Mac OS X'''

Open the [Macintosh HD]-[Library]-[Java]-[Extensions] folder.
If some of the following files

* jogl.jar
* gluegen-rt.jar
* libjogl.jnilib
* libjogl_awt.jnilib
* libjogl_cg.jnilib
* libgluegen-rt.jnilib

exist in the folder, remove them.
Here, this operation requires root privilege.

'''Windows'''

Files that should be removed are as follows.

* &lt;JRE&gt;\lib\ext\jogl.jar
* &lt;JRE&gt;\lib\ext\gluegen-rt.jar
* &lt;JRE&gt;\bin\jogl.dll
* &lt;JRE&gt;\bin\jogl_cg.dll
* &lt;JRE&gt;\bin\jogl_awt.dll
* &lt;JRE&gt;\bin\gluegen-rt.dll

Here, &lt;JRE&gt; denotes the folder that JRE has been installed; typically &lt;JRE&gt;=C:\Program Files\Java\jre6.

'''Linux'''

Files that should be removed are as follows.

* &lt;JRE&gt;/lib/ext/jogl.jar
* &lt;JRE&gt;/lib/ext/gluegen-rt.jar
* &lt;JRE&gt;/lib/&lt;arch&gt;/libjogl.so
* &lt;JRE&gt;/lib/&lt;arch&gt;/libjogl_cg.so
* &lt;JRE&gt;/lib/&lt;arch&gt;/libjogl_awt.so
* &lt;JRE&gt;/lib/&lt;arch&gt;/libjogl_drihack.so
* &lt;JRE&gt;/lib/&lt;arch&gt;/libgluegen-rt.so

Here, &lt;JRE&gt; denotes the directory that JRE has been installed; typically &lt;JRE&gt;=/usr/java/jdk1.6.0_17/jre,
and &lt;arch&gt; the processor architecture such as &lt;arch&gt;=i386.</text>
    <sha1>be46a32469ed86d1d6ede19f1abca13714e5cb14</sha1>
  </revision>
  <revision>
    <id>539</id>
    <parentid>537</parentid>
    <timestamp>2013-03-18T06:19:20Z</timestamp>
    <contributor>
      <username>IMSsato</username>
      <id>4</id>
    </contributor>
    <comment>/* JOGL library conflict */</comment>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="5371" xml:space="preserve">{| style="left"
 |__TOC__
 |}

== Latest environment is recommended ==

Using latest version of Java and jV is recommended to avoid problems.
Following issues are known for older versions of them.

* jV applet fails to start on JRE 1.6.0_15 and 1.6.0_16 by a certificate error.
* Java's file-cache functionality causes a problem on JRE 1.6.0_15 and 1.6.0_16.
* jV applet fails to start on JRE 1.6.0_21 because of a conflict with next-generation Java Plug-in.
* jV of versions eariler than 4.1 do not run as an applet on recent Mac OS.

=== JRE 1.7 is required on Mac OS 10.7 or later ===

Apple-provided Java SE 6 does not support Java applets now.
The following changes were made at Java 1.6.0_37[http://support.apple.com/kb/HT5493]:

# All the java plug-ins for every web browser provided from Apple Inc. will be removed.
# The "Java Preferences" application will be removed.

If you access a web page containing a Java applet and click on the region labeled "Missing plug-in",
you can go to a download page of JRE 1.7.
When JRE 1.7 is installed, you can use Java applets.
It is reported, however, that Java Web Start fails to start with JRE 1.7 in some cases,
and the issue is not resolved yet.

== JOGL library conflict ==

If you cannot start jV as a standalone program or view jV applets due to a failure of locating the JOGL library, try the followings.

===clear cached files===

Previously cached JOGL files may be the cause of a problem
(on JRE 1.6.0_15 and 1.6.0_16, cached JOGL files conflict with newer files placed on the server).
The following steps show how to clear cached files. 

;1) Open Java Control Panel
:In Windows, double-click the [Java] icon located at Control Panel. In Mac OS, click the [Java] icon in System Preferences.

;2) Open Java Cache Viewer
:On the Java Control Panel, select [General] tab and click [View...] button at the section of Temporary Internet Files, then Java Cache Viewer window appears.
:[[File:Java_cache_viewer.png|600px]]

;3) Remove cache files
:In Java Cache Viewer, you can switch categories with [Show:] pull-down list. Remove all cache files in [Applications] and [Resources] categories.

In old versions of Mac OS, Java Preferences utility is offered instead of Java Control Panel.
In such cases, use Java Preferences as follows.
;1) Open the Java Preferences window
:Double-click the [Java Preferences] icon, then the Java Preferences window appears. The place of [Java Preferences] depends on the version of Mac OS as following:
:{|style="border:1px solid gray;border-collapse:collapse"
!style="border:1px solid gray;padding:0 0.5em;background-color:lightyellow"|Max OS X version
!style="border:1px solid gray;padding:0 0.5em;background-color:lightyellow"|place
|-
|style="border:1px solid gray;padding:0 0.5em"|10.4
|style="border:1px solid gray;padding:0 0.5em"|[Applications]-[Utilities]-[Java]-[J2SE 5.0]
|-
|style="border:1px solid gray;padding:0 0.5em"|10.5 (before installing Java for Mac OS X 10.5 Update 4)
|style="border:1px solid gray;padding:0 0.5em"|[Applications]-[Utilities]-[Java]
|-
|style="border:1px solid gray;padding:0 0.5em"|10.5 (after installing Java for Mac OS X 10.5 Update 4 or later)
|style="border:1px solid gray;padding:0 0.5em"|[Applications]-[Utilities]
|-
|style="border:1px solid gray;padding:0 0.5em"|10.6
|style="border:1px solid gray;padding:0 0.5em"|[Applications]-[Utilities]
|}
:The contents of the [Java Preferences] differ for the version of Mac OS. In case 10.4, use the [General] tab, which is default displayed. In case 10.5 or later, click to display [Network] tab.

;2) Press 'Delete Files...' button
:The [Delete Temporary Files] window, which asks which items are to remove, will be opened.

:[[File:Javacache_del_en.png]]

;3) Leave all the checkboxs on and click 'OK' button.

;4) In some case, restoring the Java environment to the default may be also required. 
:To do it, click "Restore Defaults" button in the [General] tab.

===remove local JOGL library===

Older versions of jV asked users to install JOGL libraries locally;
however, manual installation of JOGL is not necessary for recent jV.
Locally-installed JOGL libraries of different version cause conflicts with
recent distributions of jV and should be removed.
JOGL library files are different between operating systems.

'''Mac OS X'''

Open the [Macintosh HD]-[Library]-[Java]-[Extensions] folder.
If some of the following files

* jogl.jar
* gluegen-rt.jar
* libjogl.jnilib
* libjogl_awt.jnilib
* libjogl_cg.jnilib
* libgluegen-rt.jnilib

exist in the folder, remove them.
Here, this operation requires root privilege.

'''Windows'''

Files that should be removed are as follows.

* &lt;JRE&gt;\lib\ext\jogl.jar
* &lt;JRE&gt;\lib\ext\gluegen-rt.jar
* &lt;JRE&gt;\bin\jogl.dll
* &lt;JRE&gt;\bin\jogl_cg.dll
* &lt;JRE&gt;\bin\jogl_awt.dll
* &lt;JRE&gt;\bin\gluegen-rt.dll

Here, &lt;JRE&gt; denotes the folder that JRE has been installed; typically &lt;JRE&gt;=C:\Program Files\Java\jre6.

'''Linux'''

Files that should be removed are as follows.

* &lt;JRE&gt;/lib/ext/jogl.jar
* &lt;JRE&gt;/lib/ext/gluegen-rt.jar
* &lt;JRE&gt;/lib/&lt;arch&gt;/libjogl.so
* &lt;JRE&gt;/lib/&lt;arch&gt;/libjogl_cg.so
* &lt;JRE&gt;/lib/&lt;arch&gt;/libjogl_awt.so
* &lt;JRE&gt;/lib/&lt;arch&gt;/libjogl_drihack.so
* &lt;JRE&gt;/lib/&lt;arch&gt;/libgluegen-rt.so

Here, &lt;JRE&gt; denotes the directory that JRE has been installed; typically &lt;JRE&gt;=/usr/java/jdk1.6.0_17/jre,
and &lt;arch&gt; the processor architecture such as &lt;arch&gt;=i386.</text>
    <sha1>edc960e347e41ee27264260ac75a6cda77162e3f</sha1>
  </revision>
  <revision>
    <id>540</id>
    <parentid>539</parentid>
    <timestamp>2013-03-18T06:28:02Z</timestamp>
    <contributor>
      <username>IMSsato</username>
      <id>4</id>
    </contributor>
    <comment>/* clear cached files */</comment>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="5371" xml:space="preserve">{| style="left"
 |__TOC__
 |}

== Latest environment is recommended ==

Using latest version of Java and jV is recommended to avoid problems.
Following issues are known for older versions of them.

* jV applet fails to start on JRE 1.6.0_15 and 1.6.0_16 by a certificate error.
* Java's file-cache functionality causes a problem on JRE 1.6.0_15 and 1.6.0_16.
* jV applet fails to start on JRE 1.6.0_21 because of a conflict with next-generation Java Plug-in.
* jV of versions eariler than 4.1 do not run as an applet on recent Mac OS.

=== JRE 1.7 is required on Mac OS 10.7 or later ===

Apple-provided Java SE 6 does not support Java applets now.
The following changes were made at Java 1.6.0_37[http://support.apple.com/kb/HT5493]:

# All the java plug-ins for every web browser provided from Apple Inc. will be removed.
# The "Java Preferences" application will be removed.

If you access a web page containing a Java applet and click on the region labeled "Missing plug-in",
you can go to a download page of JRE 1.7.
When JRE 1.7 is installed, you can use Java applets.
It is reported, however, that Java Web Start fails to start with JRE 1.7 in some cases,
and the issue is not resolved yet.

== JOGL library conflict ==

If you cannot start jV as a standalone program or view jV applets due to a failure of locating the JOGL library, try the followings.

===clear cached files===

Previously cached JOGL files may be the cause of a problem
(on JRE 1.6.0_15 and 1.6.0_16, cached JOGL files conflict with newer files placed on the server).
The following steps show how to clear cached files. 

;1) Open Java Control Panel
:In Windows, double-click the [Java] icon located at Control Panel. In Mac OS, click the [Java] icon in System Preferences.

;2) Open Java Cache Viewer
:On the Java Control Panel, select [General] tab and click [View...] button at the section of Temporary Internet Files, then Java Cache Viewer window appears.
:[[File:Java_cache_viewer.png|600px]]

;3) Remove cache files
:In Java Cache Viewer, you can switch categories with [Show:] pull-down list. Remove all cache files in [Applications] and [Resources] categories.

In old versions of Mac OS, Java Preferences utility is offered instead of Java Control Panel.
In such cases, use Java Preferences as follows.
;1) Open the Java Preferences window
:Double-click the [Java Preferences] icon, then the Java Preferences window appears. The place of [Java Preferences] depends on the version of Mac OS as following:
:{|style="border:1px solid gray;border-collapse:collapse"
!style="border:1px solid gray;padding:0 0.5em;background-color:lightyellow"|Mac OS X version
!style="border:1px solid gray;padding:0 0.5em;background-color:lightyellow"|place
|-
|style="border:1px solid gray;padding:0 0.5em"|10.4
|style="border:1px solid gray;padding:0 0.5em"|[Applications]-[Utilities]-[Java]-[J2SE 5.0]
|-
|style="border:1px solid gray;padding:0 0.5em"|10.5 (before installing Java for Mac OS X 10.5 Update 4)
|style="border:1px solid gray;padding:0 0.5em"|[Applications]-[Utilities]-[Java]
|-
|style="border:1px solid gray;padding:0 0.5em"|10.5 (after installing Java for Mac OS X 10.5 Update 4 or later)
|style="border:1px solid gray;padding:0 0.5em"|[Applications]-[Utilities]
|-
|style="border:1px solid gray;padding:0 0.5em"|10.6
|style="border:1px solid gray;padding:0 0.5em"|[Applications]-[Utilities]
|}
:The contents of the [Java Preferences] differ for the version of Mac OS. In case 10.4, use the [General] tab, which is default displayed. In case 10.5 or later, click to display [Network] tab.

;2) Press 'Delete Files...' button
:The [Delete Temporary Files] window, which asks which items are to remove, will be opened.

:[[File:Javacache_del_en.png]]

;3) Leave all the checkboxs on and click 'OK' button.

;4) In some case, restoring the Java environment to the default may be also required. 
:To do it, click "Restore Defaults" button in the [General] tab.

===remove local JOGL library===

Older versions of jV asked users to install JOGL libraries locally;
however, manual installation of JOGL is not necessary for recent jV.
Locally-installed JOGL libraries of different version cause conflicts with
recent distributions of jV and should be removed.
JOGL library files are different between operating systems.

'''Mac OS X'''

Open the [Macintosh HD]-[Library]-[Java]-[Extensions] folder.
If some of the following files

* jogl.jar
* gluegen-rt.jar
* libjogl.jnilib
* libjogl_awt.jnilib
* libjogl_cg.jnilib
* libgluegen-rt.jnilib

exist in the folder, remove them.
Here, this operation requires root privilege.

'''Windows'''

Files that should be removed are as follows.

* &lt;JRE&gt;\lib\ext\jogl.jar
* &lt;JRE&gt;\lib\ext\gluegen-rt.jar
* &lt;JRE&gt;\bin\jogl.dll
* &lt;JRE&gt;\bin\jogl_cg.dll
* &lt;JRE&gt;\bin\jogl_awt.dll
* &lt;JRE&gt;\bin\gluegen-rt.dll

Here, &lt;JRE&gt; denotes the folder that JRE has been installed; typically &lt;JRE&gt;=C:\Program Files\Java\jre6.

'''Linux'''

Files that should be removed are as follows.

* &lt;JRE&gt;/lib/ext/jogl.jar
* &lt;JRE&gt;/lib/ext/gluegen-rt.jar
* &lt;JRE&gt;/lib/&lt;arch&gt;/libjogl.so
* &lt;JRE&gt;/lib/&lt;arch&gt;/libjogl_cg.so
* &lt;JRE&gt;/lib/&lt;arch&gt;/libjogl_awt.so
* &lt;JRE&gt;/lib/&lt;arch&gt;/libjogl_drihack.so
* &lt;JRE&gt;/lib/&lt;arch&gt;/libgluegen-rt.so

Here, &lt;JRE&gt; denotes the directory that JRE has been installed; typically &lt;JRE&gt;=/usr/java/jdk1.6.0_17/jre,
and &lt;arch&gt; the processor architecture such as &lt;arch&gt;=i386.</text>
    <sha1>3098780ae64ae353d9e44e04e4e131123fe7c54e</sha1>
  </revision>
  <revision>
    <id>545</id>
    <parentid>540</parentid>
    <timestamp>2013-12-06T01:49:40Z</timestamp>
    <contributor>
      <username>Cudo29</username>
      <id>5</id>
    </contributor>
    <comment>An chapter of "Check the environment variable" was added.</comment>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="5749" xml:space="preserve">{| style="left"
 |__TOC__
 |}

== Latest environment is recommended ==

Using latest version of Java and jV is recommended to avoid problems.
Following issues are known for older versions of them.

* jV applet fails to start on JRE 1.6.0_15 and 1.6.0_16 by a certificate error.
* Java's file-cache functionality causes a problem on JRE 1.6.0_15 and 1.6.0_16.
* jV applet fails to start on JRE 1.6.0_21 because of a conflict with next-generation Java Plug-in.
* jV of versions eariler than 4.1 do not run as an applet on recent Mac OS.

=== JRE 1.7 is required on Mac OS 10.7 or later ===

Apple-provided Java SE 6 does not support Java applets now.
The following changes were made at Java 1.6.0_37[http://support.apple.com/kb/HT5493]:

# All the java plug-ins for every web browser provided from Apple Inc. will be removed.
# The "Java Preferences" application will be removed.

If you access a web page containing a Java applet and click on the region labeled "Missing plug-in",
you can go to a download page of JRE 1.7.
When JRE 1.7 is installed, you can use Java applets.
It is reported, however, that Java Web Start fails to start with JRE 1.7 in some cases,
and the issue is not resolved yet.

== JOGL library conflict ==

If you cannot start jV as a standalone program or view jV applets due to a failure of locating the JOGL library, try the followings.

===clear cached files===

Previously cached JOGL files may be the cause of a problem
(on JRE 1.6.0_15 and 1.6.0_16, cached JOGL files conflict with newer files placed on the server).
The following steps show how to clear cached files. 

;1) Open Java Control Panel
:In Windows, double-click the [Java] icon located at Control Panel. In Mac OS, click the [Java] icon in System Preferences.

;2) Open Java Cache Viewer
:On the Java Control Panel, select [General] tab and click [View...] button at the section of Temporary Internet Files, then Java Cache Viewer window appears.
:[[File:Java_cache_viewer.png|600px]]

;3) Remove cache files
:In Java Cache Viewer, you can switch categories with [Show:] pull-down list. Remove all cache files in [Applications] and [Resources] categories.

In old versions of Mac OS, Java Preferences utility is offered instead of Java Control Panel.
In such cases, use Java Preferences as follows.
;1) Open the Java Preferences window
:Double-click the [Java Preferences] icon, then the Java Preferences window appears. The place of [Java Preferences] depends on the version of Mac OS as following:
:{|style="border:1px solid gray;border-collapse:collapse"
!style="border:1px solid gray;padding:0 0.5em;background-color:lightyellow"|Mac OS X version
!style="border:1px solid gray;padding:0 0.5em;background-color:lightyellow"|place
|-
|style="border:1px solid gray;padding:0 0.5em"|10.4
|style="border:1px solid gray;padding:0 0.5em"|[Applications]-[Utilities]-[Java]-[J2SE 5.0]
|-
|style="border:1px solid gray;padding:0 0.5em"|10.5 (before installing Java for Mac OS X 10.5 Update 4)
|style="border:1px solid gray;padding:0 0.5em"|[Applications]-[Utilities]-[Java]
|-
|style="border:1px solid gray;padding:0 0.5em"|10.5 (after installing Java for Mac OS X 10.5 Update 4 or later)
|style="border:1px solid gray;padding:0 0.5em"|[Applications]-[Utilities]
|-
|style="border:1px solid gray;padding:0 0.5em"|10.6
|style="border:1px solid gray;padding:0 0.5em"|[Applications]-[Utilities]
|}
:The contents of the [Java Preferences] differ for the version of Mac OS. In case 10.4, use the [General] tab, which is default displayed. In case 10.5 or later, click to display [Network] tab.

;2) Press 'Delete Files...' button
:The [Delete Temporary Files] window, which asks which items are to remove, will be opened.

:[[File:Javacache_del_en.png]]

;3) Leave all the checkboxs on and click 'OK' button.

;4) In some case, restoring the Java environment to the default may be also required. 
:To do it, click "Restore Defaults" button in the [General] tab.

===remove local JOGL library===

Older versions of jV asked users to install JOGL libraries locally;
however, manual installation of JOGL is not necessary for recent jV.
Locally-installed JOGL libraries of different version cause conflicts with
recent distributions of jV and should be removed.
JOGL library files are different between operating systems.

'''Mac OS X'''

Open the [Macintosh HD]-[Library]-[Java]-[Extensions] folder.
If some of the following files

* jogl.jar
* gluegen-rt.jar
* libjogl.jnilib
* libjogl_awt.jnilib
* libjogl_cg.jnilib
* libgluegen-rt.jnilib

exist in the folder, remove them.
Here, this operation requires root privilege.

'''Windows'''

Files that should be removed are as follows.

* &lt;JRE&gt;\lib\ext\jogl.jar
* &lt;JRE&gt;\lib\ext\gluegen-rt.jar
* &lt;JRE&gt;\bin\jogl.dll
* &lt;JRE&gt;\bin\jogl_cg.dll
* &lt;JRE&gt;\bin\jogl_awt.dll
* &lt;JRE&gt;\bin\gluegen-rt.dll

Here, &lt;JRE&gt; denotes the folder that JRE has been installed; typically &lt;JRE&gt;=C:\Program Files\Java\jre6.

'''Linux'''

Files that should be removed are as follows.

* &lt;JRE&gt;/lib/ext/jogl.jar
* &lt;JRE&gt;/lib/ext/gluegen-rt.jar
* &lt;JRE&gt;/lib/&lt;arch&gt;/libjogl.so
* &lt;JRE&gt;/lib/&lt;arch&gt;/libjogl_cg.so
* &lt;JRE&gt;/lib/&lt;arch&gt;/libjogl_awt.so
* &lt;JRE&gt;/lib/&lt;arch&gt;/libjogl_drihack.so
* &lt;JRE&gt;/lib/&lt;arch&gt;/libgluegen-rt.so

Here, &lt;JRE&gt; denotes the directory that JRE has been installed; typically &lt;JRE&gt;=/usr/java/jdk1.6.0_17/jre,
and &lt;arch&gt; the processor architecture such as &lt;arch&gt;=i386.

==Check the environment variable==
In some environment, especially Windows, you can't launch the stand alone jar version of jV.
If you fell on such trouble, please check the environment variant includes the path of java.

;The name of environment variant
* PATH
* JAVA_HOME
;The value that should be added
:The path of java(.exe). e.g: C:¥Program Files (x86)¥java¥jre7¥bin</text>
    <sha1>2019ee7efd96e9fca02dd54940d4bfc74de94425</sha1>
  </revision>
  <revision>
    <id>546</id>
    <parentid>545</parentid>
    <timestamp>2014-01-08T03:13:33Z</timestamp>
    <contributor>
      <username>Cudo29</username>
      <id>5</id>
    </contributor>
    <comment>/* Radio button/Pull down menu to switch displaying manner doesn't work */ Added new section.</comment>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="6063" xml:space="preserve">{| style="left"
 |__TOC__
 |}

== Latest environment is recommended ==

Using latest version of Java and jV is recommended to avoid problems.
Following issues are known for older versions of them.

* jV applet fails to start on JRE 1.6.0_15 and 1.6.0_16 by a certificate error.
* Java's file-cache functionality causes a problem on JRE 1.6.0_15 and 1.6.0_16.
* jV applet fails to start on JRE 1.6.0_21 because of a conflict with next-generation Java Plug-in.
* jV of versions eariler than 4.1 do not run as an applet on recent Mac OS.

=== JRE 1.7 is required on Mac OS 10.7 or later ===

Apple-provided Java SE 6 does not support Java applets now.
The following changes were made at Java 1.6.0_37[http://support.apple.com/kb/HT5493]:

# All the java plug-ins for every web browser provided from Apple Inc. will be removed.
# The "Java Preferences" application will be removed.

If you access a web page containing a Java applet and click on the region labeled "Missing plug-in",
you can go to a download page of JRE 1.7.
When JRE 1.7 is installed, you can use Java applets.
It is reported, however, that Java Web Start fails to start with JRE 1.7 in some cases,
and the issue is not resolved yet.

== JOGL library conflict ==

If you cannot start jV as a standalone program or view jV applets due to a failure of locating the JOGL library, try the followings.

===clear cached files===

Previously cached JOGL files may be the cause of a problem
(on JRE 1.6.0_15 and 1.6.0_16, cached JOGL files conflict with newer files placed on the server).
The following steps show how to clear cached files. 

;1) Open Java Control Panel
:In Windows, double-click the [Java] icon located at Control Panel. In Mac OS, click the [Java] icon in System Preferences.

;2) Open Java Cache Viewer
:On the Java Control Panel, select [General] tab and click [View...] button at the section of Temporary Internet Files, then Java Cache Viewer window appears.
:[[File:Java_cache_viewer.png|600px]]

;3) Remove cache files
:In Java Cache Viewer, you can switch categories with [Show:] pull-down list. Remove all cache files in [Applications] and [Resources] categories.

In old versions of Mac OS, Java Preferences utility is offered instead of Java Control Panel.
In such cases, use Java Preferences as follows.
;1) Open the Java Preferences window
:Double-click the [Java Preferences] icon, then the Java Preferences window appears. The place of [Java Preferences] depends on the version of Mac OS as following:
:{|style="border:1px solid gray;border-collapse:collapse"
!style="border:1px solid gray;padding:0 0.5em;background-color:lightyellow"|Mac OS X version
!style="border:1px solid gray;padding:0 0.5em;background-color:lightyellow"|place
|-
|style="border:1px solid gray;padding:0 0.5em"|10.4
|style="border:1px solid gray;padding:0 0.5em"|[Applications]-[Utilities]-[Java]-[J2SE 5.0]
|-
|style="border:1px solid gray;padding:0 0.5em"|10.5 (before installing Java for Mac OS X 10.5 Update 4)
|style="border:1px solid gray;padding:0 0.5em"|[Applications]-[Utilities]-[Java]
|-
|style="border:1px solid gray;padding:0 0.5em"|10.5 (after installing Java for Mac OS X 10.5 Update 4 or later)
|style="border:1px solid gray;padding:0 0.5em"|[Applications]-[Utilities]
|-
|style="border:1px solid gray;padding:0 0.5em"|10.6
|style="border:1px solid gray;padding:0 0.5em"|[Applications]-[Utilities]
|}
:The contents of the [Java Preferences] differ for the version of Mac OS. In case 10.4, use the [General] tab, which is default displayed. In case 10.5 or later, click to display [Network] tab.

;2) Press 'Delete Files...' button
:The [Delete Temporary Files] window, which asks which items are to remove, will be opened.

:[[File:Javacache_del_en.png]]

;3) Leave all the checkboxs on and click 'OK' button.

;4) In some case, restoring the Java environment to the default may be also required. 
:To do it, click "Restore Defaults" button in the [General] tab.

===remove local JOGL library===

Older versions of jV asked users to install JOGL libraries locally;
however, manual installation of JOGL is not necessary for recent jV.
Locally-installed JOGL libraries of different version cause conflicts with
recent distributions of jV and should be removed.
JOGL library files are different between operating systems.

'''Mac OS X'''

Open the [Macintosh HD]-[Library]-[Java]-[Extensions] folder.
If some of the following files

* jogl.jar
* gluegen-rt.jar
* libjogl.jnilib
* libjogl_awt.jnilib
* libjogl_cg.jnilib
* libgluegen-rt.jnilib

exist in the folder, remove them.
Here, this operation requires root privilege.

'''Windows'''

Files that should be removed are as follows.

* &lt;JRE&gt;\lib\ext\jogl.jar
* &lt;JRE&gt;\lib\ext\gluegen-rt.jar
* &lt;JRE&gt;\bin\jogl.dll
* &lt;JRE&gt;\bin\jogl_cg.dll
* &lt;JRE&gt;\bin\jogl_awt.dll
* &lt;JRE&gt;\bin\gluegen-rt.dll

Here, &lt;JRE&gt; denotes the folder that JRE has been installed; typically &lt;JRE&gt;=C:\Program Files\Java\jre6.

'''Linux'''

Files that should be removed are as follows.

* &lt;JRE&gt;/lib/ext/jogl.jar
* &lt;JRE&gt;/lib/ext/gluegen-rt.jar
* &lt;JRE&gt;/lib/&lt;arch&gt;/libjogl.so
* &lt;JRE&gt;/lib/&lt;arch&gt;/libjogl_cg.so
* &lt;JRE&gt;/lib/&lt;arch&gt;/libjogl_awt.so
* &lt;JRE&gt;/lib/&lt;arch&gt;/libjogl_drihack.so
* &lt;JRE&gt;/lib/&lt;arch&gt;/libgluegen-rt.so

Here, &lt;JRE&gt; denotes the directory that JRE has been installed; typically &lt;JRE&gt;=/usr/java/jdk1.6.0_17/jre,
and &lt;arch&gt; the processor architecture such as &lt;arch&gt;=i386.

==Check the environment variable==
In some environment, especially Windows, you can't launch the stand alone jar version of jV.
If you fell on such trouble, please check the environment variant includes the path of java.

;The name of environment variant
* PATH
* JAVA_HOME
;The value that should be added
:The path of java(.exe). e.g: C:¥Program Files (x86)¥java¥jre7¥bin

==Radio button/Pull down menu to switch displaying manner doesn't work==
When you browse jV applet pages such as in PDBj Mine and the radio button or pull down menu doesn't work,
please try following procedures.

# Close the jV applet page.
# Terminate all running Java Applet application.
# Open the page again.</text>
    <sha1>b19187e555b4e3f1dc992088cf7f98c0432dbca7</sha1>
  </revision>
</page>
<page arvcontinue="20120326072111|504">
  <title>Use jV applet with JNLP file</title>
  <ns>0</ns>
  <id>68</id>
  <revision>
    <id>512</id>
    <parentid>499</parentid>
    <timestamp>2013-02-25T05:05:50Z</timestamp>
    <contributor>
      <username>IMSsato</username>
      <id>4</id>
    </contributor>
    <minor/>
    <comment>moved [[Use jV with next-generation Java Plug-in]] to [[Use jV applet with JNLP file]]</comment>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="2156" xml:space="preserve">A brief introduction to use jV as applet with next-generation Java Plug-in.
Note that the next-generation Java Plug-in is not available before JRE 1.6.0_10.

== Example ==
The following code snippet shows how to embed jV applet in a web page.

 &lt;applet name="jVwindow" height="600" width="600" code="org.pdbj.viewer.gui.ViewerApplet"&gt;
   &lt;param name="jnlp_href" value="jV-applet.jnlp"/&gt;
   &lt;param name="java_arguments" value="-Dsun.java2d.noddraw=true"/&gt;
   &amp;lt;!-- replace the following with an appropriate URL --&gt;
   &lt;param name="pdbmlURL" value="http://eprots.protein.osaka-u.ac.jp/Rep_PDBML/1ashA1.xml.gz"&gt;
   &lt;param name="commands" value="cartoon;color group" name="commands"&gt;
   &lt;script type="text/javascript"&gt;
   &amp;lt;!-- 
   if(navigator.userAgent.indexOf("Mac") != -1 ){
     document.write('&lt;param name="newt" value="true"/&gt;');
   }
   //--&gt;
   &lt;/script&gt;
 &lt;/applet&gt;

Note that jV version 4.1 requires an applet parameter newt set to true when the user's OS is Mac OS X.
The example assumes that a file named jV-applet.jnlp is placed at the same location as the HTML file that contains above applet tag. The contents of jV-applet.jnlp is as follows.

 &lt;?xml version="1.0" encoding="UTF-8"?&gt;
 &lt;jnlp href="jV-applet.jnlp"&gt;
   &lt;information&gt;
     &lt;title&gt;jV&lt;/title&gt;
     &lt;vendor&gt;Protein Data Bank Japan&lt;/vendor&gt;
     &lt;homepage href="http://ef-site.hgc.jp/jV/"/&gt;
     &lt;description&gt;Program to display molecular graphics of proteins and nucleic acids&lt;/description&gt;
     &lt;description kind="short"&gt;&lt;/description&gt;
     &lt;offline-allowed/&gt;
   &lt;/information&gt;
   &lt;resources&gt;
     &lt;j2se href="http://java.sun.com/products/autodl/j2se" version="1.4+"/&gt;
     &lt;property name="sun.java2d.noddraw" value="true"/&gt;
     &lt;jar href="jv4_1.jar"/&gt;
     &lt;extension name="jogl-all-awt" href="http://jogamp.org/deployment/jogamp-current/jogl-all-awt.jnlp" /&gt;
   &lt;/resources&gt;
   &lt;applet-desc
       name="jV"
       main-class="org.pdbj.viewer.gui.ViewerApplet"
       width="500"
       height="500"&gt;
   &lt;/applet-desc&gt;
 &lt;/jnlp&gt;

Here, applet-desc tag has name, width and height attributes. These are required, however, their values are overridden by those of applet tag in HTML.</text>
    <sha1>35843c4f6475270cf57d8571d672bf9b41d2f7b1</sha1>
  </revision>
  <revision>
    <id>515</id>
    <parentid>512</parentid>
    <timestamp>2013-02-25T05:10:28Z</timestamp>
    <contributor>
      <username>IMSsato</username>
      <id>4</id>
    </contributor>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="2314" xml:space="preserve">A brief introduction to use jV as applet with JNLP file.
Note that JNLP file works with the next-generation Java Plug-in and is not available before JRE 1.6.0_10.
If you place multiple applets on a single web page, using applet-launcher rather than JNLP file is
recommended because of a start-up stability problem.

== Example ==
The following code snippet shows how to embed jV applet in a web page.

 &lt;applet name="jVwindow" height="600" width="600" code="org.pdbj.viewer.gui.ViewerApplet"&gt;
   &lt;param name="jnlp_href" value="jV-applet.jnlp"/&gt;
   &lt;param name="java_arguments" value="-Dsun.java2d.noddraw=true"/&gt;
   &amp;lt;!-- replace the following with an appropriate URL --&gt;
   &lt;param name="pdbmlURL" value="http://eprots.protein.osaka-u.ac.jp/Rep_PDBML/1ashA1.xml.gz"&gt;
   &lt;param name="commands" value="cartoon;color group" name="commands"&gt;
   &lt;script type="text/javascript"&gt;
   &amp;lt;!-- 
   if(navigator.userAgent.indexOf("Mac") != -1 ){
     document.write('&lt;param name="newt" value="true"/&gt;');
   }
   //--&gt;
   &lt;/script&gt;
 &lt;/applet&gt;

Note that jV version 4.1 requires an applet parameter newt set to true when the user's OS is Mac OS X.
The example assumes that a file named jV-applet.jnlp is placed at the same location as the HTML file that contains above applet tag. The contents of jV-applet.jnlp is as follows.

 &lt;?xml version="1.0" encoding="UTF-8"?&gt;
 &lt;jnlp href="jV-applet.jnlp"&gt;
   &lt;information&gt;
     &lt;title&gt;jV&lt;/title&gt;
     &lt;vendor&gt;Protein Data Bank Japan&lt;/vendor&gt;
     &lt;homepage href="http://ef-site.hgc.jp/jV/"/&gt;
     &lt;description&gt;Program to display molecular graphics of proteins and nucleic acids&lt;/description&gt;
     &lt;description kind="short"&gt;&lt;/description&gt;
     &lt;offline-allowed/&gt;
   &lt;/information&gt;
   &lt;resources&gt;
     &lt;j2se href="http://java.sun.com/products/autodl/j2se" version="1.4+"/&gt;
     &lt;property name="sun.java2d.noddraw" value="true"/&gt;
     &lt;jar href="jv4_1.jar"/&gt;
     &lt;extension name="jogl-all-awt" href="http://jogamp.org/deployment/jogamp-current/jogl-all-awt.jnlp" /&gt;
   &lt;/resources&gt;
   &lt;applet-desc
       name="jV"
       main-class="org.pdbj.viewer.gui.ViewerApplet"
       width="500"
       height="500"&gt;
   &lt;/applet-desc&gt;
 &lt;/jnlp&gt;

Here, applet-desc tag has name, width and height attributes. These are required, however, their values are overridden by those of applet tag in HTML.</text>
    <sha1>1ad8d7a966bd51ed8a80c3062076601edcd1c183</sha1>
  </revision>
  <revision>
    <id>519</id>
    <parentid>515</parentid>
    <timestamp>2013-02-25T05:12:02Z</timestamp>
    <contributor>
      <username>IMSsato</username>
      <id>4</id>
    </contributor>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="2360" xml:space="preserve">A brief introduction to use jV as applet with JNLP file.
Note that JNLP file works with the next-generation Java Plug-in and is not available before JRE 1.6.0_10.
If you place multiple applets on a single web page, using applet-launcher (see [[Use jV applet with applet launcher]]
)
rather than JNLP file is recommended because of a start-up stability problem.

== Example ==
The following code snippet shows how to embed jV applet in a web page.

 &lt;applet name="jVwindow" height="600" width="600" code="org.pdbj.viewer.gui.ViewerApplet"&gt;
   &lt;param name="jnlp_href" value="jV-applet.jnlp"/&gt;
   &lt;param name="java_arguments" value="-Dsun.java2d.noddraw=true"/&gt;
   &amp;lt;!-- replace the following with an appropriate URL --&gt;
   &lt;param name="pdbmlURL" value="http://eprots.protein.osaka-u.ac.jp/Rep_PDBML/1ashA1.xml.gz"&gt;
   &lt;param name="commands" value="cartoon;color group" name="commands"&gt;
   &lt;script type="text/javascript"&gt;
   &amp;lt;!-- 
   if(navigator.userAgent.indexOf("Mac") != -1 ){
     document.write('&lt;param name="newt" value="true"/&gt;');
   }
   //--&gt;
   &lt;/script&gt;
 &lt;/applet&gt;

Note that jV version 4.1 requires an applet parameter newt set to true when the user's OS is Mac OS X.
The example assumes that a file named jV-applet.jnlp is placed at the same location as the HTML file that contains above applet tag. The contents of jV-applet.jnlp is as follows.

 &lt;?xml version="1.0" encoding="UTF-8"?&gt;
 &lt;jnlp href="jV-applet.jnlp"&gt;
   &lt;information&gt;
     &lt;title&gt;jV&lt;/title&gt;
     &lt;vendor&gt;Protein Data Bank Japan&lt;/vendor&gt;
     &lt;homepage href="http://ef-site.hgc.jp/jV/"/&gt;
     &lt;description&gt;Program to display molecular graphics of proteins and nucleic acids&lt;/description&gt;
     &lt;description kind="short"&gt;&lt;/description&gt;
     &lt;offline-allowed/&gt;
   &lt;/information&gt;
   &lt;resources&gt;
     &lt;j2se href="http://java.sun.com/products/autodl/j2se" version="1.4+"/&gt;
     &lt;property name="sun.java2d.noddraw" value="true"/&gt;
     &lt;jar href="jv4_1.jar"/&gt;
     &lt;extension name="jogl-all-awt" href="http://jogamp.org/deployment/jogamp-current/jogl-all-awt.jnlp" /&gt;
   &lt;/resources&gt;
   &lt;applet-desc
       name="jV"
       main-class="org.pdbj.viewer.gui.ViewerApplet"
       width="500"
       height="500"&gt;
   &lt;/applet-desc&gt;
 &lt;/jnlp&gt;

Here, applet-desc tag has name, width and height attributes. These are required, however, their values are overridden by those of applet tag in HTML.</text>
    <sha1>760e9d2b7d80305b245b5e1e94d0702b4c95e01f</sha1>
  </revision>
  <revision>
    <id>543</id>
    <parentid>519</parentid>
    <timestamp>2013-10-22T02:57:07Z</timestamp>
    <contributor>
      <username>IMSsato</username>
      <id>4</id>
    </contributor>
    <comment>/* Example */</comment>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="2414" xml:space="preserve">A brief introduction to use jV as applet with JNLP file.
Note that JNLP file works with the next-generation Java Plug-in and is not available before JRE 1.6.0_10.
If you place multiple applets on a single web page, using applet-launcher (see [[Use jV applet with applet launcher]]
)
rather than JNLP file is recommended because of a start-up stability problem.

== Example ==
The following code snippet shows how to embed jV applet in a web page.

 &lt;applet name="jVwindow" height="600" width="600" code="org.pdbj.viewer.gui.ViewerApplet"&gt;
   &lt;param name="jnlp_href" value="jV-applet.jnlp"/&gt;
   &lt;param name="java_arguments" value="-Dsun.java2d.noddraw=true"/&gt;
   &amp;lt;!-- replace the following with an appropriate URL --&gt;
   &lt;param name="pdbmlURL" value="http://eprots.protein.osaka-u.ac.jp/Rep_PDBML/1ashA1.xml.gz"&gt;
   &lt;param name="commands" value="cartoon;color group" name="commands"&gt;
   &lt;script type="text/javascript"&gt;
   &amp;lt;!-- 
   if(navigator.userAgent.indexOf("Mac") != -1 ){
     document.write('&lt;param name="newt" value="true"/&gt;');
   }
   //--&gt;
   &lt;/script&gt;
 &lt;/applet&gt;

Note that jV version 4.1 requires an applet parameter newt set to true when the user's OS is Mac OS X.
The example assumes that a file named jV-applet.jnlp is placed at the same location as the HTML file that contains above applet tag. The contents of jV-applet.jnlp is as follows.

 &lt;?xml version="1.0" encoding="UTF-8"?&gt;
 &lt;jnlp href="jV-applet.jnlp"&gt;
   &lt;information&gt;
     &lt;title&gt;jV&lt;/title&gt;
     &lt;vendor&gt;Protein Data Bank Japan&lt;/vendor&gt;
     &lt;homepage href="http://ef-site.hgc.jp/jV/"/&gt;
     &lt;description&gt;Program to display molecular graphics of proteins and nucleic acids&lt;/description&gt;
     &lt;description kind="short"&gt;&lt;/description&gt;
     &lt;offline-allowed/&gt;
   &lt;/information&gt;
   &lt;security&gt;
     &lt;all-permissions /&gt;
   &lt;/security&gt;
   &lt;resources&gt;
     &lt;j2se href="http://java.sun.com/products/autodl/j2se" version="1.6+"/&gt;
     &lt;property name="sun.java2d.noddraw" value="true"/&gt;
     &lt;jar href="jv4_1.jar"/&gt;
     &lt;extension name="jogl-all-awt" href="http://jogamp.org/deployment/jogamp-current/jogl-all-awt.jnlp" /&gt;
   &lt;/resources&gt;
   &lt;applet-desc
       name="jV"
       main-class="org.pdbj.viewer.gui.ViewerApplet"
       width="500"
       height="500"&gt;
   &lt;/applet-desc&gt;
 &lt;/jnlp&gt;

Here, applet-desc tag has name, width and height attributes. These are required, however, their values are overridden by those of applet tag in HTML.</text>
    <sha1>4e2ad06c4a596dd0c1964865a6c2405e816b70de</sha1>
  </revision>
  <revision>
    <id>544</id>
    <parentid>543</parentid>
    <timestamp>2013-10-22T02:57:33Z</timestamp>
    <contributor>
      <username>IMSsato</username>
      <id>4</id>
    </contributor>
    <comment>/* Example */</comment>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="2413" xml:space="preserve">A brief introduction to use jV as applet with JNLP file.
Note that JNLP file works with the next-generation Java Plug-in and is not available before JRE 1.6.0_10.
If you place multiple applets on a single web page, using applet-launcher (see [[Use jV applet with applet launcher]]
)
rather than JNLP file is recommended because of a start-up stability problem.

== Example ==
The following code snippet shows how to embed jV applet in a web page.

 &lt;applet name="jVwindow" height="600" width="600" code="org.pdbj.viewer.gui.ViewerApplet"&gt;
   &lt;param name="jnlp_href" value="jV-applet.jnlp"/&gt;
   &lt;param name="java_arguments" value="-Dsun.java2d.noddraw=true"/&gt;
   &amp;lt;!-- replace the following with an appropriate URL --&gt;
   &lt;param name="pdbmlURL" value="http://eprots.protein.osaka-u.ac.jp/Rep_PDBML/1ashA1.xml.gz"&gt;
   &lt;param name="commands" value="cartoon;color group" name="commands"&gt;
   &lt;script type="text/javascript"&gt;
   &amp;lt;!-- 
   if(navigator.userAgent.indexOf("Mac") != -1 ){
     document.write('&lt;param name="newt" value="true"/&gt;');
   }
   //--&gt;
   &lt;/script&gt;
 &lt;/applet&gt;

Note that jV version 4.1 requires an applet parameter newt set to true when the user's OS is Mac OS X.
The example assumes that a file named jV-applet.jnlp is placed at the same location as the HTML file that contains above applet tag. The contents of jV-applet.jnlp is as follows.

 &lt;?xml version="1.0" encoding="UTF-8"?&gt;
 &lt;jnlp href="jV-applet.jnlp"&gt;
   &lt;information&gt;
     &lt;title&gt;jV&lt;/title&gt;
     &lt;vendor&gt;Protein Data Bank Japan&lt;/vendor&gt;
     &lt;homepage href="http://ef-site.hgc.jp/jV/"/&gt;
     &lt;description&gt;Program to display molecular graphics of proteins and nucleic acids&lt;/description&gt;
     &lt;description kind="short"&gt;&lt;/description&gt;
     &lt;offline-allowed/&gt;
   &lt;/information&gt;
   &lt;security&gt;
     &lt;all-permissions/&gt;
   &lt;/security&gt;
   &lt;resources&gt;
     &lt;j2se href="http://java.sun.com/products/autodl/j2se" version="1.6+"/&gt;
     &lt;property name="sun.java2d.noddraw" value="true"/&gt;
     &lt;jar href="jv4_1.jar"/&gt;
     &lt;extension name="jogl-all-awt" href="http://jogamp.org/deployment/jogamp-current/jogl-all-awt.jnlp" /&gt;
   &lt;/resources&gt;
   &lt;applet-desc
       name="jV"
       main-class="org.pdbj.viewer.gui.ViewerApplet"
       width="500"
       height="500"&gt;
   &lt;/applet-desc&gt;
 &lt;/jnlp&gt;

Here, applet-desc tag has name, width and height attributes. These are required, however, their values are overridden by those of applet tag in HTML.</text>
    <sha1>8169840ec1afb3d055d27f5c0f5f6fda777e5ef1</sha1>
  </revision>
  <revision>
    <id>549</id>
    <parentid>544</parentid>
    <timestamp>2014-02-25T04:58:41Z</timestamp>
    <contributor>
      <username>IMSsato</username>
      <id>4</id>
    </contributor>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="2166" xml:space="preserve">'''Note: [[Use jV applet with object tag]] is more preferable.'''

A brief introduction to use jV as applet with JNLP file.
Note that JNLP file works with the next-generation Java Plug-in and is not available before JRE 1.6.0_10.
If you place multiple applets on a single web page, using applet-launcher (see [[Use jV applet with applet launcher]]
)
rather than JNLP file is recommended because of a start-up stability problem.

== Example ==
The following code snippet shows how to embed jV applet in a web page.

 &lt;applet name="jVwindow" height="600" width="600" code="org.pdbj.viewer.gui.ViewerApplet"&gt;
   &lt;param name="jnlp_href" value="jV-applet.jnlp"/&gt;
   &lt;param name="java_arguments" value="-Dsun.java2d.noddraw=true"/&gt;
   &amp;lt;!-- replace the following with an appropriate URL --&gt;
   &lt;param name="pdbmlURL" value="http://pdbj.org/XML/all/1ash.xml.gz"&gt;
   &lt;param name="commands" value="cartoon;color group"&gt;
 &lt;/applet&gt;

The example assumes that a file named jV-applet.jnlp is placed at the same location as the HTML file that contains above applet tag. The contents of jV-applet.jnlp is as follows.

 &lt;?xml version="1.0" encoding="UTF-8"?&gt;
 &lt;jnlp href="jV-applet.jnlp"&gt;
   &lt;information&gt;
     &lt;title&gt;jV&lt;/title&gt;
     &lt;vendor&gt;Protein Data Bank Japan&lt;/vendor&gt;
     &lt;homepage href="http://ef-site.hgc.jp/jV/"/&gt;
     &lt;description&gt;Program to display molecular graphics of proteins and nucleic acids&lt;/description&gt;
     &lt;description kind="short"&gt;&lt;/description&gt;
     &lt;offline-allowed/&gt;
   &lt;/information&gt;
   &lt;security&gt;
     &lt;all-permissions/&gt;
   &lt;/security&gt;
   &lt;resources&gt;
     &lt;j2se href="http://java.sun.com/products/autodl/j2se" version="1.6+"/&gt;
     &lt;property name="sun.java2d.noddraw" value="true"/&gt;
     &lt;jar href="jv4_3_1p2_signed.jar"/&gt;
     &lt;extension name="jogl-all-awt" href="http://jogamp.org/deployment/jogamp-current/jogl-all-awt.jnlp" /&gt;
   &lt;/resources&gt;
   &lt;applet-desc
       name="jV"
       main-class="org.pdbj.viewer.gui.ViewerApplet"
       width="500"
       height="500"&gt;
   &lt;/applet-desc&gt;
 &lt;/jnlp&gt;

Here, applet-desc tag has name, width and height attributes. These are required, however, their values are overridden by those of applet tag in HTML.</text>
    <sha1>357d36cdc0c67439b04848637b20c22351c7920d</sha1>
  </revision>
  <revision>
    <id>550</id>
    <parentid>549</parentid>
    <timestamp>2014-02-25T04:59:33Z</timestamp>
    <contributor>
      <username>IMSsato</username>
      <id>4</id>
    </contributor>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="2054" xml:space="preserve">'''Note: [[Use jV applet with object tag]] is more preferable.'''

A brief introduction to use jV as applet with JNLP file.
Note that JNLP file works with the next-generation Java Plug-in and is not available before JRE 1.6.0_10.
If you place multiple applets in a single web page, JNLP file does not work properly.

== Example ==
The following code snippet shows how to embed jV applet in a web page.

 &lt;applet name="jVwindow" height="600" width="600" code="org.pdbj.viewer.gui.ViewerApplet"&gt;
   &lt;param name="jnlp_href" value="jV-applet.jnlp"/&gt;
   &lt;param name="java_arguments" value="-Dsun.java2d.noddraw=true"/&gt;
   &amp;lt;!-- replace the following with an appropriate URL --&gt;
   &lt;param name="pdbmlURL" value="http://pdbj.org/XML/all/1ash.xml.gz"&gt;
   &lt;param name="commands" value="cartoon;color group"&gt;
 &lt;/applet&gt;

The example assumes that a file named jV-applet.jnlp is placed at the same location as the HTML file that contains above applet tag. The contents of jV-applet.jnlp is as follows.

 &lt;?xml version="1.0" encoding="UTF-8"?&gt;
 &lt;jnlp href="jV-applet.jnlp"&gt;
   &lt;information&gt;
     &lt;title&gt;jV&lt;/title&gt;
     &lt;vendor&gt;Protein Data Bank Japan&lt;/vendor&gt;
     &lt;homepage href="http://ef-site.hgc.jp/jV/"/&gt;
     &lt;description&gt;Program to display molecular graphics of proteins and nucleic acids&lt;/description&gt;
     &lt;description kind="short"&gt;&lt;/description&gt;
     &lt;offline-allowed/&gt;
   &lt;/information&gt;
   &lt;security&gt;
     &lt;all-permissions/&gt;
   &lt;/security&gt;
   &lt;resources&gt;
     &lt;j2se href="http://java.sun.com/products/autodl/j2se" version="1.6+"/&gt;
     &lt;property name="sun.java2d.noddraw" value="true"/&gt;
     &lt;jar href="jv4_3_1p2_signed.jar"/&gt;
     &lt;extension name="jogl-all-awt" href="http://jogamp.org/deployment/jogamp-current/jogl-all-awt.jnlp" /&gt;
   &lt;/resources&gt;
   &lt;applet-desc
       name="jV"
       main-class="org.pdbj.viewer.gui.ViewerApplet"
       width="500"
       height="500"&gt;
   &lt;/applet-desc&gt;
 &lt;/jnlp&gt;

Here, applet-desc tag has name, width and height attributes. These are required, however, their values are overridden by those of applet tag in HTML.</text>
    <sha1>af28075b1007f3320efae0c026082755cc23c3c4</sha1>
  </revision>
</page>
<page arvcontinue="20120326072111|504">
  <title>Use jV with next-generation Java Plug-in</title>
  <ns>0</ns>
  <id>74</id>
  <revision>
    <id>513</id>
    <timestamp>2013-02-25T05:05:50Z</timestamp>
    <contributor>
      <username>IMSsato</username>
      <id>4</id>
    </contributor>
    <comment>moved [[Use jV with next-generation Java Plug-in]] to [[Use jV applet with JNLP file]]</comment>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="42" xml:space="preserve">#REDIRECT [[Use jV applet with JNLP file]]</text>
    <sha1>665dc974a48c7ecb9f59343ddd9b7332c594c444</sha1>
  </revision>
</page>
<page arvcontinue="20120326072111|504">
  <title>How to use</title>
  <ns>0</ns>
  <id>11</id>
  <revision>
    <id>514</id>
    <parentid>449</parentid>
    <timestamp>2013-02-25T05:06:32Z</timestamp>
    <contributor>
      <username>IMSsato</username>
      <id>4</id>
    </contributor>
    <comment>/* Some examples */</comment>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="1148" xml:space="preserve">The following table shows how to do the minimum things with jV; the mouse controls.
For the detail, see the reference manual and User's guide.&lt;br /&gt;
{| class="wikitable" border="1" style="margin:0 auto" 
 ! Action !! Window, Linux !! Mac OS X 
 |-
 ! style="text-align:left" | rotate around X,Y axes
 | left drag || drag
 |-
 ! style="text-align:left" | rotate around Z axis
 | Shift + right drag || Shift + command + drag
 |-
 ! style="text-align:left" | translate along X,Y axes
 | right drag || command + drag
 |-
 ! style="text-align:left" | translate along Z axis (zoom in/out)
 | Shift + left drag || Shift + drag
 |-
 ! style="text-align:left" | translate slab plane along Z axis
 | (Alt or Ctrl) + left drag || Alt + drag
 |}


== Reference manual ==
# [[Introduction]]
# [[Command List]]
# [[Atom Expression]]
# [[Vertex Expression]]
# [[Color Expression]]
# [[Use as Applet]]


== User's Guide ==
# [[Tutorials]]
# [[GUI]]
# [[Document type of the polygon file]]
# [[Functional site information for molecules]]


== Some examples ==
# [[Basic examples]]
# [[Animation]]
# [[Use jV applet with JNLP file]]
# [[Use jV with applet launcher]]</text>
    <sha1>459b65493de261d1a168eb1801bd5e05ef45a4ec</sha1>
  </revision>
  <revision>
    <id>518</id>
    <parentid>514</parentid>
    <timestamp>2013-02-25T05:11:21Z</timestamp>
    <contributor>
      <username>IMSsato</username>
      <id>4</id>
    </contributor>
    <comment>/* Some examples */</comment>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="1155" xml:space="preserve">The following table shows how to do the minimum things with jV; the mouse controls.
For the detail, see the reference manual and User's guide.&lt;br /&gt;
{| class="wikitable" border="1" style="margin:0 auto" 
 ! Action !! Window, Linux !! Mac OS X 
 |-
 ! style="text-align:left" | rotate around X,Y axes
 | left drag || drag
 |-
 ! style="text-align:left" | rotate around Z axis
 | Shift + right drag || Shift + command + drag
 |-
 ! style="text-align:left" | translate along X,Y axes
 | right drag || command + drag
 |-
 ! style="text-align:left" | translate along Z axis (zoom in/out)
 | Shift + left drag || Shift + drag
 |-
 ! style="text-align:left" | translate slab plane along Z axis
 | (Alt or Ctrl) + left drag || Alt + drag
 |}


== Reference manual ==
# [[Introduction]]
# [[Command List]]
# [[Atom Expression]]
# [[Vertex Expression]]
# [[Color Expression]]
# [[Use as Applet]]


== User's Guide ==
# [[Tutorials]]
# [[GUI]]
# [[Document type of the polygon file]]
# [[Functional site information for molecules]]


== Some examples ==
# [[Basic examples]]
# [[Animation]]
# [[Use jV applet with JNLP file]]
# [[Use jV applet with applet launcher]]</text>
    <sha1>8d740342ec00c6198f6edb811ab3aed6f6cdf9c9</sha1>
  </revision>
  <revision>
    <id>548</id>
    <parentid>518</parentid>
    <timestamp>2014-02-25T04:53:56Z</timestamp>
    <contributor>
      <username>IMSsato</username>
      <id>4</id>
    </contributor>
    <comment>/* Some examples */</comment>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="1191" xml:space="preserve">The following table shows how to do the minimum things with jV; the mouse controls.
For the detail, see the reference manual and User's guide.&lt;br /&gt;
{| class="wikitable" border="1" style="margin:0 auto" 
 ! Action !! Window, Linux !! Mac OS X 
 |-
 ! style="text-align:left" | rotate around X,Y axes
 | left drag || drag
 |-
 ! style="text-align:left" | rotate around Z axis
 | Shift + right drag || Shift + command + drag
 |-
 ! style="text-align:left" | translate along X,Y axes
 | right drag || command + drag
 |-
 ! style="text-align:left" | translate along Z axis (zoom in/out)
 | Shift + left drag || Shift + drag
 |-
 ! style="text-align:left" | translate slab plane along Z axis
 | (Alt or Ctrl) + left drag || Alt + drag
 |}


== Reference manual ==
# [[Introduction]]
# [[Command List]]
# [[Atom Expression]]
# [[Vertex Expression]]
# [[Color Expression]]
# [[Use as Applet]]


== User's Guide ==
# [[Tutorials]]
# [[GUI]]
# [[Document type of the polygon file]]
# [[Functional site information for molecules]]


== Some examples ==
# [[Basic examples]]
# [[Animation]]
# [[Use jV applet with object tag]]
# [[Use jV applet with JNLP file]]
# [[Use jV applet with applet launcher]]</text>
    <sha1>6ca8a3fa5956a9e112c77253579cfe4cd10f734d</sha1>
  </revision>
</page>
<page arvcontinue="20120326072111|504">
  <title>Use jV applet with applet launcher</title>
  <ns>0</ns>
  <id>16</id>
  <revision>
    <id>516</id>
    <parentid>491</parentid>
    <timestamp>2013-02-25T05:10:59Z</timestamp>
    <contributor>
      <username>IMSsato</username>
      <id>4</id>
    </contributor>
    <minor/>
    <comment>moved [[Use jV with applet launcher]] to [[Use jV applet with applet launcher]]</comment>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="2105" xml:space="preserve">A brief introduction to use jV in applet.

== Minimum Example ==
One way to use jV applet is to use with applet-launcher. jV after v3.6 is fully compatible with applet-launcher.

 &lt;applet
   hspace="0" vspace="0" align="middle"
   name="jVwindow" height="600" width="600"
   archive="http://jogamp.org/deployment/jogamp-current/jar/applet-launcher.jar,
            http://jogamp.org/deployment/jogamp-current/jar/jogl.all.jar,
            http://jogamp.org/deployment/jogamp-current/jar/gluegen-rt.jar,
            '''jv4_1.jar'''"
   code="org.jdesktop.applet.util.JNLPAppletLauncher"&gt;
 &amp;lt;!-- param for applet-launcher --&gt;
   &lt;param name="subapplet.classname" value="'''org.pdbj.viewer.gui.ViewerApplet'''"&gt;
   &lt;param name="subapplet.displayname" value="jV applet"&gt;
   &lt;param name="noddraw.check" value="true"/&gt;
   &lt;param name="noddraw.check.silent" value="true"/&gt;
   &lt;param name="java_arguments" value="-Dsun.java2d.noddraw=true"/&gt;
   &lt;param name="progressbar" value="true"/&gt;
   &lt;param name="jnlpNumExtensions" value="1"/&gt;
   &lt;param name="jnlpExtension1"
    value="http://jogamp.org/deployment/jogamp-current/jogl-all-awt.jnlp"/&gt;
 '''&amp;lt;!-- param for jV --&gt;'''
   '''&lt;param value="" name="pdbURL"&gt;'''
    '''&amp;lt;!-- replace the following with an appropriate URL --&gt;'''
   '''&lt;param name="pdbmlURL" value="http://eprots.protein.osaka-u.ac.jp/Rep_PDBML/1ashA1.xml.gz"&gt;'''
   '''&lt;param value="" name="polygonURL"&gt;'''
   '''&lt;param value="set picking ident;background black;wireframe off;cartoon;color group" name="commands"&gt;'''
   '''&lt;script type="text/javascript"&gt;'''
   '''&amp;lt;!--'''
   '''if(navigator.userAgent.indexOf("Mac") != -1 ){'''
   '''  document.write('&lt;param name="newt" value="true"/&gt;');'''
   '''}'''
   '''//--&gt;'''
   '''&lt;/script&gt;'''
 &lt;/applet&gt;

Upper part is almost same as the usual usage of applet launcher. See the [http://jogamp.org/applet-launcher/www/ applet-launcher page] for details. The latter part is for jV parameters. Note that jV version 4.1 requires an applet parameter newt set to true when the user's OS is Mac OS X.

Only the &lt;B&gt;bold face&lt;/B&gt; part is specific for jV.</text>
    <sha1>22db916a2473d831f5dcf874aff1831d51635ec0</sha1>
  </revision>
  <revision>
    <id>520</id>
    <parentid>516</parentid>
    <timestamp>2013-02-25T05:26:11Z</timestamp>
    <contributor>
      <username>IMSsato</username>
      <id>4</id>
    </contributor>
    <comment>/* Minimum Example */</comment>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="2327" xml:space="preserve">A brief introduction to use jV in applet.

== Minimum Example ==
One way to use jV applet is to use with applet-launcher. jV after v3.6 is fully compatible with applet-launcher.

 &lt;applet
   hspace="0" vspace="0" align="middle"
   name="jVwindow" height="600" width="600"
   archive="http://jogamp.org/deployment/jogamp-current/jar/applet-launcher.jar,
            http://jogamp.org/deployment/jogamp-current/jar/jogl-all.jar,
            http://jogamp.org/deployment/jogamp-current/jar/gluegen-rt.jar,
            '''jv4_2_1.jar'''"
   code="'''org.pdbj.viewer.gui.GLInitJNLPAppletLauncher'''"&gt;
 &amp;lt;!-- param for applet-launcher --&gt;
   &lt;param name="subapplet.classname" value="'''org.pdbj.viewer.gui.ViewerApplet'''"&gt;
   &lt;param name="subapplet.displayname" value="jV applet"&gt;
   &lt;param name="noddraw.check" value="true"/&gt;
   &lt;param name="noddraw.check.silent" value="true"/&gt;
   &lt;param name="java_arguments" value="-Dsun.java2d.noddraw=true"/&gt;
   &lt;param name="progressbar" value="true"/&gt;
   &lt;param name="jnlpNumExtensions" value="1"/&gt;
   &lt;param name="jnlpExtension1"
    value="http://jogamp.org/deployment/jogamp-current/jogl-all-awt.jnlp"/&gt;
 '''&amp;lt;!-- param for jV --&gt;'''
   '''&lt;param value="" name="pdbURL"&gt;'''
    '''&amp;lt;!-- replace the following with an appropriate URL --&gt;'''
   '''&lt;param name="pdbmlURL" value="http://eprots.protein.osaka-u.ac.jp/Rep_PDBML/1ashA1.xml.gz"&gt;'''
   '''&lt;param value="" name="polygonURL"&gt;'''
   '''&lt;param value="set picking ident;background black;wireframe off;cartoon;color group" name="commands"&gt;'''
   '''&lt;script type="text/javascript"&gt;'''
   '''&amp;lt;!--'''
   '''if(navigator.userAgent.indexOf("Mac") != -1 ){'''
   '''  document.write('&lt;param name="newt" value="true"/&gt;');'''
   '''}'''
   '''//--&gt;'''
   '''&lt;/script&gt;'''
 &lt;/applet&gt;

Upper part is almost same as the usual usage of applet launcher. See the [http://jogamp.org/applet-launcher/www/ applet-launcher page] for details. 
Notice, however, that we specify org.pdbj.viewer.gui.GLInitJNLPAppletLauncher class to the code attribute rather than org.jdesktop.applet.util.JNLPAppletLauncher class to avoid an initialization problem.
The latter part is for jV parameters. From jV version 4.1, the program requires an applet parameter newt set to true when the user's OS is Mac OS X.

Only the &lt;B&gt;bold face&lt;/B&gt; part is specific for jV.</text>
    <sha1>808ff71decaf6491e2a61a359af668402baf360b</sha1>
  </revision>
  <revision>
    <id>551</id>
    <parentid>520</parentid>
    <timestamp>2014-02-25T05:03:30Z</timestamp>
    <contributor>
      <username>IMSsato</username>
      <id>4</id>
    </contributor>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="1925" xml:space="preserve">'''Note: [[Use jV applet with object tag]] is more preferable.'''

A brief introduction to use jV in applet with applet-launcher.

== Example ==
One way to use jV applet is to use with applet-launcher. jV after v3.6 is fully compatible with applet-launcher.

 &lt;applet
   hspace="0" vspace="0" align="middle"
   name="jVwindow" height="600" width="600"
   archive="http://jogamp.org/deployment/jogamp-current/jar/applet-launcher.jar,
            http://jogamp.org/deployment/jogamp-current/jar/jogl-all.jar,
            http://jogamp.org/deployment/jogamp-current/jar/gluegen-rt.jar,
            '''jv4_3_1p2_signed.jar'''"
   code="'''org.pdbj.viewer.gui.GLInitJNLPAppletLauncher'''"&gt;
 &amp;lt;!-- param for applet-launcher --&gt;
   &lt;param name="subapplet.classname" value="'''org.pdbj.viewer.gui.ViewerApplet'''"&gt;
   &lt;param name="subapplet.displayname" value="jV applet"&gt;
   &lt;param name="noddraw.check" value="true"/&gt;
   &lt;param name="noddraw.check.silent" value="true"/&gt;
   &lt;param name="java_arguments" value="-Dsun.java2d.noddraw=true"/&gt;
   &lt;param name="progressbar" value="true"/&gt;
   &lt;param name="jnlpNumExtensions" value="1"/&gt;
   &lt;param name="jnlpExtension1"
    value="http://jogamp.org/deployment/jogamp-current/jogl-all-awt.jnlp"/&gt;
 '''&amp;lt;!-- param for jV --&gt;'''
    '''&amp;lt;!-- replace the following with an appropriate URL --&gt;'''
   '''&lt;param name="pdbmlURL" value="http://pdbj.org/XML/all/1ash.xml.gz"&gt;'''
   '''&lt;param name="commands" value="cartoon;color group"&gt;'''
 &lt;/applet&gt;

Upper part is almost same as the usual usage of applet launcher. See the [http://jogamp.org/applet-launcher/www/ applet-launcher page] for details. 
Notice, however, that we specify org.pdbj.viewer.gui.GLInitJNLPAppletLauncher class to the code attribute rather than org.jdesktop.applet.util.JNLPAppletLauncher class to avoid an initialization problem.
The latter part is for jV parameters.

Only the &lt;B&gt;bold face&lt;/B&gt; part is specific for jV.</text>
    <sha1>4fd86aff59485ec178a0ba0aea9c2c15695b7301</sha1>
  </revision>
</page>
<page arvcontinue="20120326072111|504">
  <title>Use jV with applet launcher</title>
  <ns>0</ns>
  <id>75</id>
  <revision>
    <id>517</id>
    <timestamp>2013-02-25T05:10:59Z</timestamp>
    <contributor>
      <username>IMSsato</username>
      <id>4</id>
    </contributor>
    <comment>moved [[Use jV with applet launcher]] to [[Use jV applet with applet launcher]]</comment>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="48" xml:space="preserve">#REDIRECT [[Use jV applet with applet launcher]]</text>
    <sha1>5c28106a37c41f09753c134b8ee92b6f74b4962c</sha1>
  </revision>
</page>
<page arvcontinue="20120326072111|504">
  <title>Installation of jV</title>
  <ns>0</ns>
  <id>38</id>
  <revision>
    <id>521</id>
    <parentid>484</parentid>
    <timestamp>2013-02-25T05:26:51Z</timestamp>
    <contributor>
      <username>IMSsato</username>
      <id>4</id>
    </contributor>
    <comment>/* System requirements */</comment>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="766" xml:space="preserve">__NOTOC__
== System requirements ==
jV runs on the Java Runtime Environment (JRE) with JOGL API. The version requirements are as follows.
* [http://java.sun.com/j2se/ JRE] (includes Java Plug-in) 1.6 or later
* [http://jogamp.org/jogl/www/ JOGL] API 2.0-rc11 or later 
These softwares are available on typical operation systems such as Windows (XP/Vista/7), Mac OS X 10.6 or later, and Red Hat Linux 7.3 or later.

== Installation ==
From the version 3.8.3, binary distribution of jV contains the JOGL library
and pre-installation of JOGL is not necessary.
Just JRE is required on your computer in advance.
With JRE properly installed, you can download the binary distribution of jV 
and immediately use jV by running a start-up script contained in the distribution.</text>
    <sha1>4dd8c6bac8842fd13471c64b38688e67e5a8fa56</sha1>
  </revision>
  <revision>
    <id>541</id>
    <parentid>521</parentid>
    <timestamp>2013-05-28T06:13:48Z</timestamp>
    <contributor>
      <username>IMSsato</username>
      <id>4</id>
    </contributor>
    <comment>/* System requirements */</comment>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="806" xml:space="preserve">__NOTOC__
== System requirements ==
jV runs on the Java Runtime Environment (JRE) with JOGL API. The version requirements are as follows.
* [http://www.oracle.com/technetwork/java/javase/overview/index.html JRE] (includes Java Plug-in) 1.6 or later
* [http://jogamp.org/jogl/www/ JOGL] API 2.0-rc11 or later 
These softwares are available on typical operation systems such as Windows (XP/Vista/7), Mac OS X 10.6 or later, and Red Hat Linux 7.3 or later.

== Installation ==
From the version 3.8.3, binary distribution of jV contains the JOGL library
and pre-installation of JOGL is not necessary.
Just JRE is required on your computer in advance.
With JRE properly installed, you can download the binary distribution of jV 
and immediately use jV by running a start-up script contained in the distribution.</text>
    <sha1>9d2bea61b3b092abe4a7e8312b3fc7a8116c0f24</sha1>
  </revision>
  <revision>
    <id>552</id>
    <parentid>541</parentid>
    <timestamp>2014-02-25T06:31:14Z</timestamp>
    <contributor>
      <username>IMSsato</username>
      <id>4</id>
    </contributor>
    <comment>/* System requirements */</comment>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="803" xml:space="preserve">__NOTOC__
== System requirements ==
jV runs on the Java Runtime Environment (JRE) with JOGL API. The version requirements are as follows.
* [http://www.oracle.com/technetwork/java/javase/overview/index.html JRE] (includes Java Plug-in) 1.6 or later
* [http://jogamp.org/jogl/www/ JOGL] API 2.1.3 or later 
These softwares are available on typical operation systems such as Windows (XP/Vista/7), Mac OS X 10.6 or later, and Red Hat Linux 7.3 or later.

== Installation ==
From the version 3.8.3, binary distribution of jV contains the JOGL library
and pre-installation of JOGL is not necessary.
Just JRE is required on your computer in advance.
With JRE properly installed, you can download the binary distribution of jV 
and immediately use jV by running a start-up script contained in the distribution.</text>
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  </revision>
</page>
<page arvcontinue="20120326072111|504">
  <title>File:Java cache viewer.png</title>
  <ns>6</ns>
  <id>76</id>
  <revision>
    <id>538</id>
    <timestamp>2013-03-18T06:16:12Z</timestamp>
    <contributor>
      <username>IMSsato</username>
      <id>4</id>
    </contributor>
    <model>wikitext</model>
    <format>text/x-wiki</format>
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  </revision>
</page>
<page arvcontinue="20120326072111|504">
  <title>Use jV applet with object tag</title>
  <ns>0</ns>
  <id>77</id>
  <revision>
    <id>547</id>
    <timestamp>2014-02-25T04:53:34Z</timestamp>
    <contributor>
      <username>IMSsato</username>
      <id>4</id>
    </contributor>
    <comment>Created page with 'A brief introduction to use jV as applet with object tag.  == Example == The following code snippet shows how to embed jV applet in a web page.   &lt;object type="application/x-java…'</comment>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="805" xml:space="preserve">A brief introduction to use jV as applet with object tag.

== Example ==
The following code snippet shows how to embed jV applet in a web page.

 &lt;object type="application/x-java-applet;version=1.6"
         name="jVwindow" width="600" height="600"&gt;
   &lt;param name="java_arguments" value="-Dsun.java2d.noddraw=true"&gt;
   &lt;param name="code" value="org.pdbj.viewer.gui.ViewerApplet"&gt;
   &lt;param name="archive"
          value="./jv4_3_1p2_signed.jar,
                 http://jogamp.org/deployment/jogamp-current/jar/jogl-all.jar,
                 http://jogamp.org/deployment/jogamp-current/jar/gluegen-rt.jar"&gt;
   &amp;lt;!-- replace the following with an appropriate URL --&gt;
   &lt;param name="pdbmlURL" value="http://pdbj.org/XML/all/1ash.xml.gz"&gt;
   &lt;param name="commands" value="cartoon;color group"&gt;
 &lt;/object&gt;</text>
    <sha1>ca5ab66683301b328eaa74eaf6a0abe8eb3425bd</sha1>
  </revision>
</page>
<page arvcontinue="20140430014530|554">
  <title>Release note</title>
  <ns>0</ns>
  <id>17</id>
  <revision>
    <id>554</id>
    <parentid>529</parentid>
    <timestamp>2014-04-30T01:45:30Z</timestamp>
    <contributor>
      <username>IMSsato</username>
      <id>4</id>
    </contributor>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="5336" xml:space="preserve">Changes and improvements have been made as follows.

* version 3.1
** The following commands have been added; 'animrange', 'set adjustview', 'show godata', and 'show xps3'.
** The xPSSS expression has been added in order to select a group of atoms.
** Several public methods have been added to the applet so as to append molecule or polygon files after the applet started.
** The applet can send information about mouse-picked atoms to JavaScript.
* version 3.1.1
** Some problems in GUI menu [Options]-[Hetero Atoms] and [Hydrogens] have been fixed.
** Some problems in 'trace' command have been fixed.
* version 3.1.2
** eF-site ID has been changed to a new format.
* version 3.1.3
** Some problems in xps3 atom selection have been fixed.
* version 3.1.4
** Some problems in finalization process of openGL rendering have been fixed.
* version 3.1.5
** The output of 'show xps3' command has been modified.
** Some problems in 'save png/jpeg' command have been fixed.
* version 3.1.6
** Some problems in loading an empty polygon file have been fixed.
* version 3.1.7
** Some problems in initialization process of the applet have been fixed.
* version 3.2
** 'show site' command has been added.
* version 3.3 beta 1
** Availabe JOGL version is restricted to JSR-231 beta 5 only.
* version 3.3
** Both the previous JOGL (version 1.1.1) and JSR-231 are available.
** The following commands have been added; 'set viewpoint', 'show viewpoint', 'set imagesize', and 'show imagesize'.
* version 3.3.1
** Some problems in reading a pdbMLplus file have been fixed.
* version 3.4
** PDB format version 3 can be processed.
* version 3.5
** Discrimination of DNA and RNA linking nucleotides is based on [http://remediation.wwpdb.org/ccd.html Chemical Component Dictionary] for PDB format version 3.
** The default representation of the cartoon model has been changed. Commands 'set cartoon_loop_tube', 'set cartoon_round' and 'set ribbonback' have been added.
** The default parameters of lighting have been changed. Commands 'set ambient', 'set diffuse1', 'set diffuse1_direction', 'set diffuse2' and 'set diffuse1_direction' have been added.
** Commands 'set pdbml_noatom_url', 'set pdbml_extatom_url', 'set pdbml_plus_url', 'set efsite_url', 'set ext_site_url', 'show pdbml_url', 'show efsite_url' and 'show ext_site_url' have been added.
** The command-line option '-stdin' has been added to receive commands from stdin stream.
* version 3.6
** Users can specify the JavaScript function name used in Applet-to-JavaScript Communication.
** Applet parameter 'file_load_message' has been added.
* version 3.6.1
** Predefined set of residues has been modified.
** Old JOGL API is not supported.
* version 3.6.2
** Latest version of PDBML can be processed.
** Some problems in mouse control on Mac have been fixed.
* version 3.6.3
** Molecule file parsing has been modified to detect chain breaks properly by reading the 'label_asym_id' column in PDBML and the TER line in PDB flat file, respectively.
* version 3.6.4
** Some problems in GUI menu on Mac have been fixed.
* version 3.6.5
** The jV applet can invoke a JavaScript function when it started.
* version 3.7
** Commands 'pdbj_describe' and 'pdbj_execute' have been added.
** Keyword 'xps3' have been replaced by 'pdbj'.
* version 3.7.1
** Default PDBML URLs have been changed.
* version 3.7.2
** Some problems in creating png/jpeg image files have been fixed.
* version 3.8
** Command 'displayatom' has been added.
** The signed jV applet can save PNG/JPEG image files.
* version 3.8.1
** In commands 'cartoon', 'ribbons' and 'trace', a backbone will be drawn instead when a chain does not have enough atoms to draw those models.
** Recognition of amino acids is based on [http://remediation.wwpdb.org/ccd.html Chemical Component Dictionary].
* version 3.8.2
** Command 'ball_and_stick' has been added.
* version 3.8.3
** Binary distribution contains the JOGL library and pre-installation of JOGL is not necessary to use jV.
* version 4.0
** The program supports PDB format version 4.0.
** Atom expression has been extended to handle case-sensitive chain ID and label_asym_id in PDBML.
* version 4.1
** The program runs with new JOGL library (2.0-rc4 or later) which enables jV applets to run on Mac.
** From this release, the program requires JRE 1.6 or later.
** Command 'add_backbone' has been added.
** The program uses MODRES data and chem_comp/type data (PDBML only) to determine residue types.
* version 4.2
** The program reads polygon CGO (PyMOL-specific Compiled Graphics Objects) files distributed at eF-site system. Command 'load polygon_cgo' has been added.
** A parameter 'pdbid' and a method 'loadFTP' have been added to applet.
** When the program loads a PDBML noatom file whose directory is 'all-noatom' or 'XML-noatom', the coordinate file is retrieved from the corresponding directory; '../all-extatom' or '../XML-extatom', respectively.
* version 4.2.1
** The program runs with new JOGL library (2.0-rc11).
* version 4.3
** Anaglyph 3D rendering is added to 'stereo' command.
* version 4.3.1
** A workaround for a cache problem in JRE 1.7 has been added.
* version 4.4
** The program can read and write mmCIF format files.
** The program handles biomolecule structures when reading and writing a molecule file.
** The default setting of PDBMLplus URL has been changed.</text>
    <sha1>df798c210298e2afee3665e5d1a0f145c2f2f98b</sha1>
  </revision>
  <revision>
    <id>566</id>
    <parentid>554</parentid>
    <timestamp>2014-11-11T02:42:44Z</timestamp>
    <contributor>
      <username>IMSsato</username>
      <id>4</id>
    </contributor>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="5611" xml:space="preserve">Changes and improvements have been made as follows.

* version 3.1
** The following commands have been added; 'animrange', 'set adjustview', 'show godata', and 'show xps3'.
** The xPSSS expression has been added in order to select a group of atoms.
** Several public methods have been added to the applet so as to append molecule or polygon files after the applet started.
** The applet can send information about mouse-picked atoms to JavaScript.
* version 3.1.1
** Some problems in GUI menu [Options]-[Hetero Atoms] and [Hydrogens] have been fixed.
** Some problems in 'trace' command have been fixed.
* version 3.1.2
** eF-site ID has been changed to a new format.
* version 3.1.3
** Some problems in xps3 atom selection have been fixed.
* version 3.1.4
** Some problems in finalization process of openGL rendering have been fixed.
* version 3.1.5
** The output of 'show xps3' command has been modified.
** Some problems in 'save png/jpeg' command have been fixed.
* version 3.1.6
** Some problems in loading an empty polygon file have been fixed.
* version 3.1.7
** Some problems in initialization process of the applet have been fixed.
* version 3.2
** 'show site' command has been added.
* version 3.3 beta 1
** Availabe JOGL version is restricted to JSR-231 beta 5 only.
* version 3.3
** Both the previous JOGL (version 1.1.1) and JSR-231 are available.
** The following commands have been added; 'set viewpoint', 'show viewpoint', 'set imagesize', and 'show imagesize'.
* version 3.3.1
** Some problems in reading a pdbMLplus file have been fixed.
* version 3.4
** PDB format version 3 can be processed.
* version 3.5
** Discrimination of DNA and RNA linking nucleotides is based on [http://remediation.wwpdb.org/ccd.html Chemical Component Dictionary] for PDB format version 3.
** The default representation of the cartoon model has been changed. Commands 'set cartoon_loop_tube', 'set cartoon_round' and 'set ribbonback' have been added.
** The default parameters of lighting have been changed. Commands 'set ambient', 'set diffuse1', 'set diffuse1_direction', 'set diffuse2' and 'set diffuse1_direction' have been added.
** Commands 'set pdbml_noatom_url', 'set pdbml_extatom_url', 'set pdbml_plus_url', 'set efsite_url', 'set ext_site_url', 'show pdbml_url', 'show efsite_url' and 'show ext_site_url' have been added.
** The command-line option '-stdin' has been added to receive commands from stdin stream.
* version 3.6
** Users can specify the JavaScript function name used in Applet-to-JavaScript Communication.
** Applet parameter 'file_load_message' has been added.
* version 3.6.1
** Predefined set of residues has been modified.
** Old JOGL API is not supported.
* version 3.6.2
** Latest version of PDBML can be processed.
** Some problems in mouse control on Mac have been fixed.
* version 3.6.3
** Molecule file parsing has been modified to detect chain breaks properly by reading the 'label_asym_id' column in PDBML and the TER line in PDB flat file, respectively.
* version 3.6.4
** Some problems in GUI menu on Mac have been fixed.
* version 3.6.5
** The jV applet can invoke a JavaScript function when it started.
* version 3.7
** Commands 'pdbj_describe' and 'pdbj_execute' have been added.
** Keyword 'xps3' have been replaced by 'pdbj'.
* version 3.7.1
** Default PDBML URLs have been changed.
* version 3.7.2
** Some problems in creating png/jpeg image files have been fixed.
* version 3.8
** Command 'displayatom' has been added.
** The signed jV applet can save PNG/JPEG image files.
* version 3.8.1
** In commands 'cartoon', 'ribbons' and 'trace', a backbone will be drawn instead when a chain does not have enough atoms to draw those models.
** Recognition of amino acids is based on [http://remediation.wwpdb.org/ccd.html Chemical Component Dictionary].
* version 3.8.2
** Command 'ball_and_stick' has been added.
* version 3.8.3
** Binary distribution contains the JOGL library and pre-installation of JOGL is not necessary to use jV.
* version 4.0
** The program supports PDB format version 4.0.
** Atom expression has been extended to handle case-sensitive chain ID and label_asym_id in PDBML.
* version 4.1
** The program runs with new JOGL library (2.0-rc4 or later) which enables jV applets to run on Mac.
** From this release, the program requires JRE 1.6 or later.
** Command 'add_backbone' has been added.
** The program uses MODRES data and chem_comp/type data (PDBML only) to determine residue types.
* version 4.2
** The program reads polygon CGO (PyMOL-specific Compiled Graphics Objects) files distributed at eF-site system. Command 'load polygon_cgo' has been added.
** A parameter 'pdbid' and a method 'loadFTP' have been added to applet.
** When the program loads a PDBML noatom file whose directory is 'all-noatom' or 'XML-noatom', the coordinate file is retrieved from the corresponding directory; '../all-extatom' or '../XML-extatom', respectively.
* version 4.2.1
** The program runs with new JOGL library (2.0-rc11).
* version 4.3
** Anaglyph 3D rendering is added to 'stereo' command.
* version 4.3.1
** A workaround for a cache problem in JRE 1.7 has been added.
* version 4.4
** The program can read and write mmCIF format files.
** The program handles biomolecule structures when reading and writing a molecule file.
** The default setting of PDBMLplus URL has been changed.
* version 4.4.1
** Some problems in reading mmCIF files have been fixed.
** The behavior of mouse picking when measuring the distance between two atoms has been changed. Rotation and translation of molecules between two mouse pickings do not affect the distance measurement.</text>
    <sha1>feba0509fb77cc27eb635fe6f46571a383a77733</sha1>
  </revision>
  <revision>
    <id>571</id>
    <parentid>566</parentid>
    <timestamp>2014-12-03T03:05:28Z</timestamp>
    <contributor>
      <username>IMSsato</username>
      <id>4</id>
    </contributor>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="5683" xml:space="preserve">Changes and improvements have been made as follows.

* version 3.1
** The following commands have been added; 'animrange', 'set adjustview', 'show godata', and 'show xps3'.
** The xPSSS expression has been added in order to select a group of atoms.
** Several public methods have been added to the applet so as to append molecule or polygon files after the applet started.
** The applet can send information about mouse-picked atoms to JavaScript.
* version 3.1.1
** Some problems in GUI menu [Options]-[Hetero Atoms] and [Hydrogens] have been fixed.
** Some problems in 'trace' command have been fixed.
* version 3.1.2
** eF-site ID has been changed to a new format.
* version 3.1.3
** Some problems in xps3 atom selection have been fixed.
* version 3.1.4
** Some problems in finalization process of openGL rendering have been fixed.
* version 3.1.5
** The output of 'show xps3' command has been modified.
** Some problems in 'save png/jpeg' command have been fixed.
* version 3.1.6
** Some problems in loading an empty polygon file have been fixed.
* version 3.1.7
** Some problems in initialization process of the applet have been fixed.
* version 3.2
** 'show site' command has been added.
* version 3.3 beta 1
** Availabe JOGL version is restricted to JSR-231 beta 5 only.
* version 3.3
** Both the previous JOGL (version 1.1.1) and JSR-231 are available.
** The following commands have been added; 'set viewpoint', 'show viewpoint', 'set imagesize', and 'show imagesize'.
* version 3.3.1
** Some problems in reading a pdbMLplus file have been fixed.
* version 3.4
** PDB format version 3 can be processed.
* version 3.5
** Discrimination of DNA and RNA linking nucleotides is based on [http://remediation.wwpdb.org/ccd.html Chemical Component Dictionary] for PDB format version 3.
** The default representation of the cartoon model has been changed. Commands 'set cartoon_loop_tube', 'set cartoon_round' and 'set ribbonback' have been added.
** The default parameters of lighting have been changed. Commands 'set ambient', 'set diffuse1', 'set diffuse1_direction', 'set diffuse2' and 'set diffuse1_direction' have been added.
** Commands 'set pdbml_noatom_url', 'set pdbml_extatom_url', 'set pdbml_plus_url', 'set efsite_url', 'set ext_site_url', 'show pdbml_url', 'show efsite_url' and 'show ext_site_url' have been added.
** The command-line option '-stdin' has been added to receive commands from stdin stream.
* version 3.6
** Users can specify the JavaScript function name used in Applet-to-JavaScript Communication.
** Applet parameter 'file_load_message' has been added.
* version 3.6.1
** Predefined set of residues has been modified.
** Old JOGL API is not supported.
* version 3.6.2
** Latest version of PDBML can be processed.
** Some problems in mouse control on Mac have been fixed.
* version 3.6.3
** Molecule file parsing has been modified to detect chain breaks properly by reading the 'label_asym_id' column in PDBML and the TER line in PDB flat file, respectively.
* version 3.6.4
** Some problems in GUI menu on Mac have been fixed.
* version 3.6.5
** The jV applet can invoke a JavaScript function when it started.
* version 3.7
** Commands 'pdbj_describe' and 'pdbj_execute' have been added.
** Keyword 'xps3' have been replaced by 'pdbj'.
* version 3.7.1
** Default PDBML URLs have been changed.
* version 3.7.2
** Some problems in creating png/jpeg image files have been fixed.
* version 3.8
** Command 'displayatom' has been added.
** The signed jV applet can save PNG/JPEG image files.
* version 3.8.1
** In commands 'cartoon', 'ribbons' and 'trace', a backbone will be drawn instead when a chain does not have enough atoms to draw those models.
** Recognition of amino acids is based on [http://remediation.wwpdb.org/ccd.html Chemical Component Dictionary].
* version 3.8.2
** Command 'ball_and_stick' has been added.
* version 3.8.3
** Binary distribution contains the JOGL library and pre-installation of JOGL is not necessary to use jV.
* version 4.0
** The program supports PDB format version 4.0.
** Atom expression has been extended to handle case-sensitive chain ID and label_asym_id in PDBML.
* version 4.1
** The program runs with new JOGL library (2.0-rc4 or later) which enables jV applets to run on Mac.
** From this release, the program requires JRE 1.6 or later.
** Command 'add_backbone' has been added.
** The program uses MODRES data and chem_comp/type data (PDBML only) to determine residue types.
* version 4.2
** The program reads polygon CGO (PyMOL-specific Compiled Graphics Objects) files distributed at eF-site system. Command 'load polygon_cgo' has been added.
** A parameter 'pdbid' and a method 'loadFTP' have been added to applet.
** When the program loads a PDBML noatom file whose directory is 'all-noatom' or 'XML-noatom', the coordinate file is retrieved from the corresponding directory; '../all-extatom' or '../XML-extatom', respectively.
* version 4.2.1
** The program runs with new JOGL library (2.0-rc11).
* version 4.3
** Anaglyph 3D rendering is added to 'stereo' command.
* version 4.3.1
** A workaround for a cache problem in JRE 1.7 has been added.
* version 4.4
** The program can read and write mmCIF format files.
** The program handles biomolecule structures when reading and writing a molecule file.
** The default setting of PDBMLplus URL has been changed.
* version 4.4.1
** Some problems in reading mmCIF files have been fixed.
** The behavior of mouse picking when measuring the distance between two atoms has been changed. Rotation and translation of molecules between two mouse pickings do not affect the distance measurement.
* version 4.4.2
** The program files are signed with a new certificate.</text>
    <sha1>8509ffebe566515085279f958d6f0350b416ea64</sha1>
  </revision>
  <revision>
    <id>599</id>
    <parentid>571</parentid>
    <timestamp>2015-02-24T06:31:59Z</timestamp>
    <contributor>
      <username>IMSsato</username>
      <id>4</id>
    </contributor>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="5754" xml:space="preserve">Changes and improvements have been made as follows.

* version 3.1
** The following commands have been added; 'animrange', 'set adjustview', 'show godata', and 'show xps3'.
** The xPSSS expression has been added in order to select a group of atoms.
** Several public methods have been added to the applet so as to append molecule or polygon files after the applet started.
** The applet can send information about mouse-picked atoms to JavaScript.
* version 3.1.1
** Some problems in GUI menu [Options]-[Hetero Atoms] and [Hydrogens] have been fixed.
** Some problems in 'trace' command have been fixed.
* version 3.1.2
** eF-site ID has been changed to a new format.
* version 3.1.3
** Some problems in xps3 atom selection have been fixed.
* version 3.1.4
** Some problems in finalization process of openGL rendering have been fixed.
* version 3.1.5
** The output of 'show xps3' command has been modified.
** Some problems in 'save png/jpeg' command have been fixed.
* version 3.1.6
** Some problems in loading an empty polygon file have been fixed.
* version 3.1.7
** Some problems in initialization process of the applet have been fixed.
* version 3.2
** 'show site' command has been added.
* version 3.3 beta 1
** Availabe JOGL version is restricted to JSR-231 beta 5 only.
* version 3.3
** Both the previous JOGL (version 1.1.1) and JSR-231 are available.
** The following commands have been added; 'set viewpoint', 'show viewpoint', 'set imagesize', and 'show imagesize'.
* version 3.3.1
** Some problems in reading a pdbMLplus file have been fixed.
* version 3.4
** PDB format version 3 can be processed.
* version 3.5
** Discrimination of DNA and RNA linking nucleotides is based on [http://remediation.wwpdb.org/ccd.html Chemical Component Dictionary] for PDB format version 3.
** The default representation of the cartoon model has been changed. Commands 'set cartoon_loop_tube', 'set cartoon_round' and 'set ribbonback' have been added.
** The default parameters of lighting have been changed. Commands 'set ambient', 'set diffuse1', 'set diffuse1_direction', 'set diffuse2' and 'set diffuse1_direction' have been added.
** Commands 'set pdbml_noatom_url', 'set pdbml_extatom_url', 'set pdbml_plus_url', 'set efsite_url', 'set ext_site_url', 'show pdbml_url', 'show efsite_url' and 'show ext_site_url' have been added.
** The command-line option '-stdin' has been added to receive commands from stdin stream.
* version 3.6
** Users can specify the JavaScript function name used in Applet-to-JavaScript Communication.
** Applet parameter 'file_load_message' has been added.
* version 3.6.1
** Predefined set of residues has been modified.
** Old JOGL API is not supported.
* version 3.6.2
** Latest version of PDBML can be processed.
** Some problems in mouse control on Mac have been fixed.
* version 3.6.3
** Molecule file parsing has been modified to detect chain breaks properly by reading the 'label_asym_id' column in PDBML and the TER line in PDB flat file, respectively.
* version 3.6.4
** Some problems in GUI menu on Mac have been fixed.
* version 3.6.5
** The jV applet can invoke a JavaScript function when it started.
* version 3.7
** Commands 'pdbj_describe' and 'pdbj_execute' have been added.
** Keyword 'xps3' have been replaced by 'pdbj'.
* version 3.7.1
** Default PDBML URLs have been changed.
* version 3.7.2
** Some problems in creating png/jpeg image files have been fixed.
* version 3.8
** Command 'displayatom' has been added.
** The signed jV applet can save PNG/JPEG image files.
* version 3.8.1
** In commands 'cartoon', 'ribbons' and 'trace', a backbone will be drawn instead when a chain does not have enough atoms to draw those models.
** Recognition of amino acids is based on [http://remediation.wwpdb.org/ccd.html Chemical Component Dictionary].
* version 3.8.2
** Command 'ball_and_stick' has been added.
* version 3.8.3
** Binary distribution contains the JOGL library and pre-installation of JOGL is not necessary to use jV.
* version 4.0
** The program supports PDB format version 4.0.
** Atom expression has been extended to handle case-sensitive chain ID and label_asym_id in PDBML.
* version 4.1
** The program runs with new JOGL library (2.0-rc4 or later) which enables jV applets to run on Mac.
** From this release, the program requires JRE 1.6 or later.
** Command 'add_backbone' has been added.
** The program uses MODRES data and chem_comp/type data (PDBML only) to determine residue types.
* version 4.2
** The program reads polygon CGO (PyMOL-specific Compiled Graphics Objects) files distributed at eF-site system. Command 'load polygon_cgo' has been added.
** A parameter 'pdbid' and a method 'loadFTP' have been added to applet.
** When the program loads a PDBML noatom file whose directory is 'all-noatom' or 'XML-noatom', the coordinate file is retrieved from the corresponding directory; '../all-extatom' or '../XML-extatom', respectively.
* version 4.2.1
** The program runs with new JOGL library (2.0-rc11).
* version 4.3
** Anaglyph 3D rendering is added to 'stereo' command.
* version 4.3.1
** A workaround for a cache problem in JRE 1.7 has been added.
* version 4.4
** The program can read and write mmCIF format files.
** The program handles biomolecule structures when reading and writing a molecule file.
** The default setting of PDBMLplus URL has been changed.
* version 4.4.1
** Some problems in reading mmCIF files have been fixed.
** The behavior of mouse picking when measuring the distance between two atoms has been changed. Rotation and translation of molecules between two mouse pickings do not affect the distance measurement.
* version 4.4.2
** The program files are signed with a new certificate.
* version 4.4.3
** Some problems in writing PDB files have been fixed.</text>
    <sha1>aaafedca19788a7e77d66e88dca79ca30d1604b6</sha1>
  </revision>
</page>
<page arvcontinue="20140430014530|554">
  <title>Introduction</title>
  <ns>0</ns>
  <id>44</id>
  <revision>
    <id>555</id>
    <parentid>496</parentid>
    <timestamp>2014-04-30T01:45:53Z</timestamp>
    <contributor>
      <username>IMSsato</username>
      <id>4</id>
    </contributor>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="1897" xml:space="preserve">jV is an interactive 3D viewer program to visualize protein and nucleic acid molecules. The program reads in a PDBML file that is an XML format for PDB. Usual PDB format files are also accepted. More than one molecule files can be opened and displayed at the same time and their display models and transforms can be operated separately. In addition to molecule files, a polygon file written in XML can be read and displayed. More than one polygon files can be opened at the same time and superposed on molecule images. The [http://ef-site.hgc.jp/eF-site/schema/polygon12.xsd XML schema] of the polygon file is available. jV can perform an animation of molecules. The animation file is a PDB format file in which each frame is separated by a MODEL line.

jV runs on Java Runtime Environment ([http://java.sun.com/javase/ JRE]) and can be used both as a standalone program and an applet. The 3D rendering is performed with the use of [http://jogamp.org/jogl/www/ JOGL] API. The version requirements are as follows.

* JRE (includes Java Plug-in) 1.6 or later
* JOGL 2.1.3 or later

Here, [http://java.sun.com/products/plugin/ Java Plug-in] is required in order to use the program as an applet.

The program allows an interactive mouse control and command execution. The commnad syntax follows that of [http://www.rasmol.org/ Rasmol] with some modifications. In order to handle the transform of each molecule and polygon separately, every files are set to be either selected or not selected. The transform operation commands, such as rotate or translate, act only on selected files. On the other hand, every atoms in a molecule are also set to be either selected or not selected independently of whether the molecule itself is selected or not selected. Only selected atoms are the target of display model operations, such as wireframe or spacefill commands, and coloring operations.

[[Release note]]</text>
    <sha1>44229361197cae5f4ce5ffec9fb236979d3b4203</sha1>
  </revision>
  <revision>
    <id>560</id>
    <parentid>555</parentid>
    <timestamp>2014-04-30T02:17:18Z</timestamp>
    <contributor>
      <username>IMSsato</username>
      <id>4</id>
    </contributor>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="1896" xml:space="preserve">jV is an interactive 3D viewer program to visualize protein and nucleic acid molecules. The program reads in a PDBML file that is an XML format for PDB. Usual PDB format files are also accepted. More than one molecule files can be opened and displayed at the same time and their display models and transforms can be operated separately. In addition to molecule files, a polygon file written in XML can be read and displayed. More than one polygon files can be opened at the same time and superposed on molecule images. The [http://ef-site.hgc.jp/eF-site/schema/polygon12.xsd XML schema] of the polygon file is available. jV can perform an animation of molecules. The animation file is a PDB format file in which each frame is separated by a MODEL line.

jV runs on Java Runtime Environment ([http://www.oracle.com/technetwork/java/javase/overview/index.html JRE]) and can be used both as a standalone program and an applet. The 3D rendering is performed with the use of [http://jogamp.org/jogl/www/ JOGL] API. The version requirements are as follows.

* JRE (includes Java Plug-in) 1.6 or later
* JOGL 2.1.3 or later

Here, Java Plug-in is required in order to use the program as an applet.

The program allows an interactive mouse control and command execution. The commnad syntax follows that of [http://www.rasmol.org/ Rasmol] with some modifications. In order to handle the transform of each molecule and polygon separately, every files are set to be either selected or not selected. The transform operation commands, such as rotate or translate, act only on selected files. On the other hand, every atoms in a molecule are also set to be either selected or not selected independently of whether the molecule itself is selected or not selected. Only selected atoms are the target of display model operations, such as wireframe or spacefill commands, and coloring operations.

[[Release note]]</text>
    <sha1>5e9c9e508fcf2b1226dcee652e88d07d874788d5</sha1>
  </revision>
  <revision>
    <id>561</id>
    <parentid>560</parentid>
    <timestamp>2014-04-30T02:23:07Z</timestamp>
    <contributor>
      <username>IMSsato</username>
      <id>4</id>
    </contributor>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="1935" xml:space="preserve">jV is an interactive 3D viewer program to visualize protein and nucleic acid molecules. The program reads in a PDBML file that is an XML format for PDB. Usual PDB format files are also accepted. More than one molecule files can be opened and displayed at the same time and their display models and transforms can be operated separately. In addition to molecule files, a polygon file written in XML can be read and displayed. More than one polygon files can be opened at the same time and superposed on molecule images. The [http://ef-site.hgc.jp/eF-site/schema/polygon12.xsd XML schema] of the polygon file is available. jV can perform an animation of molecules. The animation file is a PDB format file in which each frame is separated by a MODEL line.

jV runs on Java Runtime Environment ([http://www.oracle.com/technetwork/java/javase/overview/index.html JRE]) and can be used both as a standalone program and an applet. The 3D rendering is performed with the use of [http://jogamp.org/jogl/www/ JOGL] API. The version requirements are as follows.

* JRE (includes Java Plug-in) 1.6 or later
* JOGL 2.1.3 or later

Here, [http://java.sun.com/products/plugin/ Java Plug-in] is required in order to use the program as an applet.

The program allows an interactive mouse control and command execution. The commnad syntax follows that of [http://www.rasmol.org/ Rasmol] with some modifications. In order to handle the transform of each molecule and polygon separately, every files are set to be either selected or not selected. The transform operation commands, such as rotate or translate, act only on selected files. On the other hand, every atoms in a molecule are also set to be either selected or not selected independently of whether the molecule itself is selected or not selected. Only selected atoms are the target of display model operations, such as wireframe or spacefill commands, and coloring operations.

[[Release note]]</text>
    <sha1>90bcc017f5d786f81981fa7b9cb0259fe71a2e01</sha1>
  </revision>
  <revision>
    <id>565</id>
    <parentid>561</parentid>
    <timestamp>2014-11-11T02:41:50Z</timestamp>
    <contributor>
      <username>IMSsato</username>
      <id>4</id>
    </contributor>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="1935" xml:space="preserve">jV is an interactive 3D viewer program to visualize protein and nucleic acid molecules. The program reads in a PDBML file that is an XML format for PDB. Usual PDB format files are also accepted. More than one molecule files can be opened and displayed at the same time and their display models and transforms can be operated separately. In addition to molecule files, a polygon file written in XML can be read and displayed. More than one polygon files can be opened at the same time and superposed on molecule images. The [http://ef-site.hgc.jp/eF-site/schema/polygon12.xsd XML schema] of the polygon file is available. jV can perform an animation of molecules. The animation file is a PDB format file in which each frame is separated by a MODEL line.

jV runs on Java Runtime Environment ([http://www.oracle.com/technetwork/java/javase/overview/index.html JRE]) and can be used both as a standalone program and an applet. The 3D rendering is performed with the use of [http://jogamp.org/jogl/www/ JOGL] API. The version requirements are as follows.

* JRE (includes Java Plug-in) 1.6 or later
* JOGL 2.2.4 or later

Here, [http://java.sun.com/products/plugin/ Java Plug-in] is required in order to use the program as an applet.

The program allows an interactive mouse control and command execution. The commnad syntax follows that of [http://www.rasmol.org/ Rasmol] with some modifications. In order to handle the transform of each molecule and polygon separately, every files are set to be either selected or not selected. The transform operation commands, such as rotate or translate, act only on selected files. On the other hand, every atoms in a molecule are also set to be either selected or not selected independently of whether the molecule itself is selected or not selected. Only selected atoms are the target of display model operations, such as wireframe or spacefill commands, and coloring operations.

[[Release note]]</text>
    <sha1>b9066e5986b5ba76432cf0a5b3527a0ab8c631c2</sha1>
  </revision>
  <revision>
    <id>593</id>
    <parentid>565</parentid>
    <timestamp>2015-02-23T07:46:49Z</timestamp>
    <contributor>
      <username>IMSsato</username>
      <id>4</id>
    </contributor>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="1921" xml:space="preserve">jV is an interactive 3D viewer program to visualize protein and nucleic acid molecules. The program reads in a PDBML file that is an XML format for PDB. Usual PDB format files are also accepted. More than one molecule files can be opened and displayed at the same time and their display models and transforms can be operated separately. In addition to molecule files, a polygon file written in XML can be read and displayed. More than one polygon files can be opened at the same time and superposed on molecule images. The [http://www.pdbj.org/jv/polygonSchema XML schema] of the polygon file is available. jV can perform an animation of molecules. The animation file is a PDB format file in which each frame is separated by a MODEL line.

jV runs on Java Runtime Environment ([http://www.oracle.com/technetwork/java/javase/overview/index.html JRE]) and can be used both as a standalone program and an applet. The 3D rendering is performed with the use of [http://jogamp.org/jogl/www/ JOGL] API. The version requirements are as follows.

* JRE (includes Java Plug-in) 1.6 or later
* JOGL 2.2.4 or later

Here, [http://java.sun.com/products/plugin/ Java Plug-in] is required in order to use the program as an applet.

The program allows an interactive mouse control and command execution. The commnad syntax follows that of [http://www.rasmol.org/ Rasmol] with some modifications. In order to handle the transform of each molecule and polygon separately, every files are set to be either selected or not selected. The transform operation commands, such as rotate or translate, act only on selected files. On the other hand, every atoms in a molecule are also set to be either selected or not selected independently of whether the molecule itself is selected or not selected. Only selected atoms are the target of display model operations, such as wireframe or spacefill commands, and coloring operations.

[[Release note]]</text>
    <sha1>5be09cc725b44fc7f2f21f088a426d4ad0649840</sha1>
  </revision>
  <revision>
    <id>603</id>
    <parentid>593</parentid>
    <timestamp>2015-10-01T01:42:10Z</timestamp>
    <contributor>
      <username>IMSsato</username>
      <id>4</id>
    </contributor>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="1881" xml:space="preserve">jV is an interactive 3D viewer program to visualize protein and nucleic acid molecules. The program reads in a PDBML file that is an XML format for PDB. Usual PDB format files are also accepted. More than one molecule files can be opened and displayed at the same time and their display models and transforms can be operated separately. In addition to molecule files, a polygon file written in XML can be read and displayed. More than one polygon files can be opened at the same time and superposed on molecule images. The [http://www.pdbj.org/jv/polygonSchema XML schema] of the polygon file is available. jV can perform an animation of molecules. The animation file is a PDB format file in which each frame is separated by a MODEL line.

jV runs on Java Runtime Environment ([http://java.com/download/ JRE]) and can be used both as a standalone program and an applet. The 3D rendering is performed with the use of [http://jogamp.org/jogl/www/ JOGL] API. The version requirements are as follows.

* JRE (includes Java Plug-in) 1.6 or later
* JOGL 2.2.4 or later

Here, [http://java.sun.com/products/plugin/ Java Plug-in] is required in order to use the program as an applet.

The program allows an interactive mouse control and command execution. The commnad syntax follows that of [http://www.rasmol.org/ Rasmol] with some modifications. In order to handle the transform of each molecule and polygon separately, every files are set to be either selected or not selected. The transform operation commands, such as rotate or translate, act only on selected files. On the other hand, every atoms in a molecule are also set to be either selected or not selected independently of whether the molecule itself is selected or not selected. Only selected atoms are the target of display model operations, such as wireframe or spacefill commands, and coloring operations.

[[Release note]]</text>
    <sha1>c01c7b409c6f3bb3b9ff0b50c7d60b8df2ab1234</sha1>
  </revision>
</page>
<page arvcontinue="20140430014530|554">
  <title>Command List</title>
  <ns>0</ns>
  <id>20</id>
  <revision>
    <id>556</id>
    <parentid>507</parentid>
    <timestamp>2014-04-30T01:49:35Z</timestamp>
    <contributor>
      <username>IMSsato</username>
      <id>4</id>
    </contributor>
    <comment>/* load */</comment>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="25053" xml:space="preserve"> {| style="float:right"
  |__TOC__
  |}
Command usage of jV follows that of [http://www.rasmol.org/ Rasmol] with some modifications. In the following part, command arguments that can take an arbitrary value are denoted as &lt;value&gt; for example, arguments restricted to several possible values are listed with / as a delimiter, and arguments that can be omitted are put in brackets {}. Commands, [[#exit|exit]], [[#load|load]], [[#quit|quit]], [[#save|save]], [[#script|script]], and [[#write|write]], are not available in applet circumstance.

== add_backboe ==
 add_backbone {&lt;residue_name&gt; {&lt;atom_names&gt;}}
Adds backbone atom names to predefined ones for the specified residue. The &lt;atom_names&gt; is a comma-delimited list of atom names. Omitting the &lt;atom_names&gt; means to reset the residue to the initial setting. When no arguments are given, the current settings are shown.

== anim ==
 anim forward {&lt;value&gt;}
Starts animation forward. If the &lt;value&gt; is given, just move frames forward by the specified amount.

 anim backward {&lt;value&gt;}
Starts animation backward. If the &lt;value&gt; is given, just move frames backward by the specified amount.

 anim stop
Stops animation.

== animframe ==
 animframe &lt;frame&gt; {&lt;file_ID&gt;}
Sets the frame of all animation files for the specified value. When &lt;file_ID&gt; is given, only the specified file is processed.

== animmode ==
 animmode once
Sets the behavior of animation for 'once'. When the frame reaches the last one, animation is stopped.

 animmode loop
Sets the behavior of animation for 'loop'. When the frame reaches the last one, animation is reset to the first frame and continues playing.

 animmode swing
Sets the behavior of animation for 'swing'. When the frame reaches the last one, the direction of animation is reversed.

== animrange ==
 animrange &lt;init_frame&gt;-&lt;term_frame&gt; {&lt;file_IDs&gt;}
Sets the range of all animation files. When is given, only the specified file is processed.

== animselect ==
 animselect {-a/-r} &lt;file_IDs&gt;
Selects the specified files and makes the others not selected. More than one file IDs can be specified by putting commas as the delimiter. When the option -a or -r is specified, only the selection status of the specified files are modified, selected or not selected, respectively, and the others remain unchanged.

== animspeed ==
 animspeed &lt;speed&gt;
Sets the animation speed. The argument should be an integer value from 1 to 20.

== animstep ==
 animstep &lt;step&gt; {&lt;file_ID&gt;}
Sets the step of all animation files for the specified value. When &lt;file_ID&gt; is given, only the specified file is processed.

== backbone ==
 backbone {on/true}
Turns on the selected backbone bonds.

 backbone off/false
Turns off the selected backbone bonds.

 backbone &lt;radius&gt;
Turns on the selected backbone bonds with the specified raidus (angstrom or Rasmol unit). The maximum parameter value is 2.0.

== background ==
 background &lt;color&gt;
Changes the background color. The color may be given as RGB values [r,g,b], or predefined color names.

== ball_and_stick ==
 ball_and_stick {on/true}
Turns on the ball and stick image of the selected atoms with ball radius 0.5 and stick radius 0.2 in angstrom.

 ball_and_stick off/false
Turns off the ball and stick image of the selected atoms.

 ball_and_stick &lt;ball_radius&gt; &lt;stick_radius&gt;
Turns on the ball and stick image of the selected atoms with the specified ball radius and stick radius (angstrom or Rasmol unit). The maximum parameter value is 3.0 and 2.0, respectively.

== cartoon ==
 cartoon {on/true}
Turns on the thick ribbons for the selected residues. When a chain does not have enough atoms to draw the ribbon model, a backbone will be shown instead.

 cartoon off/false
Turns off the thick ribbons for the selected residues.

 cartoon &lt;half_width&gt;
Turns on the thick ribbons for the selected residues with the specified half width (angstrom or Rasmol unit). The maximum parameter value is 4.0.

== center ==
 center {-r/-s} {&lt;atom_expression&gt;}
Sets the center of rotation and the center of the screen to the center of a group of atoms specified by the [[Atom Expression|atom expression]]. When the option -r or -s is specified, only the center of rotation or the center of the screen is modified, respectively.

 center {-r} [x, y, z]
Moves the center of rotation and the center of the screen from the current position by the specified amount. When the option -r is specified, only the center of rotation is modified.

 center {-r} {x, y, z}
Sets the center of rotation and the center of the screen to the specified coordinates. When the option -r is specified, only the center of rotation is modified.

 center -s [x, y]
Moves the center of the screen from the current position by the specified amount.

 center -s {x, y}
Sets the center of the screen to the specified coordinates.

== color ==
 color {atoms} &lt;color&gt;
Sets the color of the selected atoms. The color may be given as RGB values [r,g,b], predefined color names, or predefined color schemes; amino, chain, charge, cpk, group, shapely, structure, and temperature.

 color bonds/backbone/ribbons/hbonds/ssbonds &lt;color&gt;
Sets the color of the specified object. The color may be given as RGB values [r,g,b] or predefined color names. For hydrogen bonds, color scheme 'type' can be specified.

 color bonds/backbone/ribbons/hbonds/ssbonds none
Resets the color of the specified object.

== colorvertex ==
 colorvertex &lt;color&gt;
Sets the color of the selected vertices. The color may be given as RGB values [r,g,b] or predefined color names.

 colorvertex none
Resets the color of the selected vertices.

== cpk ==
 cpk
A synonym of the [[#spacefill|spacefill]] command.

== define ==
 define &lt;name&gt; &lt;atom_expression&gt;
Associates an arbitrary set of atoms specified by the [[Atom Expression|atom expression]] with a unique name.

== display ==
 display all
Displays the image of all files.

 display none
Turns off the image of all files.

 display {-a/-r} &lt;file_IDs&gt;
Displays the image of the specified files and turns off the others. More than one file IDs can be specified by putting commas as the delimiter. When the option -a or -r is specified, turns the image of the specified files on or off, respectively, and the others remain unchanged.

== displayatom ==
 displayatom {on/true}
Displays the selected atoms.

 displayatom off/false
Turns off the selected atoms.

== displayvertex ==
 displayvertex {on/true}
Displays the selected vertices.

 displayvertex off/false
Turns off the selected vertices.

== echo ==
 echo &lt;string&gt;
Echoes the specified message back to the message area.

== exit ==
 exit
Terminates the application.

== fit ==
 fit &lt;file1_ID&gt; &lt;file2_ID&gt;
Sets the transform matrix of file1 identical to that of file2. 

== fselect ==
 fselect all
Selects all files.

 fselect none
Selects no files.

 fselect {-a/-r} &lt;file_IDs&gt;
Selects the specified files and makes the others not selected. More than one file IDs can be specified by putting commas as the delimiter. When the option -a or -r is specified, only the selection status of the specified files are modified, selected or not selected, respectively, and the others remain unchanged.

== hbonds ==
 hbonds {on/true}
Turns on the selected hydrogen bonds.

 hbonds off/false
Turns off the selected hydrogen bonds.

 hbonds &lt;radius&gt;
Turns on the selected hydrogen bonds with the specified raidus (angstrom or Rasmol unit). The maximum parameter value is 2.0. 

== load ==
 load {pdbml} &lt;filename&gt; {fit &lt;file_ID&gt;} {biomolecule &lt;assembly_ID&gt;} {filter &lt;atom_expression&gt;} 
Opens a PDBML file. URL can be used to open a remote file. The transform matrix is copied from the file specified by 'fit'. A biomolecule structure can be specified by 'biomolecule'. For a biomolecule structure, a distinct model ID is assigned to each transform operation, which is listed by 'show information' command. Only atoms that matches a given filter are loaded. The filter takes any atom expressions except some keywords (bonded, helix, sheet, turn, within and pdbj:). The atom expression should be double-quoted or enclosed in a parenthesis when it contains spaces. 

 load mmcif &lt;filename&gt; {fit &lt;file_ID&gt;} {biomolecule &lt;assembly_ID&gt;} {filter &lt;atom_expression&gt;} 
Opens a mmCIF file. URL can be used to open a remote file. The transform matrix is copied from the file specified by 'fit'. A biomolecule structure can be specified by 'biomolecule'. For a biomolecule structure, a distinct model ID is assigned to each transform operation, which is listed by 'show information' command. Only atoms that matches a given filter are loaded. The filter takes any atom expressions except some keywords (bonded, helix, sheet, turn, within and pdbj:). The atom expression should be double-quoted or enclosed in a parenthesis when it contains spaces. 

 load pdb &lt;filename&gt; {fit &lt;file_ID&gt;} {filter &lt;atom_expression&gt;} 
Opens a PDB file. URL can be used to open a remote file. The transform matrix is copied from the file specified by 'fit'. Only atoms that matches a given filter are loaded. The filter takes any atom expressions except some keywords (bonded, helix, sheet, turn, within and pdbj:). The atom expression should be double-quoted or enclosed in a parenthesis when it contains spaces. 

 load polygon &lt;filename&gt; {fit &lt;file_ID&gt;}
Opens a polygon file. URL can be used to open a remote file. The transform matrix is copied from the file specified by 'fit'. 

 load polygon_cgo &lt;filename&gt; {fit &lt;file_ID&gt;}
Opens a polygon CGO file distributed at eF-site system. URL can be used to open a remote file. The transform matrix is copied from the file specified by 'fit'. 

 load animation &lt;filename&gt; {fit &lt;file_ID&gt;} {filter &lt;atom_expression&gt;}
Opens an animation file. URL can be used to open a remote file. The transform matrix is copied from the file specified by 'fit'. Only atoms that matches a given filter are loaded. The filter takes any atom expressions except some keywords (bonded, helix, sheet, turn, within and pdbj:). The atom expression should be double-quoted or enclosed in a parenthesis when it contains spaces. 

 load ftp &lt;PDB_code&gt; {fit &lt;file_ID&gt;} {biomolecule &lt;assembly_ID&gt;} {filter &lt;atom_expression&gt;} 
Retrieves a PDBML file from the PDBj FTP site and opens it. The transform matrix is copied from the file specified by 'fit'. A biomolecule structure can be specified by 'biomolecule'. For a biomolecule structure, a distinct model ID is assigned to each transform operation, which is listed by 'show information' command. Only atoms that matches a given filter are loaded. The filter takes any atom expressions except some keywords (bonded, helix, sheet, turn, within and pdbj:). The atom expression should be double-quoted or enclosed in a parenthesis when it contains spaces.

 load efsite &lt;efsite_ID&gt; 
Retrieves the PDB file and efvet file from eF-site database.

== pause ==
 pause
Stops the execution of a script file until any key is pressed to restart. 

== pdbj_describe ==
 pdbj_describe &lt;file_id&gt; {&lt;name&gt;} 
Shows the document for the jV_command in PDBMLplus specified by file ID and name. When the name is not specified, all available names are listed.

== pdbj_execute ==
 pdbj_execute &lt;file_id&gt; &lt;name&gt; 
Executes the jV_command in PDBMLplus specified by file ID and name.

== quit ==
 quit
A synonym of the [[#exit|exit]] command.

== refresh ==
 refresh
Redraws all images. 

== reset ==
=== default ===
 reset
Restores the original viewing transformation of all images, the center of rotation, and the view point. 

=== cartoon ===
 reset cartoon
Restores the thickness of the cartoon representation. 

=== line_width ===
 reset line_width
Restores the width of lines in polygon images. 

=== pickradius ===
 reset pickradius
Restores the mouse-pickable region of each atom. 

=== point_size ===
 reset point_size
Restores the size of points in polygon images. 

=== polyline_width ===
 reset polyline_width
Restores the width of polylines in polygon images. 

=== transparency ===
 reset transparency
Restores the transparency of polygon images.

 reset point_transparency
Restores the transparency of points in polygon images.

 reset line_transparency
Restores the transparency of lines in polygon images.

 reset triangle_transparency
Restores the transparency of triangles in polygon images.

 reset quad_transparency
Restores the transparency of quads in polygon images.

 reset polyline_transparency
Restores the transparency of polylines in polygon images. 

== ribbons ==
 ribbons {on/true}
Turns on the ribbon surfaces for the selected residues. When a chain does not have enough atoms to draw the ribbon model, a backbone will be shown instead.

 ribbons off/false
Turns off the ribbon surfaces for the selected residues.

 ribbons &lt;half_width&gt;
Turns on the ribbon surfaces for the selected residues with the specified half width (angstrom or Rasmol unit). The maximum parameter value is 4.0.

== rotate ==
 rotate x/y/z &lt;angle&gt;
Rotates images about the specified axis by the specified angle in degrees. 

== save ==
 save {pdb} &lt;filename&gt;
Saves the currently selected set of atoms in a PDB format file.

 save script &lt;filename&gt;
Creates a script file that reproduces the currently displayed image.

 save png &lt;filename&gt;
Creates a PNG image file of the currently displayed image.

 save jpeg &lt;filename&gt; {&lt;quality&gt;}
Creates a JPEG image file of the currently displayed image. The compression quality can be specified, 0 &lt; quality &lt;= 1, where 'quality = 1' means no compression. 

== script ==
 script &lt;filename&gt;
Opens and executes the specified script file. URL can be used to open a remote file. 

== select ==
 select
Selects all atoms. Whether hetero atoms and hydrogens are selected or not depends on the internal parameters, hetero and hydrogen, respectively.

 select all
Selects all atoms including hetero atoms and hydrogens.

 select none
Selects no atoms.

 select &lt;atom_expression&gt;
Selects a group of atoms specified by the [[Atom Expression|atom expression]].

== selectvertex ==
 selectvertex {all}
Selects all vertices.

 selectvertex none
Selects no vertices.

 selectvertex &lt;vertex_expression&gt;
Selects a group of vertices specified by the [[Vertex Expression|vertex expression]].

== set ==
=== ambient ===
 set ambient {&lt;value&gt;}
Sets the amount of ambient light. The value must be between 0 and 100. When the parameter is not specified, it is restored to the default value 33.

=== adjustview ===
 set adjustview on
The view point is automatically adjusted when a new file is loaded.

 set adjustview off
The view point is kept unchanged when a new file is loaded. 

=== background ===
 set background &lt;color&gt;
Changes the background color. The color may be given as RGB values [r,g,b], or predefined color names. 

=== bondmode ===
 set bondmode and
Specifies how to select an individual bonds. A bond is selected when both atoms connected by the bond are selected.

 set bondmode or
Specifies how to select an individual bonds. A bond is selected when either of the connected atoms is selected. 

=== cartoon ===
 set cartoon {&lt;value&gt;}
Specifies the thickness of the cartoon representation (angstrom or Rasmol unit). The maximum parameter value is 2.0. When the parameter is not specified, it is restored to the default value. 

=== cartoon_loop_tube ===
 set cartoon_loop_tube on
The loop region is drawn as tube in the cartoon representation.

 set cartoon_loop_tube off
The loop region is drawn as square pillar in the cartoon representation.

=== cartoon_round ===
 set cartoon_round on
Square pillar with round edge is drawn in the cartoon representation (except beta strands). 

 set cartoon_round off
Square pillar is drawn in the cartoon representation.

=== center ===
 set center &lt;atom_expression&gt;
Sets the default center of the selected files to the center of a group of atoms specified by the [[Atom Expression|atom expression]].

 set center [x, y, z]
Sets the default center of the selected files to the specified coordinates.

=== diffuse1 ===
 set diffuse1 {&lt;value&gt;}
Sets the amount of the first diffuse light. The value must be between 0 and 100. When the parameter is not specified, it is restored to the default value 50.

=== diffuse1_direction ===
 set diffuse1_direction {[x, y, z]}
Sets the direction of the first diffuse light. When the parameter is not specified, it is restored to the default value [-1, -1, -1].

=== diffuse2 ===
 set diffuse2 {&lt;value&gt;}
Sets the amount of the second diffuse light. The value must be between 0 and 100. When the parameter is not specified, it is restored to the default value 50.

=== diffuse2_direction ===
 set diffuse2_direction {[x, y, z]}
Sets the direction of the second diffuse light. When the parameter is not specified, it is restored to the default value [-1, -1, -1].

=== drawlevel ===
 set drawlevel &lt;value&gt;
Specifies precision of the rendering of spheres and cylinders. The value may be given as an integer (minimum 5) that stands for the number of straight line segments to represent an arc of 180 degrees. 

=== efsite_url ===
 set efsite_url &lt;URL&gt;
Sets the URL for eF-site.

=== ext_site_url ===
 set ext_site_url &lt;prefix&gt; &lt;URL&gt;
Sets the URL for an external database site.

=== hbonds ===
 set hbonds backbone
Hydrogen bonds are displayed between backbones.

 set hbonds sidechain
Hydrogen bonds are displayed between sidechains. 

=== hetero ===
 set hetero on
Sets the default behavior of the select command such that hetero atoms are selected.

 set hetero off
Sets the default behavior of the select command such that hetero atoms are not selected. 

=== hydrogen ===
 set hydrogen on
Sets the default behavior of the select command such that hydrogens are selected.

 set hydrogen off
Sets the default behavior of the select command such that hydrogens are not selected. 

=== imagesize ===
 set imagesize &lt;width&gt; &lt;height&gt;
Sets the size of the 3D-rendering panel in pixels. The size will be set within the screen size with the width being an even integer. 

=== line_width ===
 set line_width &lt;value&gt;
Sets the width of lines in polygon images. The &lt;value&gt; should be larger than 0. 

=== loadcenter ===
 set loadcenter on
When a file is opened, sets the default center of that file to the center of all files that have already opened.

 set loadcenter off
When a file is opened, sets the default center of that file according to its own coordiantes. 

=== pdbml_noatom_url ===
 set pdbml_noatom_url &lt;URL&gt;
Sets the URL for PDBML noatom files.

=== pdbml_extatom_url ===
 set pdbml_extatom_url &lt;URL&gt;
Sets the URL for PDBML extatom files.

=== pdbml_plus_url ===
 set pdbml_plus_url &lt;URL&gt;
Sets the URL for PDBMLplus files.

=== picking ===
 set picking off
Turns off the mouse picking.

 set picking ident
Sets the mouse picking behavior to show atom identification.

 set picking coord
Sets the mouse picking behavior to show atom coordinates with identification.

 set picking distance
Sets the mouse picking behavior to show the distance between atoms successively picked.

 set picking center
Sets the mouse picking behavior to specify the center of rotation and center of the screen.

 set picking select
Sets the mouse picking behavior to select the file that contains the atom picked. 

=== pickradius ===
 set pickradius &lt;value&gt;
Sets the mouse-pickable region of each atom to be the sphere centered to each atom with the specified radius (angstrom or Rasmol unit). 

=== point_size ===
 set point_size &lt;value&gt;
Sets the size of points in polygon images. The &lt;value&gt; should be larger than 0. 

=== polyline_width ===
 set polyline_width &lt;value&gt;
Sets the width of polylines in polygon images. The &lt;value&gt; should be larger than 0. 

=== projection ===
 set projection perspective
Sets the projection mode for a perspective projection.

 set projection parallel {&lt;size&gt;}
Sets the projection mode for a parallel projection. The size of image (fit to the height of the screen) can be specified (angstrom or Rasmol unit). 

=== ribbonback ===
 set ribbonback &lt;color&gt;
Sets the color of the back of ribbon models. The color may be given as RGB values [r,g,b] or predefined color names.

 set ribbonback none
Resets the color of the back of ribbon models.

=== specular ===
 set specular on/true
Enables the display of specular highlights on solid objects.

 set specular off/false
Disables the display of specular highlights on solid objects.

 set specular &lt;value&gt;
Enables the display of specular highlights on solid objects. The value between 0 and 100 specifies the specular color in gray scale with 0 and 100 being black and white, respectively. The default value is 50.0. 

=== specpower ===
 set specpower &lt;value&gt;
Sets the shininess of solid objects. The value between 0 and 100 specifies a material reflection coefficient with 0 being diffuse surfaces and 100 being shiny surfaces. 

=== ssbonds ===
 set ssbonds backbone
Disulfide bonds are displayed between backbones.

 set ssbonds sidechain
Disulfide bonds are displayed between sidechains. 

=== stereo ===
 set stereo
A synonym of the [[#stereo_2|stereo]] command.

=== transparency ===
 set transparency &lt;value&gt;
Sets the transparency of polygon images.

 set point_transparency &lt;value&gt;
Sets the transparency of points in polygon images.

 set line_transparency &lt;value&gt;
Sets the transparency of lines in polygon images.

 set triangle_transparency &lt;value&gt;
Sets the transparency of triangles in polygon images.

 set quad_transparency &lt;value&gt;
Sets the transparency of quads in polygon images.

 set polyline_transparency &lt;value&gt;
Sets the transparency of polylines in polygon images. 

=== viewpoint ===
 set viewpoint {x, y, z}
Sets the viewpoint to the specified coordinates. 

== show ==
 show godata
Displays gene ontology data of molecules.

 show imagesize
Displays the size of the 3D-rendering panel.

 show information
Displays a detail discription of molecules.

 show site {&lt;prefix&gt;:&lt;db&gt;:&lt;category&gt;}
Displays site information in an external database.

 show transform
Displays the transform matrix of molecules.

 show viewpoint
Displays the current viewpoint.

 show pdbj
Displays keywords available in [[Atom Expression#PDBj expression|PDBj expression]].

== slab ==
 slab {on/true}
Enables the z-clipping plane of molecules and polygons.

 slab off/false
Disables the z-clipping plane of molecules and polygons.

 slab &lt;ratio&gt;
Sets the position of the z-clipping plane of molecules and polygons. The parameter may be given as a number from 0 to 100. The values 0 and 100 represent that image as a whole is completely invisible and visible, respectively.

 slab -v &lt;value&gt;
Sets the position of the z-clipping plane of molecules and polygons by specifying the z coordinate value. 

== spacefill ==
 spacefill {on/true}
Turns on the ball image of the selected atoms.

 spacefill off/false
Turns off the ball image of the selected atoms.

 spacefill &lt;radius&gt;
Turns on the ball image of the selected atoms with the specified radius (angstrom or Rasmol unit). The maximum parameter value is 3.0.

 spacefill temperature
Turns on the ball image of the selected atoms using the temperature factor as radius. 

== ssbonds ==
 ssbonds {on/true}
Turns on the selected disulfide bonds.

 ssbonds off/false
Turns off the selected disulfide bonds.

 ssbonds &lt;radius&gt;
Turns on the selected disulfide bonds with the specified raidus (angstrom or Rasmol unit). The maximum parameter value is 2.0. 

== stereo ==
 stereo {on/true}
Enables stereo display. This command without arguments cycles three state; 'stereo off', 'stereo on' in cross-eyed mode and 'stereo on' in parallel-eyed mode.

 stereo off/false
Disables stereo display.

 stereo &lt;angle&gt;
Enables stereo display with the specified separation angle. Positive and negative values represent cross-eyed and parallel-eyed viewing, respectively.


== structure ==
 structure
Estimates the secondary structure using Kabsch and Sander's DSSP algorithm. 

== trace ==
 trace {on/true}
Turns on a tube representation for the selected residues. When a chain does not have enough atoms to draw the tube model, a backbone will be shown instead.

 trace off/false
Turns off a tube representation for the selected residues.

 trace &lt;radius&gt;
Turns on a tube representation for the selected residues with the specified radius (angstrom or Rasmol unit). The maximum parameter value is 2.0.

== translate ==
 translate x/y/z &lt;value&gt;
Moves images along the specified axis by the specified amount (angstrom). 

== wireframe ==
 wireframe {on/true}
Turns on the selected bonds.

 wireframe off/false
Turns off the selected bonds.

 wireframe &lt;radius&gt;
Turns on the selected bonds with the specified raidus (angstrom or Rasmol unit). The maximum parameter value is 2.0. 

== write ==
 write
A synonym of the [[#save|save]] command.

== zap ==
 zap {&lt;file_IDs&gt;}
Closes the specified files. More than one file IDs can be specified by putting commas as the delimiter. When the paraneter is absent, all files are closed. 

== zoom ==
 zoom {&lt;value&gt;}
Sets the magnification of the image as a whole. The value stands for the magnification as a percentage of the current scale. The minimum parameter value is 10.0.</text>
    <sha1>29772a4d8af48c39be654818a827988b664f6051</sha1>
  </revision>
  <revision>
    <id>567</id>
    <parentid>556</parentid>
    <timestamp>2014-11-11T02:43:52Z</timestamp>
    <contributor>
      <username>IMSsato</username>
      <id>4</id>
    </contributor>
    <comment>/* picking */</comment>
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  |}
Command usage of jV follows that of [http://www.rasmol.org/ Rasmol] with some modifications. In the following part, command arguments that can take an arbitrary value are denoted as &lt;value&gt; for example, arguments restricted to several possible values are listed with / as a delimiter, and arguments that can be omitted are put in brackets {}. Commands, [[#exit|exit]], [[#load|load]], [[#quit|quit]], [[#save|save]], [[#script|script]], and [[#write|write]], are not available in applet circumstance.

== add_backboe ==
 add_backbone {&lt;residue_name&gt; {&lt;atom_names&gt;}}
Adds backbone atom names to predefined ones for the specified residue. The &lt;atom_names&gt; is a comma-delimited list of atom names. Omitting the &lt;atom_names&gt; means to reset the residue to the initial setting. When no arguments are given, the current settings are shown.

== anim ==
 anim forward {&lt;value&gt;}
Starts animation forward. If the &lt;value&gt; is given, just move frames forward by the specified amount.

 anim backward {&lt;value&gt;}
Starts animation backward. If the &lt;value&gt; is given, just move frames backward by the specified amount.

 anim stop
Stops animation.

== animframe ==
 animframe &lt;frame&gt; {&lt;file_ID&gt;}
Sets the frame of all animation files for the specified value. When &lt;file_ID&gt; is given, only the specified file is processed.

== animmode ==
 animmode once
Sets the behavior of animation for 'once'. When the frame reaches the last one, animation is stopped.

 animmode loop
Sets the behavior of animation for 'loop'. When the frame reaches the last one, animation is reset to the first frame and continues playing.

 animmode swing
Sets the behavior of animation for 'swing'. When the frame reaches the last one, the direction of animation is reversed.

== animrange ==
 animrange &lt;init_frame&gt;-&lt;term_frame&gt; {&lt;file_IDs&gt;}
Sets the range of all animation files. When is given, only the specified file is processed.

== animselect ==
 animselect {-a/-r} &lt;file_IDs&gt;
Selects the specified files and makes the others not selected. More than one file IDs can be specified by putting commas as the delimiter. When the option -a or -r is specified, only the selection status of the specified files are modified, selected or not selected, respectively, and the others remain unchanged.

== animspeed ==
 animspeed &lt;speed&gt;
Sets the animation speed. The argument should be an integer value from 1 to 20.

== animstep ==
 animstep &lt;step&gt; {&lt;file_ID&gt;}
Sets the step of all animation files for the specified value. When &lt;file_ID&gt; is given, only the specified file is processed.

== backbone ==
 backbone {on/true}
Turns on the selected backbone bonds.

 backbone off/false
Turns off the selected backbone bonds.

 backbone &lt;radius&gt;
Turns on the selected backbone bonds with the specified raidus (angstrom or Rasmol unit). The maximum parameter value is 2.0.

== background ==
 background &lt;color&gt;
Changes the background color. The color may be given as RGB values [r,g,b], or predefined color names.

== ball_and_stick ==
 ball_and_stick {on/true}
Turns on the ball and stick image of the selected atoms with ball radius 0.5 and stick radius 0.2 in angstrom.

 ball_and_stick off/false
Turns off the ball and stick image of the selected atoms.

 ball_and_stick &lt;ball_radius&gt; &lt;stick_radius&gt;
Turns on the ball and stick image of the selected atoms with the specified ball radius and stick radius (angstrom or Rasmol unit). The maximum parameter value is 3.0 and 2.0, respectively.

== cartoon ==
 cartoon {on/true}
Turns on the thick ribbons for the selected residues. When a chain does not have enough atoms to draw the ribbon model, a backbone will be shown instead.

 cartoon off/false
Turns off the thick ribbons for the selected residues.

 cartoon &lt;half_width&gt;
Turns on the thick ribbons for the selected residues with the specified half width (angstrom or Rasmol unit). The maximum parameter value is 4.0.

== center ==
 center {-r/-s} {&lt;atom_expression&gt;}
Sets the center of rotation and the center of the screen to the center of a group of atoms specified by the [[Atom Expression|atom expression]]. When the option -r or -s is specified, only the center of rotation or the center of the screen is modified, respectively.

 center {-r} [x, y, z]
Moves the center of rotation and the center of the screen from the current position by the specified amount. When the option -r is specified, only the center of rotation is modified.

 center {-r} {x, y, z}
Sets the center of rotation and the center of the screen to the specified coordinates. When the option -r is specified, only the center of rotation is modified.

 center -s [x, y]
Moves the center of the screen from the current position by the specified amount.

 center -s {x, y}
Sets the center of the screen to the specified coordinates.

== color ==
 color {atoms} &lt;color&gt;
Sets the color of the selected atoms. The color may be given as RGB values [r,g,b], predefined color names, or predefined color schemes; amino, chain, charge, cpk, group, shapely, structure, and temperature.

 color bonds/backbone/ribbons/hbonds/ssbonds &lt;color&gt;
Sets the color of the specified object. The color may be given as RGB values [r,g,b] or predefined color names. For hydrogen bonds, color scheme 'type' can be specified.

 color bonds/backbone/ribbons/hbonds/ssbonds none
Resets the color of the specified object.

== colorvertex ==
 colorvertex &lt;color&gt;
Sets the color of the selected vertices. The color may be given as RGB values [r,g,b] or predefined color names.

 colorvertex none
Resets the color of the selected vertices.

== cpk ==
 cpk
A synonym of the [[#spacefill|spacefill]] command.

== define ==
 define &lt;name&gt; &lt;atom_expression&gt;
Associates an arbitrary set of atoms specified by the [[Atom Expression|atom expression]] with a unique name.

== display ==
 display all
Displays the image of all files.

 display none
Turns off the image of all files.

 display {-a/-r} &lt;file_IDs&gt;
Displays the image of the specified files and turns off the others. More than one file IDs can be specified by putting commas as the delimiter. When the option -a or -r is specified, turns the image of the specified files on or off, respectively, and the others remain unchanged.

== displayatom ==
 displayatom {on/true}
Displays the selected atoms.

 displayatom off/false
Turns off the selected atoms.

== displayvertex ==
 displayvertex {on/true}
Displays the selected vertices.

 displayvertex off/false
Turns off the selected vertices.

== echo ==
 echo &lt;string&gt;
Echoes the specified message back to the message area.

== exit ==
 exit
Terminates the application.

== fit ==
 fit &lt;file1_ID&gt; &lt;file2_ID&gt;
Sets the transform matrix of file1 identical to that of file2. 

== fselect ==
 fselect all
Selects all files.

 fselect none
Selects no files.

 fselect {-a/-r} &lt;file_IDs&gt;
Selects the specified files and makes the others not selected. More than one file IDs can be specified by putting commas as the delimiter. When the option -a or -r is specified, only the selection status of the specified files are modified, selected or not selected, respectively, and the others remain unchanged.

== hbonds ==
 hbonds {on/true}
Turns on the selected hydrogen bonds.

 hbonds off/false
Turns off the selected hydrogen bonds.

 hbonds &lt;radius&gt;
Turns on the selected hydrogen bonds with the specified raidus (angstrom or Rasmol unit). The maximum parameter value is 2.0. 

== load ==
 load {pdbml} &lt;filename&gt; {fit &lt;file_ID&gt;} {biomolecule &lt;assembly_ID&gt;} {filter &lt;atom_expression&gt;} 
Opens a PDBML file. URL can be used to open a remote file. The transform matrix is copied from the file specified by 'fit'. A biomolecule structure can be specified by 'biomolecule'. For a biomolecule structure, a distinct model ID is assigned to each transform operation, which is listed by 'show information' command. Only atoms that matches a given filter are loaded. The filter takes any atom expressions except some keywords (bonded, helix, sheet, turn, within and pdbj:). The atom expression should be double-quoted or enclosed in a parenthesis when it contains spaces. 

 load mmcif &lt;filename&gt; {fit &lt;file_ID&gt;} {biomolecule &lt;assembly_ID&gt;} {filter &lt;atom_expression&gt;} 
Opens a mmCIF file. URL can be used to open a remote file. The transform matrix is copied from the file specified by 'fit'. A biomolecule structure can be specified by 'biomolecule'. For a biomolecule structure, a distinct model ID is assigned to each transform operation, which is listed by 'show information' command. Only atoms that matches a given filter are loaded. The filter takes any atom expressions except some keywords (bonded, helix, sheet, turn, within and pdbj:). The atom expression should be double-quoted or enclosed in a parenthesis when it contains spaces. 

 load pdb &lt;filename&gt; {fit &lt;file_ID&gt;} {filter &lt;atom_expression&gt;} 
Opens a PDB file. URL can be used to open a remote file. The transform matrix is copied from the file specified by 'fit'. Only atoms that matches a given filter are loaded. The filter takes any atom expressions except some keywords (bonded, helix, sheet, turn, within and pdbj:). The atom expression should be double-quoted or enclosed in a parenthesis when it contains spaces. 

 load polygon &lt;filename&gt; {fit &lt;file_ID&gt;}
Opens a polygon file. URL can be used to open a remote file. The transform matrix is copied from the file specified by 'fit'. 

 load polygon_cgo &lt;filename&gt; {fit &lt;file_ID&gt;}
Opens a polygon CGO file distributed at eF-site system. URL can be used to open a remote file. The transform matrix is copied from the file specified by 'fit'. 

 load animation &lt;filename&gt; {fit &lt;file_ID&gt;} {filter &lt;atom_expression&gt;}
Opens an animation file. URL can be used to open a remote file. The transform matrix is copied from the file specified by 'fit'. Only atoms that matches a given filter are loaded. The filter takes any atom expressions except some keywords (bonded, helix, sheet, turn, within and pdbj:). The atom expression should be double-quoted or enclosed in a parenthesis when it contains spaces. 

 load ftp &lt;PDB_code&gt; {fit &lt;file_ID&gt;} {biomolecule &lt;assembly_ID&gt;} {filter &lt;atom_expression&gt;} 
Retrieves a PDBML file from the PDBj FTP site and opens it. The transform matrix is copied from the file specified by 'fit'. A biomolecule structure can be specified by 'biomolecule'. For a biomolecule structure, a distinct model ID is assigned to each transform operation, which is listed by 'show information' command. Only atoms that matches a given filter are loaded. The filter takes any atom expressions except some keywords (bonded, helix, sheet, turn, within and pdbj:). The atom expression should be double-quoted or enclosed in a parenthesis when it contains spaces.

 load efsite &lt;efsite_ID&gt; 
Retrieves the PDB file and efvet file from eF-site database.

== pause ==
 pause
Stops the execution of a script file until any key is pressed to restart. 

== pdbj_describe ==
 pdbj_describe &lt;file_id&gt; {&lt;name&gt;} 
Shows the document for the jV_command in PDBMLplus specified by file ID and name. When the name is not specified, all available names are listed.

== pdbj_execute ==
 pdbj_execute &lt;file_id&gt; &lt;name&gt; 
Executes the jV_command in PDBMLplus specified by file ID and name.

== quit ==
 quit
A synonym of the [[#exit|exit]] command.

== refresh ==
 refresh
Redraws all images. 

== reset ==
=== default ===
 reset
Restores the original viewing transformation of all images, the center of rotation, and the view point. 

=== cartoon ===
 reset cartoon
Restores the thickness of the cartoon representation. 

=== line_width ===
 reset line_width
Restores the width of lines in polygon images. 

=== pickradius ===
 reset pickradius
Restores the mouse-pickable region of each atom. 

=== point_size ===
 reset point_size
Restores the size of points in polygon images. 

=== polyline_width ===
 reset polyline_width
Restores the width of polylines in polygon images. 

=== transparency ===
 reset transparency
Restores the transparency of polygon images.

 reset point_transparency
Restores the transparency of points in polygon images.

 reset line_transparency
Restores the transparency of lines in polygon images.

 reset triangle_transparency
Restores the transparency of triangles in polygon images.

 reset quad_transparency
Restores the transparency of quads in polygon images.

 reset polyline_transparency
Restores the transparency of polylines in polygon images. 

== ribbons ==
 ribbons {on/true}
Turns on the ribbon surfaces for the selected residues. When a chain does not have enough atoms to draw the ribbon model, a backbone will be shown instead.

 ribbons off/false
Turns off the ribbon surfaces for the selected residues.

 ribbons &lt;half_width&gt;
Turns on the ribbon surfaces for the selected residues with the specified half width (angstrom or Rasmol unit). The maximum parameter value is 4.0.

== rotate ==
 rotate x/y/z &lt;angle&gt;
Rotates images about the specified axis by the specified angle in degrees. 

== save ==
 save {pdb} &lt;filename&gt;
Saves the currently selected set of atoms in a PDB format file.

 save script &lt;filename&gt;
Creates a script file that reproduces the currently displayed image.

 save png &lt;filename&gt;
Creates a PNG image file of the currently displayed image.

 save jpeg &lt;filename&gt; {&lt;quality&gt;}
Creates a JPEG image file of the currently displayed image. The compression quality can be specified, 0 &lt; quality &lt;= 1, where 'quality = 1' means no compression. 

== script ==
 script &lt;filename&gt;
Opens and executes the specified script file. URL can be used to open a remote file. 

== select ==
 select
Selects all atoms. Whether hetero atoms and hydrogens are selected or not depends on the internal parameters, hetero and hydrogen, respectively.

 select all
Selects all atoms including hetero atoms and hydrogens.

 select none
Selects no atoms.

 select &lt;atom_expression&gt;
Selects a group of atoms specified by the [[Atom Expression|atom expression]].

== selectvertex ==
 selectvertex {all}
Selects all vertices.

 selectvertex none
Selects no vertices.

 selectvertex &lt;vertex_expression&gt;
Selects a group of vertices specified by the [[Vertex Expression|vertex expression]].

== set ==
=== ambient ===
 set ambient {&lt;value&gt;}
Sets the amount of ambient light. The value must be between 0 and 100. When the parameter is not specified, it is restored to the default value 33.

=== adjustview ===
 set adjustview on
The view point is automatically adjusted when a new file is loaded.

 set adjustview off
The view point is kept unchanged when a new file is loaded. 

=== background ===
 set background &lt;color&gt;
Changes the background color. The color may be given as RGB values [r,g,b], or predefined color names. 

=== bondmode ===
 set bondmode and
Specifies how to select an individual bonds. A bond is selected when both atoms connected by the bond are selected.

 set bondmode or
Specifies how to select an individual bonds. A bond is selected when either of the connected atoms is selected. 

=== cartoon ===
 set cartoon {&lt;value&gt;}
Specifies the thickness of the cartoon representation (angstrom or Rasmol unit). The maximum parameter value is 2.0. When the parameter is not specified, it is restored to the default value. 

=== cartoon_loop_tube ===
 set cartoon_loop_tube on
The loop region is drawn as tube in the cartoon representation.

 set cartoon_loop_tube off
The loop region is drawn as square pillar in the cartoon representation.

=== cartoon_round ===
 set cartoon_round on
Square pillar with round edge is drawn in the cartoon representation (except beta strands). 

 set cartoon_round off
Square pillar is drawn in the cartoon representation.

=== center ===
 set center &lt;atom_expression&gt;
Sets the default center of the selected files to the center of a group of atoms specified by the [[Atom Expression|atom expression]].

 set center [x, y, z]
Sets the default center of the selected files to the specified coordinates.

=== diffuse1 ===
 set diffuse1 {&lt;value&gt;}
Sets the amount of the first diffuse light. The value must be between 0 and 100. When the parameter is not specified, it is restored to the default value 50.

=== diffuse1_direction ===
 set diffuse1_direction {[x, y, z]}
Sets the direction of the first diffuse light. When the parameter is not specified, it is restored to the default value [-1, -1, -1].

=== diffuse2 ===
 set diffuse2 {&lt;value&gt;}
Sets the amount of the second diffuse light. The value must be between 0 and 100. When the parameter is not specified, it is restored to the default value 50.

=== diffuse2_direction ===
 set diffuse2_direction {[x, y, z]}
Sets the direction of the second diffuse light. When the parameter is not specified, it is restored to the default value [-1, -1, -1].

=== drawlevel ===
 set drawlevel &lt;value&gt;
Specifies precision of the rendering of spheres and cylinders. The value may be given as an integer (minimum 5) that stands for the number of straight line segments to represent an arc of 180 degrees. 

=== efsite_url ===
 set efsite_url &lt;URL&gt;
Sets the URL for eF-site.

=== ext_site_url ===
 set ext_site_url &lt;prefix&gt; &lt;URL&gt;
Sets the URL for an external database site.

=== hbonds ===
 set hbonds backbone
Hydrogen bonds are displayed between backbones.

 set hbonds sidechain
Hydrogen bonds are displayed between sidechains. 

=== hetero ===
 set hetero on
Sets the default behavior of the select command such that hetero atoms are selected.

 set hetero off
Sets the default behavior of the select command such that hetero atoms are not selected. 

=== hydrogen ===
 set hydrogen on
Sets the default behavior of the select command such that hydrogens are selected.

 set hydrogen off
Sets the default behavior of the select command such that hydrogens are not selected. 

=== imagesize ===
 set imagesize &lt;width&gt; &lt;height&gt;
Sets the size of the 3D-rendering panel in pixels. The size will be set within the screen size with the width being an even integer. 

=== line_width ===
 set line_width &lt;value&gt;
Sets the width of lines in polygon images. The &lt;value&gt; should be larger than 0. 

=== loadcenter ===
 set loadcenter on
When a file is opened, sets the default center of that file to the center of all files that have already opened.

 set loadcenter off
When a file is opened, sets the default center of that file according to its own coordiantes. 

=== pdbml_noatom_url ===
 set pdbml_noatom_url &lt;URL&gt;
Sets the URL for PDBML noatom files.

=== pdbml_extatom_url ===
 set pdbml_extatom_url &lt;URL&gt;
Sets the URL for PDBML extatom files.

=== pdbml_plus_url ===
 set pdbml_plus_url &lt;URL&gt;
Sets the URL for PDBMLplus files.

=== picking ===
 set picking off
Turns off the mouse picking.

 set picking ident
Sets the mouse picking behavior to show atom identification.

 set picking coord
Sets the mouse picking behavior to show atom coordinates with identification.

 set picking distance
Sets the mouse picking behavior to show the distance between atoms successively picked.
Rotation and translation of molecules between two mouse pickings do not affect the distance measurement.

 set picking center
Sets the mouse picking behavior to specify the center of rotation and center of the screen.

 set picking select
Sets the mouse picking behavior to select the file that contains the atom picked.

=== pickradius ===
 set pickradius &lt;value&gt;
Sets the mouse-pickable region of each atom to be the sphere centered to each atom with the specified radius (angstrom or Rasmol unit). 

=== point_size ===
 set point_size &lt;value&gt;
Sets the size of points in polygon images. The &lt;value&gt; should be larger than 0. 

=== polyline_width ===
 set polyline_width &lt;value&gt;
Sets the width of polylines in polygon images. The &lt;value&gt; should be larger than 0. 

=== projection ===
 set projection perspective
Sets the projection mode for a perspective projection.

 set projection parallel {&lt;size&gt;}
Sets the projection mode for a parallel projection. The size of image (fit to the height of the screen) can be specified (angstrom or Rasmol unit). 

=== ribbonback ===
 set ribbonback &lt;color&gt;
Sets the color of the back of ribbon models. The color may be given as RGB values [r,g,b] or predefined color names.

 set ribbonback none
Resets the color of the back of ribbon models.

=== specular ===
 set specular on/true
Enables the display of specular highlights on solid objects.

 set specular off/false
Disables the display of specular highlights on solid objects.

 set specular &lt;value&gt;
Enables the display of specular highlights on solid objects. The value between 0 and 100 specifies the specular color in gray scale with 0 and 100 being black and white, respectively. The default value is 50.0. 

=== specpower ===
 set specpower &lt;value&gt;
Sets the shininess of solid objects. The value between 0 and 100 specifies a material reflection coefficient with 0 being diffuse surfaces and 100 being shiny surfaces. 

=== ssbonds ===
 set ssbonds backbone
Disulfide bonds are displayed between backbones.

 set ssbonds sidechain
Disulfide bonds are displayed between sidechains. 

=== stereo ===
 set stereo
A synonym of the [[#stereo_2|stereo]] command.

=== transparency ===
 set transparency &lt;value&gt;
Sets the transparency of polygon images.

 set point_transparency &lt;value&gt;
Sets the transparency of points in polygon images.

 set line_transparency &lt;value&gt;
Sets the transparency of lines in polygon images.

 set triangle_transparency &lt;value&gt;
Sets the transparency of triangles in polygon images.

 set quad_transparency &lt;value&gt;
Sets the transparency of quads in polygon images.

 set polyline_transparency &lt;value&gt;
Sets the transparency of polylines in polygon images. 

=== viewpoint ===
 set viewpoint {x, y, z}
Sets the viewpoint to the specified coordinates. 

== show ==
 show godata
Displays gene ontology data of molecules.

 show imagesize
Displays the size of the 3D-rendering panel.

 show information
Displays a detail discription of molecules.

 show site {&lt;prefix&gt;:&lt;db&gt;:&lt;category&gt;}
Displays site information in an external database.

 show transform
Displays the transform matrix of molecules.

 show viewpoint
Displays the current viewpoint.

 show pdbj
Displays keywords available in [[Atom Expression#PDBj expression|PDBj expression]].

== slab ==
 slab {on/true}
Enables the z-clipping plane of molecules and polygons.

 slab off/false
Disables the z-clipping plane of molecules and polygons.

 slab &lt;ratio&gt;
Sets the position of the z-clipping plane of molecules and polygons. The parameter may be given as a number from 0 to 100. The values 0 and 100 represent that image as a whole is completely invisible and visible, respectively.

 slab -v &lt;value&gt;
Sets the position of the z-clipping plane of molecules and polygons by specifying the z coordinate value. 

== spacefill ==
 spacefill {on/true}
Turns on the ball image of the selected atoms.

 spacefill off/false
Turns off the ball image of the selected atoms.

 spacefill &lt;radius&gt;
Turns on the ball image of the selected atoms with the specified radius (angstrom or Rasmol unit). The maximum parameter value is 3.0.

 spacefill temperature
Turns on the ball image of the selected atoms using the temperature factor as radius. 

== ssbonds ==
 ssbonds {on/true}
Turns on the selected disulfide bonds.

 ssbonds off/false
Turns off the selected disulfide bonds.

 ssbonds &lt;radius&gt;
Turns on the selected disulfide bonds with the specified raidus (angstrom or Rasmol unit). The maximum parameter value is 2.0. 

== stereo ==
 stereo {on/true}
Enables stereo display. This command without arguments cycles three state; 'stereo off', 'stereo on' in cross-eyed mode and 'stereo on' in parallel-eyed mode.

 stereo off/false
Disables stereo display.

 stereo &lt;angle&gt;
Enables stereo display with the specified separation angle. Positive and negative values represent cross-eyed and parallel-eyed viewing, respectively.


== structure ==
 structure
Estimates the secondary structure using Kabsch and Sander's DSSP algorithm. 

== trace ==
 trace {on/true}
Turns on a tube representation for the selected residues. When a chain does not have enough atoms to draw the tube model, a backbone will be shown instead.

 trace off/false
Turns off a tube representation for the selected residues.

 trace &lt;radius&gt;
Turns on a tube representation for the selected residues with the specified radius (angstrom or Rasmol unit). The maximum parameter value is 2.0.

== translate ==
 translate x/y/z &lt;value&gt;
Moves images along the specified axis by the specified amount (angstrom). 

== wireframe ==
 wireframe {on/true}
Turns on the selected bonds.

 wireframe off/false
Turns off the selected bonds.

 wireframe &lt;radius&gt;
Turns on the selected bonds with the specified raidus (angstrom or Rasmol unit). The maximum parameter value is 2.0. 

== write ==
 write
A synonym of the [[#save|save]] command.

== zap ==
 zap {&lt;file_IDs&gt;}
Closes the specified files. More than one file IDs can be specified by putting commas as the delimiter. When the paraneter is absent, all files are closed. 

== zoom ==
 zoom {&lt;value&gt;}
Sets the magnification of the image as a whole. The value stands for the magnification as a percentage of the current scale. The minimum parameter value is 10.0.</text>
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Command usage of jV follows that of [http://www.rasmol.org/ Rasmol] with some modifications. In the following part, command arguments that can take an arbitrary value are denoted as &lt;value&gt; for example, arguments restricted to several possible values are listed with / as a delimiter, and arguments that can be omitted are put in brackets {}. Commands, [[#exit|exit]], [[#load|load]], [[#quit|quit]], [[#save|save]], [[#script|script]], and [[#write|write]], are not available in applet circumstance.

== add_backboe ==
 add_backbone {&lt;residue_name&gt; {&lt;atom_names&gt;}}
Adds backbone atom names to predefined ones for the specified residue. The &lt;atom_names&gt; is a comma-delimited list of atom names. Omitting the &lt;atom_names&gt; means to reset the residue to the initial setting. When no arguments are given, the current settings are shown.

== anim ==
 anim forward {&lt;value&gt;}
Starts animation forward. If the &lt;value&gt; is given, just move frames forward by the specified amount.

 anim backward {&lt;value&gt;}
Starts animation backward. If the &lt;value&gt; is given, just move frames backward by the specified amount.

 anim stop
Stops animation.

== animframe ==
 animframe &lt;frame&gt; {&lt;file_ID&gt;}
Sets the frame of all animation files for the specified value. When &lt;file_ID&gt; is given, only the specified file is processed.

== animmode ==
 animmode once
Sets the behavior of animation for 'once'. When the frame reaches the last one, animation is stopped.

 animmode loop
Sets the behavior of animation for 'loop'. When the frame reaches the last one, animation is reset to the first frame and continues playing.

 animmode swing
Sets the behavior of animation for 'swing'. When the frame reaches the last one, the direction of animation is reversed.

== animrange ==
 animrange &lt;init_frame&gt;-&lt;term_frame&gt; {&lt;file_IDs&gt;}
Sets the range of all animation files. When is given, only the specified file is processed.

== animselect ==
 animselect {-a/-r} &lt;file_IDs&gt;
Selects the specified files and makes the others not selected. More than one file IDs can be specified by putting commas as the delimiter. When the option -a or -r is specified, only the selection status of the specified files are modified, selected or not selected, respectively, and the others remain unchanged.

== animspeed ==
 animspeed &lt;speed&gt;
Sets the animation speed. The argument should be an integer value from 1 to 20.

== animstep ==
 animstep &lt;step&gt; {&lt;file_ID&gt;}
Sets the step of all animation files for the specified value. When &lt;file_ID&gt; is given, only the specified file is processed.

== backbone ==
 backbone {on/true}
Turns on the selected backbone bonds.

 backbone off/false
Turns off the selected backbone bonds.

 backbone &lt;radius&gt;
Turns on the selected backbone bonds with the specified raidus (angstrom or Rasmol unit). The maximum parameter value is 2.0.

== background ==
 background &lt;color&gt;
Changes the background color. The color may be given as RGB values [r,g,b], or predefined color names.

== ball_and_stick ==
 ball_and_stick {on/true}
Turns on the ball and stick image of the selected atoms with ball radius 0.5 and stick radius 0.2 in angstrom.

 ball_and_stick off/false
Turns off the ball and stick image of the selected atoms.

 ball_and_stick &lt;ball_radius&gt; &lt;stick_radius&gt;
Turns on the ball and stick image of the selected atoms with the specified ball radius and stick radius (angstrom or Rasmol unit). The maximum parameter value is 3.0 and 2.0, respectively.

== cartoon ==
 cartoon {on/true}
Turns on the thick ribbons for the selected residues. When a chain does not have enough atoms to draw the ribbon model, a backbone will be shown instead.

 cartoon off/false
Turns off the thick ribbons for the selected residues.

 cartoon &lt;half_width&gt;
Turns on the thick ribbons for the selected residues with the specified half width (angstrom or Rasmol unit). The maximum parameter value is 4.0.

== center ==
 center {-r/-s} {&lt;atom_expression&gt;}
Sets the center of rotation and the center of the screen to the center of a group of atoms specified by the [[Atom Expression|atom expression]]. When the option -r or -s is specified, only the center of rotation or the center of the screen is modified, respectively.

 center {-r} [x, y, z]
Moves the center of rotation and the center of the screen from the current position by the specified amount. When the option -r is specified, only the center of rotation is modified.

 center {-r} {x, y, z}
Sets the center of rotation and the center of the screen to the specified coordinates. When the option -r is specified, only the center of rotation is modified.

 center -s [x, y]
Moves the center of the screen from the current position by the specified amount.

 center -s {x, y}
Sets the center of the screen to the specified coordinates.

== color ==
 color {atoms} &lt;color&gt;
Sets the color of the selected atoms. The color may be given as RGB values [r,g,b], predefined color names, or predefined color schemes; amino, chain, charge, cpk, group, shapely, structure, and temperature.

 color bonds/backbone/ribbons/hbonds/ssbonds &lt;color&gt;
Sets the color of the specified object. The color may be given as RGB values [r,g,b] or predefined color names. For hydrogen bonds, color scheme 'type' can be specified.

 color bonds/backbone/ribbons/hbonds/ssbonds none
Resets the color of the specified object.

== colorvertex ==
 colorvertex &lt;color&gt;
Sets the color of the selected vertices. The color may be given as RGB values [r,g,b] or predefined color names.

 colorvertex none
Resets the color of the selected vertices.

== cpk ==
 cpk
A synonym of the [[#spacefill|spacefill]] command.

== define ==
 define &lt;name&gt; &lt;atom_expression&gt;
Associates an arbitrary set of atoms specified by the [[Atom Expression|atom expression]] with a unique name.

== display ==
 display all
Displays the image of all files.

 display none
Turns off the image of all files.

 display {-a/-r} &lt;file_IDs&gt;
Displays the image of the specified files and turns off the others. More than one file IDs can be specified by putting commas as the delimiter. When the option -a or -r is specified, turns the image of the specified files on or off, respectively, and the others remain unchanged.

== displayatom ==
 displayatom {on/true}
Displays the selected atoms.

 displayatom off/false
Turns off the selected atoms.

== displayvertex ==
 displayvertex {on/true}
Displays the selected vertices.

 displayvertex off/false
Turns off the selected vertices.

== echo ==
 echo &lt;string&gt;
Echoes the specified message back to the message area.

== exit ==
 exit
Terminates the application.

== fit ==
 fit &lt;file1_ID&gt; &lt;file2_ID&gt;
Sets the transform matrix of file1 identical to that of file2. 

== fselect ==
 fselect all
Selects all files.

 fselect none
Selects no files.

 fselect {-a/-r} &lt;file_IDs&gt;
Selects the specified files and makes the others not selected. More than one file IDs can be specified by putting commas as the delimiter. When the option -a or -r is specified, only the selection status of the specified files are modified, selected or not selected, respectively, and the others remain unchanged.

== hbonds ==
 hbonds {on/true}
Turns on the selected hydrogen bonds.

 hbonds off/false
Turns off the selected hydrogen bonds.

 hbonds &lt;radius&gt;
Turns on the selected hydrogen bonds with the specified raidus (angstrom or Rasmol unit). The maximum parameter value is 2.0. 

== load ==
 load {pdbml} &lt;filename&gt; {fit &lt;file_ID&gt;} {biomolecule &lt;assembly_ID&gt;} {filter &lt;atom_expression&gt;} 
Opens a PDBML file. URL can be used to open a remote file. The transform matrix is copied from the file specified by 'fit'. A biomolecule structure can be specified by 'biomolecule'. For a biomolecule structure, a distinct model ID is assigned to each transform operation, which is listed by 'show information' command. Only atoms that matches a given filter are loaded. The filter takes any atom expressions except some keywords (bonded, helix, sheet, turn, within and pdbj:). The atom expression should be double-quoted or enclosed in a parenthesis when it contains spaces. 

 load mmcif &lt;filename&gt; {fit &lt;file_ID&gt;} {biomolecule &lt;assembly_ID&gt;} {filter &lt;atom_expression&gt;} 
Opens a mmCIF file. URL can be used to open a remote file. The transform matrix is copied from the file specified by 'fit'. A biomolecule structure can be specified by 'biomolecule'. For a biomolecule structure, a distinct model ID is assigned to each transform operation, which is listed by 'show information' command. Only atoms that matches a given filter are loaded. The filter takes any atom expressions except some keywords (bonded, helix, sheet, turn, within and pdbj:). The atom expression should be double-quoted or enclosed in a parenthesis when it contains spaces. 

 load pdb &lt;filename&gt; {fit &lt;file_ID&gt;} {filter &lt;atom_expression&gt;} 
Opens a PDB file. URL can be used to open a remote file. The transform matrix is copied from the file specified by 'fit'. Only atoms that matches a given filter are loaded. The filter takes any atom expressions except some keywords (bonded, helix, sheet, turn, within and pdbj:). The atom expression should be double-quoted or enclosed in a parenthesis when it contains spaces. 

 load polygon &lt;filename&gt; {fit &lt;file_ID&gt;}
Opens a polygon file. URL can be used to open a remote file. The transform matrix is copied from the file specified by 'fit'. 

 load polygon_cgo &lt;filename&gt; {fit &lt;file_ID&gt;}
Opens a polygon CGO file distributed at eF-site system. URL can be used to open a remote file. The transform matrix is copied from the file specified by 'fit'. 

 load animation &lt;filename&gt; {fit &lt;file_ID&gt;} {filter &lt;atom_expression&gt;}
Opens an animation file. URL can be used to open a remote file. The transform matrix is copied from the file specified by 'fit'. Only atoms that matches a given filter are loaded. The filter takes any atom expressions except some keywords (bonded, helix, sheet, turn, within and pdbj:). The atom expression should be double-quoted or enclosed in a parenthesis when it contains spaces. 

 load ftp &lt;PDB_code&gt; {fit &lt;file_ID&gt;} {biomolecule &lt;assembly_ID&gt;} {filter &lt;atom_expression&gt;} 
Retrieves a PDBML file from the PDBj FTP site and opens it. The transform matrix is copied from the file specified by 'fit'. A biomolecule structure can be specified by 'biomolecule'. For a biomolecule structure, a distinct model ID is assigned to each transform operation, which is listed by 'show information' command. Only atoms that matches a given filter are loaded. The filter takes any atom expressions except some keywords (bonded, helix, sheet, turn, within and pdbj:). The atom expression should be double-quoted or enclosed in a parenthesis when it contains spaces.

 load efsite &lt;efsite_ID&gt; 
Retrieves the PDB file and efvet file from eF-site database.

== pause ==
 pause
Stops the execution of a script file until any key is pressed to restart. 

== pdbj_describe ==
 pdbj_describe &lt;file_id&gt; {&lt;name&gt;} 
Shows the document for the jV_command in PDBMLplus specified by file ID and name. When the name is not specified, all available names are listed.

== pdbj_execute ==
 pdbj_execute &lt;file_id&gt; &lt;name&gt; 
Executes the jV_command in PDBMLplus specified by file ID and name.

== quit ==
 quit
A synonym of the [[#exit|exit]] command.

== refresh ==
 refresh
Redraws all images. 

== reset ==
=== default ===
 reset
Restores the original viewing transformation of all images, the center of rotation, and the view point. 

=== cartoon ===
 reset cartoon
Restores the thickness of the cartoon representation. 

=== line_width ===
 reset line_width
Restores the width of lines in polygon images. 

=== pickradius ===
 reset pickradius
Restores the mouse-pickable region of each atom. 

=== point_size ===
 reset point_size
Restores the size of points in polygon images. 

=== polyline_width ===
 reset polyline_width
Restores the width of polylines in polygon images. 

=== transparency ===
 reset transparency
Restores the transparency of polygon images.

 reset point_transparency
Restores the transparency of points in polygon images.

 reset line_transparency
Restores the transparency of lines in polygon images.

 reset triangle_transparency
Restores the transparency of triangles in polygon images.

 reset quad_transparency
Restores the transparency of quads in polygon images.

 reset polyline_transparency
Restores the transparency of polylines in polygon images. 

== ribbons ==
 ribbons {on/true}
Turns on the ribbon surfaces for the selected residues. When a chain does not have enough atoms to draw the ribbon model, a backbone will be shown instead.

 ribbons off/false
Turns off the ribbon surfaces for the selected residues.

 ribbons &lt;half_width&gt;
Turns on the ribbon surfaces for the selected residues with the specified half width (angstrom or Rasmol unit). The maximum parameter value is 4.0.

== rotate ==
 rotate x/y/z &lt;angle&gt;
Rotates images about the specified axis by the specified angle in degrees. 

== save ==
 save {pdb} &lt;filename&gt;
Saves the currently selected set of atoms in a PDB format file.

 save mmcif &lt;filename&gt;
Saves the currently selected set of atoms in a mmCIF format file.

 save script &lt;filename&gt;
Creates a script file that reproduces the currently displayed image.

 save png &lt;filename&gt;
Creates a PNG image file of the currently displayed image.

 save jpeg &lt;filename&gt; {&lt;quality&gt;}
Creates a JPEG image file of the currently displayed image. The compression quality can be specified, 0 &lt; quality &lt;= 1, where 'quality = 1' means no compression.

== script ==
 script &lt;filename&gt;
Opens and executes the specified script file. URL can be used to open a remote file. 

== select ==
 select
Selects all atoms. Whether hetero atoms and hydrogens are selected or not depends on the internal parameters, hetero and hydrogen, respectively.

 select all
Selects all atoms including hetero atoms and hydrogens.

 select none
Selects no atoms.

 select &lt;atom_expression&gt;
Selects a group of atoms specified by the [[Atom Expression|atom expression]].

== selectvertex ==
 selectvertex {all}
Selects all vertices.

 selectvertex none
Selects no vertices.

 selectvertex &lt;vertex_expression&gt;
Selects a group of vertices specified by the [[Vertex Expression|vertex expression]].

== set ==
=== ambient ===
 set ambient {&lt;value&gt;}
Sets the amount of ambient light. The value must be between 0 and 100. When the parameter is not specified, it is restored to the default value 33.

=== adjustview ===
 set adjustview on
The view point is automatically adjusted when a new file is loaded.

 set adjustview off
The view point is kept unchanged when a new file is loaded. 

=== background ===
 set background &lt;color&gt;
Changes the background color. The color may be given as RGB values [r,g,b], or predefined color names. 

=== bondmode ===
 set bondmode and
Specifies how to select an individual bonds. A bond is selected when both atoms connected by the bond are selected.

 set bondmode or
Specifies how to select an individual bonds. A bond is selected when either of the connected atoms is selected. 

=== cartoon ===
 set cartoon {&lt;value&gt;}
Specifies the thickness of the cartoon representation (angstrom or Rasmol unit). The maximum parameter value is 2.0. When the parameter is not specified, it is restored to the default value. 

=== cartoon_loop_tube ===
 set cartoon_loop_tube on
The loop region is drawn as tube in the cartoon representation.

 set cartoon_loop_tube off
The loop region is drawn as square pillar in the cartoon representation.

=== cartoon_round ===
 set cartoon_round on
Square pillar with round edge is drawn in the cartoon representation (except beta strands). 

 set cartoon_round off
Square pillar is drawn in the cartoon representation.

=== center ===
 set center &lt;atom_expression&gt;
Sets the default center of the selected files to the center of a group of atoms specified by the [[Atom Expression|atom expression]].

 set center [x, y, z]
Sets the default center of the selected files to the specified coordinates.

=== diffuse1 ===
 set diffuse1 {&lt;value&gt;}
Sets the amount of the first diffuse light. The value must be between 0 and 100. When the parameter is not specified, it is restored to the default value 50.

=== diffuse1_direction ===
 set diffuse1_direction {[x, y, z]}
Sets the direction of the first diffuse light. When the parameter is not specified, it is restored to the default value [-1, -1, -1].

=== diffuse2 ===
 set diffuse2 {&lt;value&gt;}
Sets the amount of the second diffuse light. The value must be between 0 and 100. When the parameter is not specified, it is restored to the default value 50.

=== diffuse2_direction ===
 set diffuse2_direction {[x, y, z]}
Sets the direction of the second diffuse light. When the parameter is not specified, it is restored to the default value [-1, -1, -1].

=== drawlevel ===
 set drawlevel &lt;value&gt;
Specifies precision of the rendering of spheres and cylinders. The value may be given as an integer (minimum 5) that stands for the number of straight line segments to represent an arc of 180 degrees. 

=== efsite_url ===
 set efsite_url &lt;URL&gt;
Sets the URL for eF-site.

=== ext_site_url ===
 set ext_site_url &lt;prefix&gt; &lt;URL&gt;
Sets the URL for an external database site.

=== hbonds ===
 set hbonds backbone
Hydrogen bonds are displayed between backbones.

 set hbonds sidechain
Hydrogen bonds are displayed between sidechains. 

=== hetero ===
 set hetero on
Sets the default behavior of the select command such that hetero atoms are selected.

 set hetero off
Sets the default behavior of the select command such that hetero atoms are not selected. 

=== hydrogen ===
 set hydrogen on
Sets the default behavior of the select command such that hydrogens are selected.

 set hydrogen off
Sets the default behavior of the select command such that hydrogens are not selected. 

=== imagesize ===
 set imagesize &lt;width&gt; &lt;height&gt;
Sets the size of the 3D-rendering panel in pixels. The size will be set within the screen size with the width being an even integer. 

=== line_width ===
 set line_width &lt;value&gt;
Sets the width of lines in polygon images. The &lt;value&gt; should be larger than 0. 

=== loadcenter ===
 set loadcenter on
When a file is opened, sets the default center of that file to the center of all files that have already opened.

 set loadcenter off
When a file is opened, sets the default center of that file according to its own coordiantes. 

=== pdbml_noatom_url ===
 set pdbml_noatom_url &lt;URL&gt;
Sets the URL for PDBML noatom files.

=== pdbml_extatom_url ===
 set pdbml_extatom_url &lt;URL&gt;
Sets the URL for PDBML extatom files.

=== pdbml_plus_url ===
 set pdbml_plus_url &lt;URL&gt;
Sets the URL for PDBMLplus files.

=== picking ===
 set picking off
Turns off the mouse picking.

 set picking ident
Sets the mouse picking behavior to show atom identification.

 set picking coord
Sets the mouse picking behavior to show atom coordinates with identification.

 set picking distance
Sets the mouse picking behavior to show the distance between atoms successively picked.
Rotation and translation of molecules between two mouse pickings do not affect the distance measurement.

 set picking center
Sets the mouse picking behavior to specify the center of rotation and center of the screen.

 set picking select
Sets the mouse picking behavior to select the file that contains the atom picked.

=== pickradius ===
 set pickradius &lt;value&gt;
Sets the mouse-pickable region of each atom to be the sphere centered to each atom with the specified radius (angstrom or Rasmol unit). 

=== point_size ===
 set point_size &lt;value&gt;
Sets the size of points in polygon images. The &lt;value&gt; should be larger than 0. 

=== polyline_width ===
 set polyline_width &lt;value&gt;
Sets the width of polylines in polygon images. The &lt;value&gt; should be larger than 0. 

=== projection ===
 set projection perspective
Sets the projection mode for a perspective projection.

 set projection parallel {&lt;size&gt;}
Sets the projection mode for a parallel projection. The size of image (fit to the height of the screen) can be specified (angstrom or Rasmol unit). 

=== ribbonback ===
 set ribbonback &lt;color&gt;
Sets the color of the back of ribbon models. The color may be given as RGB values [r,g,b] or predefined color names.

 set ribbonback none
Resets the color of the back of ribbon models.

=== specular ===
 set specular on/true
Enables the display of specular highlights on solid objects.

 set specular off/false
Disables the display of specular highlights on solid objects.

 set specular &lt;value&gt;
Enables the display of specular highlights on solid objects. The value between 0 and 100 specifies the specular color in gray scale with 0 and 100 being black and white, respectively. The default value is 50.0. 

=== specpower ===
 set specpower &lt;value&gt;
Sets the shininess of solid objects. The value between 0 and 100 specifies a material reflection coefficient with 0 being diffuse surfaces and 100 being shiny surfaces. 

=== ssbonds ===
 set ssbonds backbone
Disulfide bonds are displayed between backbones.

 set ssbonds sidechain
Disulfide bonds are displayed between sidechains. 

=== stereo ===
 set stereo
A synonym of the [[#stereo_2|stereo]] command.

=== transparency ===
 set transparency &lt;value&gt;
Sets the transparency of polygon images.

 set point_transparency &lt;value&gt;
Sets the transparency of points in polygon images.

 set line_transparency &lt;value&gt;
Sets the transparency of lines in polygon images.

 set triangle_transparency &lt;value&gt;
Sets the transparency of triangles in polygon images.

 set quad_transparency &lt;value&gt;
Sets the transparency of quads in polygon images.

 set polyline_transparency &lt;value&gt;
Sets the transparency of polylines in polygon images. 

=== viewpoint ===
 set viewpoint {x, y, z}
Sets the viewpoint to the specified coordinates. 

== show ==
 show godata
Displays gene ontology data of molecules.

 show imagesize
Displays the size of the 3D-rendering panel.

 show information
Displays a detail discription of molecules.

 show site {&lt;prefix&gt;:&lt;db&gt;:&lt;category&gt;}
Displays site information in an external database.

 show transform
Displays the transform matrix of molecules.

 show viewpoint
Displays the current viewpoint.

 show pdbj
Displays keywords available in [[Atom Expression#PDBj expression|PDBj expression]].

== slab ==
 slab {on/true}
Enables the z-clipping plane of molecules and polygons.

 slab off/false
Disables the z-clipping plane of molecules and polygons.

 slab &lt;ratio&gt;
Sets the position of the z-clipping plane of molecules and polygons. The parameter may be given as a number from 0 to 100. The values 0 and 100 represent that image as a whole is completely invisible and visible, respectively.

 slab -v &lt;value&gt;
Sets the position of the z-clipping plane of molecules and polygons by specifying the z coordinate value. 

== spacefill ==
 spacefill {on/true}
Turns on the ball image of the selected atoms.

 spacefill off/false
Turns off the ball image of the selected atoms.

 spacefill &lt;radius&gt;
Turns on the ball image of the selected atoms with the specified radius (angstrom or Rasmol unit). The maximum parameter value is 3.0.

 spacefill temperature
Turns on the ball image of the selected atoms using the temperature factor as radius. 

== ssbonds ==
 ssbonds {on/true}
Turns on the selected disulfide bonds.

 ssbonds off/false
Turns off the selected disulfide bonds.

 ssbonds &lt;radius&gt;
Turns on the selected disulfide bonds with the specified raidus (angstrom or Rasmol unit). The maximum parameter value is 2.0. 

== stereo ==
 stereo {on/true}
Enables stereo display. This command without arguments cycles three state; 'stereo off', 'stereo on' in cross-eyed mode and 'stereo on' in parallel-eyed mode.

 stereo off/false
Disables stereo display.

 stereo &lt;angle&gt;
Enables stereo display with the specified separation angle. Positive and negative values represent cross-eyed and parallel-eyed viewing, respectively.


== structure ==
 structure
Estimates the secondary structure using Kabsch and Sander's DSSP algorithm. 

== trace ==
 trace {on/true}
Turns on a tube representation for the selected residues. When a chain does not have enough atoms to draw the tube model, a backbone will be shown instead.

 trace off/false
Turns off a tube representation for the selected residues.

 trace &lt;radius&gt;
Turns on a tube representation for the selected residues with the specified radius (angstrom or Rasmol unit). The maximum parameter value is 2.0.

== translate ==
 translate x/y/z &lt;value&gt;
Moves images along the specified axis by the specified amount (angstrom). 

== wireframe ==
 wireframe {on/true}
Turns on the selected bonds.

 wireframe off/false
Turns off the selected bonds.

 wireframe &lt;radius&gt;
Turns on the selected bonds with the specified raidus (angstrom or Rasmol unit). The maximum parameter value is 2.0. 

== write ==
 write
A synonym of the [[#save|save]] command.

== zap ==
 zap {&lt;file_IDs&gt;}
Closes the specified files. More than one file IDs can be specified by putting commas as the delimiter. When the paraneter is absent, all files are closed. 

== zoom ==
 zoom {&lt;value&gt;}
Sets the magnification of the image as a whole. The value stands for the magnification as a percentage of the current scale. The minimum parameter value is 10.0.</text>
    <sha1>3d15c098f955bd69808277508be1b6ed0c46e27c</sha1>
  </revision>
</page>
<page arvcontinue="20140430014530|554">
  <title>Atom Expression</title>
  <ns>0</ns>
  <id>21</id>
  <revision>
    <id>557</id>
    <parentid>469</parentid>
    <timestamp>2014-04-30T01:50:59Z</timestamp>
    <contributor>
      <username>IMSsato</username>
      <id>4</id>
    </contributor>
    <comment>/* others */</comment>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="12562" xml:space="preserve">{| style="float:right"
 |__TOC__
 |}
In order to specify a group of atoms in a molecule, the following five expressions are available.

The standard boolean connectives 'and', 'or' and 'not', and brackets can be used to construct a complex expression. The boolean connectives may be abbreviated as '&amp;', '|', and '!', respectively. 

== predefined set ==
=== element name ===
Element names, such as carbon or nitrogen, can be used to select atoms. 
=== set based on residue property ===
a) amino acids in protein molecule
&lt;table border="1"&gt;
&lt;tr&gt;
&lt;td&gt;&lt;/td&gt;
&lt;td&gt;ALA&lt;/td&gt;&lt;td&gt;ARG&lt;/td&gt;&lt;td&gt;ASN&lt;/td&gt;&lt;td&gt;ASP&lt;/td&gt;&lt;td&gt;CYS&lt;/td&gt;
&lt;td&gt;GLU&lt;/td&gt;&lt;td&gt;GLN&lt;/td&gt;&lt;td&gt;GLY&lt;/td&gt;&lt;td&gt;HIS&lt;/td&gt;&lt;td&gt;ILE&lt;/td&gt;
&lt;td&gt;LEU&lt;/td&gt;&lt;td&gt;LYS&lt;/td&gt;&lt;td&gt;MET&lt;/td&gt;&lt;td&gt;PHE&lt;/td&gt;&lt;td&gt;PRO&lt;/td&gt;
&lt;td&gt;SER&lt;/td&gt;&lt;td&gt;THR&lt;/td&gt;&lt;td&gt;TRP&lt;/td&gt;&lt;td&gt;TYR&lt;/td&gt;&lt;td&gt;VAL&lt;/td&gt;
&lt;/tr&gt;
&lt;tr&gt;
&lt;td&gt;Acidic&lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;/tr&gt;
&lt;tr&gt;
&lt;td&gt;Acyclic&lt;/td&gt;
&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;
&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;
&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;&lt;/td&gt;&lt;td&gt;&lt;/td&gt;
&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;&lt;/td&gt;&lt;td&gt;&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;
&lt;/tr&gt;
&lt;tr&gt;
&lt;td&gt;Aliphatic&lt;/td&gt;
&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;
&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;
&lt;/tr&gt;
&lt;tr&gt;
&lt;td&gt;Aromatic&lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;/tr&gt;
&lt;tr&gt;
&lt;td&gt;Basic&lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;/tr&gt;
&lt;tr&gt;
&lt;td&gt;Buried&lt;/td&gt;
&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;
&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;
&lt;/tr&gt;
&lt;tr&gt;
&lt;td&gt;Charged&lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;/tr&gt;
&lt;tr&gt;
&lt;td&gt;Cyclic&lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;/tr&gt;
&lt;tr&gt;
&lt;td&gt;Hydrophobic&lt;/td&gt;
&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;
&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;
&lt;/tr&gt;
&lt;tr&gt;
&lt;td&gt;Large&lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;
&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;/tr&gt;
&lt;tr&gt;
&lt;td&gt;Medium&lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;
&lt;/tr&gt;
&lt;tr&gt;
&lt;td&gt;Negative&lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;/tr&gt;
&lt;tr&gt;
&lt;td&gt;Neutral&lt;/td&gt;
&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;
&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;
&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;
&lt;/tr&gt;
&lt;tr&gt;
&lt;td&gt;Polar&lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;
&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;/tr&gt;
&lt;tr&gt;
&lt;td&gt;Positive&lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;/tr&gt;
&lt;tr&gt;
&lt;td&gt;Small&lt;/td&gt;
&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;/tr&gt;
&lt;tr&gt;
&lt;td&gt;Surface&lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;
&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;/tr&gt;
&lt;tr&gt;
&lt;td&gt;Cysteine&lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;/tr&gt;
&lt;tr&gt;
&lt;td&gt;Amino&lt;/td&gt;
&lt;td colspan="20"&gt;above 20 amino acids + other amino acids&lt;/td&gt;
&lt;/tr&gt;
&lt;tr&gt;
&lt;td&gt;Protein&lt;/td&gt;
&lt;td colspan="20"&gt;above 'Amino' set + UNK, ACE + FOR (PDB version 2.3 only)&lt;/td&gt;
&lt;/tr&gt;
&lt;/table&gt;
Here, 'other amino acids' stands for components whose type is one of the followings in [http://remediation.wwpdb.org/ccd.html Chemical Component Dictionary].&lt;br/&gt;
D-PEPTIDE LINKING&lt;br/&gt;
D-PEPTIDE NH3 AMINO TERMINUS&lt;br/&gt;
L-PEPTIDE COOH CARBOXY TERMINUS&lt;br/&gt;
L-PEPTIDE LINKING&lt;br/&gt;
L-PEPTIDE NH3 AMINO TERMINUS&lt;br/&gt;
PEPTIDE LINKING&lt;br/&gt;
PEPTIDE-LIKE&lt;br/&gt;

b1) nucleotides (for PDB version 2.3)
&lt;table border="1"&gt;
&lt;tr&gt;
&lt;td&gt;&lt;/td&gt;
&lt;td&gt;  A&lt;/td&gt;&lt;td&gt;  C&lt;/td&gt;&lt;td&gt;  G&lt;/td&gt;&lt;td&gt;  T&lt;/td&gt;&lt;td&gt;  U&lt;/td&gt;
&lt;td&gt; +U&lt;/td&gt;&lt;td&gt;  I&lt;/td&gt;&lt;td&gt;1MA&lt;/td&gt;&lt;td&gt;5MC&lt;/td&gt;&lt;td&gt;OMC&lt;/td&gt;
&lt;td&gt;1MG&lt;/td&gt;&lt;td&gt;2MG&lt;/td&gt;&lt;td&gt;M2G&lt;/td&gt;&lt;td&gt;7MG&lt;/td&gt;&lt;td&gt;OMG&lt;/td&gt;
&lt;td&gt; YG&lt;/td&gt;&lt;td&gt;H2U&lt;/td&gt;&lt;td&gt;5MU&lt;/td&gt;&lt;td&gt;PSU&lt;/td&gt;
&lt;/tr&gt;
&lt;tr&gt;
&lt;td&gt;AT&lt;/td&gt;
&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;/tr&gt;
&lt;tr&gt;
&lt;td&gt;CG&lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;/tr&gt;
&lt;tr&gt;
&lt;td&gt;Purine&lt;/td&gt;
&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;/tr&gt;
&lt;tr&gt;
&lt;td&gt;Pyrimidine&lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;/tr&gt;
&lt;tr&gt;
&lt;td&gt;DNA&lt;/td&gt;
&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;/tr&gt;
&lt;tr&gt;
&lt;td&gt;RNA&lt;/td&gt;
&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;
&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;
&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;
&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;
&lt;/tr&gt;
&lt;tr&gt;
&lt;td&gt;Nucleic&lt;/td&gt;
&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;
&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;
&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;
&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;
&lt;/tr&gt;
&lt;/table&gt;

b2) nucleotides (for PDB version 3)
&lt;table border="1"&gt;
&lt;tr&gt;
&lt;td&gt;&lt;/td&gt;
&lt;td&gt; DA&lt;/td&gt;&lt;td&gt; DC&lt;/td&gt;&lt;td&gt; DG&lt;/td&gt;&lt;td&gt; DT&lt;/td&gt;
&lt;td&gt;  A&lt;/td&gt;&lt;td&gt;  C&lt;/td&gt;&lt;td&gt;  G&lt;/td&gt;&lt;td&gt;  U&lt;/td&gt;
&lt;td&gt;other DNA&lt;/td&gt;&lt;td&gt;other RNA&lt;/td&gt;
&lt;/tr&gt;
&lt;tr&gt;
&lt;td&gt;AT&lt;/td&gt;
&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;/tr&gt;
&lt;tr&gt;
&lt;td&gt;CG&lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;/tr&gt;
&lt;tr&gt;
&lt;td&gt;Purine&lt;/td&gt;
&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;/tr&gt;
&lt;tr&gt;
&lt;td&gt;Pyrimidine&lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;/tr&gt;
&lt;tr&gt;
&lt;td&gt;DNA&lt;/td&gt;
&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;/tr&gt;
&lt;tr&gt;
&lt;td&gt;RNA&lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;
&lt;/tr&gt;
&lt;tr&gt;
&lt;td&gt;Nucleic&lt;/td&gt;
&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;
&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;
&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;
&lt;/tr&gt;
&lt;/table&gt;
Here, 'other DNA' and 'other RNA' stand for components whose type is 
DNA LINKING and RNA LINKING respectively in [http://remediation.wwpdb.org/ccd.html Chemical Component Dictionary].&lt;br/&gt;

c) others
&lt;table border="1"&gt;
&lt;tr&gt;
&lt;td&gt;&lt;/td&gt;
&lt;td&gt;HOH&lt;/td&gt;&lt;td&gt;DOD&lt;/td&gt;&lt;td&gt;SO4&lt;/td&gt;&lt;td&gt;PO4&lt;/td&gt;
&lt;/tr&gt;
&lt;tr&gt;
&lt;td&gt;Water&lt;/td&gt;
&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;
&lt;/tr&gt;
&lt;tr&gt;
&lt;td&gt;Ions&lt;/td&gt;
&lt;td&gt; &lt;/td&gt;&lt;td&gt; &lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;
&lt;/tr&gt;
&lt;tr&gt;
&lt;td&gt;Solvent&lt;/td&gt;
&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;&lt;td&gt;*&lt;/td&gt;
&lt;/tr&gt;
&lt;/table&gt;

=== others ===
&lt;table border="1"&gt;
&lt;tr&gt;
&lt;td&gt;Alpha&lt;/td&gt;
&lt;td&gt;
atoms whose name is CA.
&lt;/td&gt;
&lt;/tr&gt;
&lt;tr&gt;
&lt;td&gt;Hetero&lt;/td&gt;
&lt;td&gt;
atoms written as HETATM in PDB files or atoms in Solvent set.
&lt;/td&gt;
&lt;/tr&gt;
&lt;tr&gt;
&lt;td&gt;Ligand&lt;/td&gt;
&lt;td&gt;
atoms in Hetero set and not in Solvent set.
&lt;/td&gt;
&lt;/tr&gt;
&lt;tr&gt;
&lt;td&gt;Backbone&lt;br&gt;Mainchain&lt;/td&gt;
&lt;td&gt;
atoms in Amino set whose name is N, CA, C or O, or atoms in Nuceic set
whose name is P,O1P,O2P,O5*,C5*,C4*,O4*,C3*,O3*,C2*,O2* or C1*.
&lt;/td&gt;
&lt;/tr&gt;
&lt;tr&gt;
&lt;td&gt;Sidechain&lt;/td&gt;
&lt;td&gt;
atoms in Amino set or Nucleic set and not in Backbone set.
&lt;/td&gt;
&lt;/tr&gt;
&lt;tr&gt;
&lt;td&gt;Alphaphospho&lt;/td&gt;
&lt;td&gt;
atoms in Protein set whose name is CA or atoms in Nuceic set whose name is P.
&lt;/td&gt;
&lt;/tr&gt;
&lt;tr&gt;
&lt;td&gt;Bonded&lt;/td&gt;
&lt;td&gt;
atoms that is connected to at least one other atom.
&lt;/td&gt;
&lt;/tr&gt;
&lt;tr&gt;
&lt;td&gt;Selected&lt;/td&gt;
&lt;td&gt;
atoms currently selected.
&lt;/td&gt;
&lt;/tr&gt;
&lt;tr&gt;
&lt;td&gt;Helix&lt;/td&gt;
&lt;td&gt;
atoms in the alpha-helix structure.
&lt;/td&gt;
&lt;/tr&gt;
&lt;tr&gt;
&lt;td&gt;Sheet&lt;/td&gt;
&lt;td&gt;
atoms in the beta-sheet structure.
&lt;/td&gt;
&lt;/tr&gt;
&lt;tr&gt;
&lt;td&gt;Turn&lt;/td&gt;
&lt;td&gt;
atoms in the turn structure.
&lt;/td&gt;
&lt;/tr&gt;
&lt;/table&gt;

== comparison operators ==
Parts of a molecule can be selected using equality, inequality and ordering operators on their properties. Possible operators are =, ==, &lt;&gt;, !=, /=, &lt;, &lt;=, &gt; and &gt;=, and possible property names are as follows.
{| border="1"
 |-
 | AtomNo || atom ID in PDB files.
 |-
 | ElemNo || atomic number.
 |-
 | ResNo || residue ID in PDB files.
 |-
 | Radius || radius of a ball image of atoms.
 |-
 | Temperature || temperature factor of atoms.
 |-
 | Model || model ID in PDB files.
 |-
 | File || File ID.
 |}

== residue range ==
A group of atoms in a molecule can be selected by the residue ID. For example, command 'select 3' selects atoms whose residue ID is 3, and 'select 3-10' selects atoms whose residue ID is larger than or equal to 3 and smaller than or equal to 10. 
Optionally, the chain ID can be specified after residue range with a colon.
For example, command 'select 3:A' selects atoms
whose residue ID is 3 in the A chain.
The chain ID can be specified in several ways (see [[#primitive_expression|primitive expression]]).

== within expression ==
A within expression selects atoms that exist within a specified distance from another set of atoms. For example, 'select within(3.0, backbone) selects atoms within a 3.0 Angstrom radius of any atom in a protein or nucleic acid backbone. 

== PDBj expression ==
A PDBj expression selects a group of atoms according to molecule's properties defined in the PDBMLplus file. It takes the following form;
 pdbj:keyword
For example, 'select pdbj:binding'. The keywords available for each molecule are obtained by the 'show pdbj' command.

== primitive expression ==
A primitive expression takes such a form as
 residue name[residue ID][:chain ID][.atom name][;alternate location][/model ID][@file ID]
Here, residue name and atom name are three letter and four letter name, respectively, and terms in square brackets can be omitted. For example, command 'select SER.CA' selects all alpha carbon atoms in serine.
Residue names that contain numeric characters should be enclosed in square brackets such as '[SO4]'.
Expressions are treated in a case-insensitive manner.
However, the chain ID can be specified case-sensitively such as 'a_A' or 'a_a',
where these mean the chains whose auth_asym_id is 'A' or 'a', respectively. 
In the same way, you can use label_asym_id to specify chains case-sensitively such as 'l_A'.
Note that the label_asym_id is available only for PDBML files and not for PDB flat files.</text>
    <sha1>6ddc1ed18cbdcc2eb4dd13a2000c46d6a3f7eb88</sha1>
  </revision>
</page>
<page arvcontinue="20140430014530|554">
  <title>Use as Applet</title>
  <ns>0</ns>
  <id>24</id>
  <revision>
    <id>558</id>
    <parentid>506</parentid>
    <timestamp>2014-04-30T01:53:38Z</timestamp>
    <contributor>
      <username>IMSsato</username>
      <id>4</id>
    </contributor>
    <comment>/* Parameters */</comment>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="5187" xml:space="preserve">{| style="float:right"
 |__TOC__
 |}

== Introduction ==
In order to use jV as an applet, [http://java.sun.com/products/plugin/ Java Plug-in] must be installed on client computers. The applet is called from usual APPLET tags, or OBJECT and EMBED tags in HTML (see [http://java.sun.com/products/plugin/ Java Plug-in] homepage), where class name that should be called is "org.pdbj.viewer.gui.ViewerApplet" class. The program has following features.
* whether to use the command line interface or not can be specified
* whether to use the file control panel or not can be specified
* whether to use the popup menu or not can be specified
* witihin applets in the same web page, mouse events can be shared
* applet can receive a command string from JaveScript
* applet can send information about mouse-picked atoms to JavaScript.

== Parameters ==
To initialize the applet, the following parameters can be specified in HTML.
{| class="wikitable" border="1"
 ! parameter !! value 
 |-
 | pdbid || PDB ID to be loaded from the PDBj FTP site (delimited by comma for more than one files). This parameter works only in a signed applet.
 |-
 | mmcifURL || URL of the mmCIF files to be loaded (delimited by comma for more than one files).
 |-
 | pdbmlURL || URL of the PDBML files to be loaded (delimited by comma for more than one files).
 |-
 | pdbURL || URL of the PDB files to be loaded (delimited by comma for more than one files).
 |-
 | polygonURL || URL of the polygon files to be loaded (delimited by comma for more than one files).
 |-
 | animURL || URL of the animation files to be loaded (delimited by comma for more than one files).
 |-
 | command_area || whether to use the command line interface or not (true or false).
 |-
 | file_control || whether to use the file control panel or not (true or false).
 |-
 | popup_menu || whether to use the popup menu or not (true or false).
 |-
 | mouse_send_to || name property of applets with which mouse events are shared (delimited by comma for more than one applets).
 |-
 | commands || initial commands that are executed when the applet starts (delimited by semicolon for more than one commands).
 |-
 | report_picking || whether to send information about mouse-picked atoms to JavaScript or not (true or false).
 |-
 | picking_receiver || JavaScript function name that receives mouse-picking data.
 |-
 | file_load_message || whether to show a message dialog while loading a file (true or false).
 |-
 | call_on_start || whether to call a JavaScript function when the applet started (true or false).
 |-
 | newt || whether to use JOGL's native windowing toolkit (true or false). At the current version, applets on Mac need this parameter set to true. On other platforms, however, this parameter must be set to fasle. Therefore the parameter should be dynamically determined in applet tags in HTML based on the platform. When set to true, two other parameters, command_area and file_control, are automatically set to false and the stereo command becomes unavailable.
|}

== JavaScript-to-Applet Communication ==
The ViewerApplet class has some public methods, which can be called from JavaScript.

 void executeCommand(String commands)

Through this method, the applet can receive some arbitrary commands (delimited by semicolon).

 void loadPDB(String fileLocation)
 void loadPDBML(String fileLocation)
 void loadFTP(String pdbId)
 void loadPolygon(String fileLocation)
 void loadPolygonCGO(String fileLocation)
 void loadAnim(String fileLocation)

Using these methods, PDB file, PDBML file, polygon file, and animation file specified by URL can be loaded respectively.
The loadFTP method receives a PDB ID and retrieves a PDBML file from the PDBj FTP site, which works only in a signed applet.

 void loadPDB(String fileLocation, int fitTo)
 void loadPDBML(String fileLocation, int fitTo)
 void loadFTP(String pdbId, int fitTo)
 void loadPolygon(String fileLocation, int fitTo)
 void loadPolygonCGO(String fileLocation, int fitTo)
 void loadAnim(String fileLocation, int fitTo)

When these methods are used, the transform matrix of the loaded file is set identical to that of the specified file.

== Applet-to-JavaScript Communication ==
In order to send the result of mouse-picking to JavaScript, the following function must be defined in JavaScript.

 function receiveMousePick(file, model, chain, res, atom, altloc, resName, atomName, x, y, z)

The function name 'receiveMousePick' is a default name. It can be changed by specifying the 'picking_receiver' parameter in APPLET or OBJECT/EMBED tags.

When the applet started, it invokes the following JavScript function 

 function jvOnStart(name)

if it is configured to do so by the applet parameter 'call_on_start'. Here the function receives the name of the applet as its argument. 

In order to enable applet-to-JavaScript communications, a new attribute 'MAYSCRIPT' is required in APPLET or OBJECT/EMBED tags (see [http://java.sun.com/j2se/1.4.2/docs/guide/plugin/developer_guide/java_js.html Java Plug-in guide]).

== Available applet code for each environment ==
Which type of applet code works or not in each environment is described [http://pdbj.org/jv/test/applet.php here].</text>
    <sha1>b7a77df7abe4d7e9661621aa0302a723f0b03eee</sha1>
  </revision>
  <revision>
    <id>559</id>
    <parentid>558</parentid>
    <timestamp>2014-04-30T01:56:03Z</timestamp>
    <contributor>
      <username>IMSsato</username>
      <id>4</id>
    </contributor>
    <comment>/* JavaScript-to-Applet Communication */</comment>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="5865" xml:space="preserve">{| style="float:right"
 |__TOC__
 |}

== Introduction ==
In order to use jV as an applet, [http://java.sun.com/products/plugin/ Java Plug-in] must be installed on client computers. The applet is called from usual APPLET tags, or OBJECT and EMBED tags in HTML (see [http://java.sun.com/products/plugin/ Java Plug-in] homepage), where class name that should be called is "org.pdbj.viewer.gui.ViewerApplet" class. The program has following features.
* whether to use the command line interface or not can be specified
* whether to use the file control panel or not can be specified
* whether to use the popup menu or not can be specified
* witihin applets in the same web page, mouse events can be shared
* applet can receive a command string from JaveScript
* applet can send information about mouse-picked atoms to JavaScript.

== Parameters ==
To initialize the applet, the following parameters can be specified in HTML.
{| class="wikitable" border="1"
 ! parameter !! value 
 |-
 | pdbid || PDB ID to be loaded from the PDBj FTP site (delimited by comma for more than one files). This parameter works only in a signed applet.
 |-
 | mmcifURL || URL of the mmCIF files to be loaded (delimited by comma for more than one files).
 |-
 | pdbmlURL || URL of the PDBML files to be loaded (delimited by comma for more than one files).
 |-
 | pdbURL || URL of the PDB files to be loaded (delimited by comma for more than one files).
 |-
 | polygonURL || URL of the polygon files to be loaded (delimited by comma for more than one files).
 |-
 | animURL || URL of the animation files to be loaded (delimited by comma for more than one files).
 |-
 | command_area || whether to use the command line interface or not (true or false).
 |-
 | file_control || whether to use the file control panel or not (true or false).
 |-
 | popup_menu || whether to use the popup menu or not (true or false).
 |-
 | mouse_send_to || name property of applets with which mouse events are shared (delimited by comma for more than one applets).
 |-
 | commands || initial commands that are executed when the applet starts (delimited by semicolon for more than one commands).
 |-
 | report_picking || whether to send information about mouse-picked atoms to JavaScript or not (true or false).
 |-
 | picking_receiver || JavaScript function name that receives mouse-picking data.
 |-
 | file_load_message || whether to show a message dialog while loading a file (true or false).
 |-
 | call_on_start || whether to call a JavaScript function when the applet started (true or false).
 |-
 | newt || whether to use JOGL's native windowing toolkit (true or false). At the current version, applets on Mac need this parameter set to true. On other platforms, however, this parameter must be set to fasle. Therefore the parameter should be dynamically determined in applet tags in HTML based on the platform. When set to true, two other parameters, command_area and file_control, are automatically set to false and the stereo command becomes unavailable.
|}

== JavaScript-to-Applet Communication ==
The ViewerApplet class has some public methods, which can be called from JavaScript.

 void executeCommand(String commands)

Through this method, the applet can receive some arbitrary commands (delimited by semicolon).

 void loadMmcif(String fileLocation)
 void loadPDB(String fileLocation)
 void loadPDBML(String fileLocation)
 void loadFTP(String pdbId)
 void loadPolygon(String fileLocation)
 void loadPolygonCGO(String fileLocation)
 void loadAnim(String fileLocation)

Using these methods, mmCIF file, PDB file, PDBML file, polygon file, and animation file specified by URL can be loaded respectively.
The loadFTP method receives a PDB ID and retrieves a PDBML file from the PDBj FTP site, which works only in a signed applet.

 void loadMmcif(String fileLocation, int fitTo)
 void loadPDB(String fileLocation, int fitTo)
 void loadPDBML(String fileLocation, int fitTo)
 void loadFTP(String pdbId, int fitTo)
 void loadPolygon(String fileLocation, int fitTo)
 void loadPolygonCGO(String fileLocation, int fitTo)
 void loadAnim(String fileLocation, int fitTo)

When these methods are used, the transform matrix of the loaded file is set identical to that of the specified file.

 void loadMmcif(String fileLocation, int fitTo, String biomolecule, String filter)
 void loadPDB(String fileLocation, int fitTo, String filter)
 void loadPDBML(String fileLocation, int fitTo, String biomolecule, String filter)
 void loadFTP(String pdbId, int fitTo, String biomolecule, String filter)
 void loadAnim(String fileLocation, int fitTo, String filter)

When these methods are used, biomolecule structure and filter can also be specified. The arguments fitTo, biomolecule and filter can be set as -1, null and null, respectively, if you do not need to use some of them.

== Applet-to-JavaScript Communication ==
In order to send the result of mouse-picking to JavaScript, the following function must be defined in JavaScript.

 function receiveMousePick(file, model, chain, res, atom, altloc, resName, atomName, x, y, z)

The function name 'receiveMousePick' is a default name. It can be changed by specifying the 'picking_receiver' parameter in APPLET or OBJECT/EMBED tags.

When the applet started, it invokes the following JavScript function 

 function jvOnStart(name)

if it is configured to do so by the applet parameter 'call_on_start'. Here the function receives the name of the applet as its argument. 

In order to enable applet-to-JavaScript communications, a new attribute 'MAYSCRIPT' is required in APPLET or OBJECT/EMBED tags (see [http://java.sun.com/j2se/1.4.2/docs/guide/plugin/developer_guide/java_js.html Java Plug-in guide]).

== Available applet code for each environment ==
Which type of applet code works or not in each environment is described [http://pdbj.org/jv/test/applet.php here].</text>
    <sha1>a8277c6e8b6c10f1613e23ebf35abc46eaf4da1f</sha1>
  </revision>
</page>
<page arvcontinue="20140430014530|554">
  <title>Main Page</title>
  <ns>0</ns>
  <id>1</id>
  <revision>
    <id>562</id>
    <parentid>553</parentid>
    <timestamp>2014-11-11T02:40:26Z</timestamp>
    <contributor>
      <username>IMSsato</username>
      <id>4</id>
    </contributor>
    <comment>/* Start up */</comment>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="6711" xml:space="preserve">&lt;big&gt;'''Welcome to jV wiki.'''&lt;/big&gt;

jV (formerly known as PDBjViewer) is a program to display molecular graphics of protein and nucleic acids. 
jV supports the following features:
* jV can read and display PDBML files, the canonical XML format for the Protein Data Bank.
* Of course, jV can read and display the traditional PDB format files, too.
* RasMol-like usability.
* jV can process more than one molecules.
* jV can display polygons specified by XML. ([http://www.pdbj.org/jv/polygonSchema XML Schema for polygons] is available.)
* Multiple polygons can be processed simultaneously, and be superimposed onto molecular images.
* Animation can be realized.
* jV runs on the Java Runtime Environment ([http://www.oracle.com/technetwork/java/javase/overview/index.html JRE]) so that it can work as a stand-alone application as well as an applet.
* The graphics of jV is based on OpenGL ([http://jogamp.org/jogl/www/ JOGL]), thereby producing fairly beautiful pictures.


The program 'jV' has been developed by [http://www.hgc.jp/~kinosita/TOP.html Kengo Kinoshita] ([http://www.is.tohoku.ac.jp/index-e.html Graduate School of Information Sciences], [http://www.tohoku.ac.jp/english/ Tohoku University]) and [http://www.protein.osaka-u.ac.jp/rcsfp/pi/ Haruki Nakamura] ([http://www.protein.osaka-u.ac.jp/index_e.php Institute for Protein Research], [http://www.osaka-u.ac.jp/eng/index.html Osaka Univeristy]), with the support from [http://biosciencedbc.jp/ JST-NBDC] and [http://www.protein.osaka-u.ac.jp/index_e.php Institute for Protein Research IPR], [http://www.osaka-u.ac.jp/eng/index.html Osaka Univeristy].
      

&lt;gallery&gt;
File:Spacefill.jpg
File:Cartoon.jpg
File:Surface.jpg
File:edmap.jpg
&lt;/gallery&gt;


== Start up ==
You can start up jV (4.4.1) with Java Web Start technology immediately from here.
* [http://ef-site.hgc.jp/eF-site/servlet/stable/jV.jnlp stable JOGL version] (recommended)
* [http://ef-site.hgc.jp/eF-site/servlet/current/jV.jnlp recent JOGL version]
The current jV requires JRE 1.6 or later.
The previous version, jV version 4.0, can run with JRE 1.4 and 1.5.
* [http://ef-site.hgc.jp/jV/stable/jV_4_0.jnlp jV 4.0]

== Basic Usage ==
You can execute basic operations such as rotation and translation with mouse action. Major actions are described in the following table:
{| style="margin:auto;border:1px solid gray"
! rowspan="2" style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap;font-weight:bold" |Action
! colspan="2" style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap;font-weight:bold" |Mouse Operation
|-
! style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap;font-weight:bold" |Windows, Linux
! style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap;font-weight:bold" |Mac OS X
|-
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |rotate around X (horizontal) axis&lt;br /&gt;rotate around Y (vertical) axis
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |left drag
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |drag
|-
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |translate along X axis (holizontally)&lt;br /&gt;translate along Y axis (vertically)
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |right drag
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |Command + drag
|-
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |translate along Z axis (zoom in/out)
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |Shift + left drag
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |Shift + drag
|}

Operations such as changing display models and colors and saving the image, can be executed with a menu. The location of the menu is at the top of the application window in Windows and at the top of screen in Mac as the stand-alone application. As an applet usage, a popup menu appears by clicking the right mouse button on the display screen, or clicking with a "Command" button in case of Mac.

{| style="margin:auto;border:0"
|-
| [[File:Jv_menu_win.png|The location of menu in jV stand-alone version in Windows.|250px]]
| [[File:Jv_menu_mac.png|The location of menu in jV stand-alone version in Mac.|250px]]
| [[File:popupmenu_en.png|The location of menu in applet version.|250px]]
|-
| style="text-align:center" |Stand-alone (Windows)
| style="text-align:center" |Stand-alone (Mac)
| style="text-align:center" |Applet
|}

Basic menu operations are following (see also [[GUI]] for details):

{| style="margin:auto;border:1px solid gray;border-collapse:collapse"
! style="padding:0 0.5em;border:1px solid gray" | Operations
! style="padding:0 0.5em;border:1px solid gray" | Menu location
|-
| style="padding:0 0.5em;border:1px solid gray" | Save a static image
| style="padding:0 0.5em;border:1px solid gray" | [File]-[Save]-[PNG/JPEG]
|-
| style="padding:0 0.5em;border:1px solid gray" | Change the expression format
| style="padding:0 0.5em;border:1px solid gray" | [File]-[Display]-[Wireframe/Backbone/Sticks/Spacefill/Ball&amp;amp;Stick/Ribbons/Cartoon]
|-
| style="padding:0 0.5em;border:1px solid gray" | Change the color
| style="padding:0 0.5em;border:1px solid gray" | [File]-[Colors]-[Monochrome/CPK/Shapely/Group/Chain/Temperature/Structure/Charge/Amino]
|}

To execute more complicated operation such as diplaying some piece of the molecule or changing some part of molecule in another style, use command line operation.

See also [[#Other resources]] for details:


== Download ==
You can also download the program and start it up locally.
In this case, installing JOGL is required in advance (see [[Installation_of_jV3 | Installation]] page).
The following links take you to the download pages. (latest version is 4.4@2014/4/16)
* [http://ef-site.hgc.jp/eF-site/servlet/DownloadViewerBinary binary (4.4)] 
* [http://ef-site.hgc.jp/eF-site/servlet/Registration source code (4.4)] (registration will be required)

== Other resources ==
* [http://ef-site.hgc.jp/eF-site/jV/jV_manual.html Manual] (html in English)
* [[How_to_use]] (in this site in English)
* [http://www.pdbj.org/jv/manual/index_ja.html Manual] (html in Japanese)
* [http://www.pdbj.org/jv/manual/jV_manual.pdf Manual] (pdf in English, for ver. 3.3)
* [http://ef-site.hgc.jp/eF-site/jV/jV3_User'sGuide.pdf User's guide] (for ver. 3.8.3 in English)</text>
    <sha1>0c1d323ae690c459fd879640c8f7f834b62ac8df</sha1>
  </revision>
  <revision>
    <id>563</id>
    <parentid>562</parentid>
    <timestamp>2014-11-11T02:40:56Z</timestamp>
    <contributor>
      <username>IMSsato</username>
      <id>4</id>
    </contributor>
    <comment>/* Download */</comment>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="6718" xml:space="preserve">&lt;big&gt;'''Welcome to jV wiki.'''&lt;/big&gt;

jV (formerly known as PDBjViewer) is a program to display molecular graphics of protein and nucleic acids. 
jV supports the following features:
* jV can read and display PDBML files, the canonical XML format for the Protein Data Bank.
* Of course, jV can read and display the traditional PDB format files, too.
* RasMol-like usability.
* jV can process more than one molecules.
* jV can display polygons specified by XML. ([http://www.pdbj.org/jv/polygonSchema XML Schema for polygons] is available.)
* Multiple polygons can be processed simultaneously, and be superimposed onto molecular images.
* Animation can be realized.
* jV runs on the Java Runtime Environment ([http://www.oracle.com/technetwork/java/javase/overview/index.html JRE]) so that it can work as a stand-alone application as well as an applet.
* The graphics of jV is based on OpenGL ([http://jogamp.org/jogl/www/ JOGL]), thereby producing fairly beautiful pictures.


The program 'jV' has been developed by [http://www.hgc.jp/~kinosita/TOP.html Kengo Kinoshita] ([http://www.is.tohoku.ac.jp/index-e.html Graduate School of Information Sciences], [http://www.tohoku.ac.jp/english/ Tohoku University]) and [http://www.protein.osaka-u.ac.jp/rcsfp/pi/ Haruki Nakamura] ([http://www.protein.osaka-u.ac.jp/index_e.php Institute for Protein Research], [http://www.osaka-u.ac.jp/eng/index.html Osaka Univeristy]), with the support from [http://biosciencedbc.jp/ JST-NBDC] and [http://www.protein.osaka-u.ac.jp/index_e.php Institute for Protein Research IPR], [http://www.osaka-u.ac.jp/eng/index.html Osaka Univeristy].
      

&lt;gallery&gt;
File:Spacefill.jpg
File:Cartoon.jpg
File:Surface.jpg
File:edmap.jpg
&lt;/gallery&gt;


== Start up ==
You can start up jV (4.4.1) with Java Web Start technology immediately from here.
* [http://ef-site.hgc.jp/eF-site/servlet/stable/jV.jnlp stable JOGL version] (recommended)
* [http://ef-site.hgc.jp/eF-site/servlet/current/jV.jnlp recent JOGL version]
The current jV requires JRE 1.6 or later.
The previous version, jV version 4.0, can run with JRE 1.4 and 1.5.
* [http://ef-site.hgc.jp/jV/stable/jV_4_0.jnlp jV 4.0]

== Basic Usage ==
You can execute basic operations such as rotation and translation with mouse action. Major actions are described in the following table:
{| style="margin:auto;border:1px solid gray"
! rowspan="2" style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap;font-weight:bold" |Action
! colspan="2" style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap;font-weight:bold" |Mouse Operation
|-
! style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap;font-weight:bold" |Windows, Linux
! style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap;font-weight:bold" |Mac OS X
|-
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |rotate around X (horizontal) axis&lt;br /&gt;rotate around Y (vertical) axis
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |left drag
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |drag
|-
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |translate along X axis (holizontally)&lt;br /&gt;translate along Y axis (vertically)
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |right drag
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |Command + drag
|-
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |translate along Z axis (zoom in/out)
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |Shift + left drag
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |Shift + drag
|}

Operations such as changing display models and colors and saving the image, can be executed with a menu. The location of the menu is at the top of the application window in Windows and at the top of screen in Mac as the stand-alone application. As an applet usage, a popup menu appears by clicking the right mouse button on the display screen, or clicking with a "Command" button in case of Mac.

{| style="margin:auto;border:0"
|-
| [[File:Jv_menu_win.png|The location of menu in jV stand-alone version in Windows.|250px]]
| [[File:Jv_menu_mac.png|The location of menu in jV stand-alone version in Mac.|250px]]
| [[File:popupmenu_en.png|The location of menu in applet version.|250px]]
|-
| style="text-align:center" |Stand-alone (Windows)
| style="text-align:center" |Stand-alone (Mac)
| style="text-align:center" |Applet
|}

Basic menu operations are following (see also [[GUI]] for details):

{| style="margin:auto;border:1px solid gray;border-collapse:collapse"
! style="padding:0 0.5em;border:1px solid gray" | Operations
! style="padding:0 0.5em;border:1px solid gray" | Menu location
|-
| style="padding:0 0.5em;border:1px solid gray" | Save a static image
| style="padding:0 0.5em;border:1px solid gray" | [File]-[Save]-[PNG/JPEG]
|-
| style="padding:0 0.5em;border:1px solid gray" | Change the expression format
| style="padding:0 0.5em;border:1px solid gray" | [File]-[Display]-[Wireframe/Backbone/Sticks/Spacefill/Ball&amp;amp;Stick/Ribbons/Cartoon]
|-
| style="padding:0 0.5em;border:1px solid gray" | Change the color
| style="padding:0 0.5em;border:1px solid gray" | [File]-[Colors]-[Monochrome/CPK/Shapely/Group/Chain/Temperature/Structure/Charge/Amino]
|}

To execute more complicated operation such as diplaying some piece of the molecule or changing some part of molecule in another style, use command line operation.

See also [[#Other resources]] for details:


== Download ==
You can also download the program and start it up locally.
In this case, installing JOGL is required in advance (see [[Installation_of_jV3 | Installation]] page).
The following links take you to the download pages. (latest version is 4.4.1@2014/11/11)
* [http://ef-site.hgc.jp/eF-site/servlet/DownloadViewerBinary binary (4.4.1)] 
* [http://ef-site.hgc.jp/eF-site/servlet/Registration source code (4.4.1)] (registration will be required)

== Other resources ==
* [http://ef-site.hgc.jp/eF-site/jV/jV_manual.html Manual] (html in English)
* [[How_to_use]] (in this site in English)
* [http://www.pdbj.org/jv/manual/index_ja.html Manual] (html in Japanese)
* [http://www.pdbj.org/jv/manual/jV_manual.pdf Manual] (pdf in English, for ver. 3.3)
* [http://ef-site.hgc.jp/eF-site/jV/jV3_User'sGuide.pdf User's guide] (for ver. 3.8.3 in English)</text>
    <sha1>16ea143dc0e54a6de3a91368d554125c2ca7d9cb</sha1>
  </revision>
  <revision>
    <id>569</id>
    <parentid>563</parentid>
    <timestamp>2014-12-03T03:04:02Z</timestamp>
    <contributor>
      <username>IMSsato</username>
      <id>4</id>
    </contributor>
    <comment>/* Start up */</comment>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="6718" xml:space="preserve">&lt;big&gt;'''Welcome to jV wiki.'''&lt;/big&gt;

jV (formerly known as PDBjViewer) is a program to display molecular graphics of protein and nucleic acids. 
jV supports the following features:
* jV can read and display PDBML files, the canonical XML format for the Protein Data Bank.
* Of course, jV can read and display the traditional PDB format files, too.
* RasMol-like usability.
* jV can process more than one molecules.
* jV can display polygons specified by XML. ([http://www.pdbj.org/jv/polygonSchema XML Schema for polygons] is available.)
* Multiple polygons can be processed simultaneously, and be superimposed onto molecular images.
* Animation can be realized.
* jV runs on the Java Runtime Environment ([http://www.oracle.com/technetwork/java/javase/overview/index.html JRE]) so that it can work as a stand-alone application as well as an applet.
* The graphics of jV is based on OpenGL ([http://jogamp.org/jogl/www/ JOGL]), thereby producing fairly beautiful pictures.


The program 'jV' has been developed by [http://www.hgc.jp/~kinosita/TOP.html Kengo Kinoshita] ([http://www.is.tohoku.ac.jp/index-e.html Graduate School of Information Sciences], [http://www.tohoku.ac.jp/english/ Tohoku University]) and [http://www.protein.osaka-u.ac.jp/rcsfp/pi/ Haruki Nakamura] ([http://www.protein.osaka-u.ac.jp/index_e.php Institute for Protein Research], [http://www.osaka-u.ac.jp/eng/index.html Osaka Univeristy]), with the support from [http://biosciencedbc.jp/ JST-NBDC] and [http://www.protein.osaka-u.ac.jp/index_e.php Institute for Protein Research IPR], [http://www.osaka-u.ac.jp/eng/index.html Osaka Univeristy].
      

&lt;gallery&gt;
File:Spacefill.jpg
File:Cartoon.jpg
File:Surface.jpg
File:edmap.jpg
&lt;/gallery&gt;


== Start up ==
You can start up jV (4.4.2) with Java Web Start technology immediately from here.
* [http://ef-site.hgc.jp/eF-site/servlet/stable/jV.jnlp stable JOGL version] (recommended)
* [http://ef-site.hgc.jp/eF-site/servlet/current/jV.jnlp recent JOGL version]
The current jV requires JRE 1.6 or later.
The previous version, jV version 4.0, can run with JRE 1.4 and 1.5.
* [http://ef-site.hgc.jp/jV/stable/jV_4_0.jnlp jV 4.0]

== Basic Usage ==
You can execute basic operations such as rotation and translation with mouse action. Major actions are described in the following table:
{| style="margin:auto;border:1px solid gray"
! rowspan="2" style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap;font-weight:bold" |Action
! colspan="2" style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap;font-weight:bold" |Mouse Operation
|-
! style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap;font-weight:bold" |Windows, Linux
! style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap;font-weight:bold" |Mac OS X
|-
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |rotate around X (horizontal) axis&lt;br /&gt;rotate around Y (vertical) axis
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |left drag
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |drag
|-
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |translate along X axis (holizontally)&lt;br /&gt;translate along Y axis (vertically)
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |right drag
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |Command + drag
|-
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |translate along Z axis (zoom in/out)
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |Shift + left drag
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |Shift + drag
|}

Operations such as changing display models and colors and saving the image, can be executed with a menu. The location of the menu is at the top of the application window in Windows and at the top of screen in Mac as the stand-alone application. As an applet usage, a popup menu appears by clicking the right mouse button on the display screen, or clicking with a "Command" button in case of Mac.

{| style="margin:auto;border:0"
|-
| [[File:Jv_menu_win.png|The location of menu in jV stand-alone version in Windows.|250px]]
| [[File:Jv_menu_mac.png|The location of menu in jV stand-alone version in Mac.|250px]]
| [[File:popupmenu_en.png|The location of menu in applet version.|250px]]
|-
| style="text-align:center" |Stand-alone (Windows)
| style="text-align:center" |Stand-alone (Mac)
| style="text-align:center" |Applet
|}

Basic menu operations are following (see also [[GUI]] for details):

{| style="margin:auto;border:1px solid gray;border-collapse:collapse"
! style="padding:0 0.5em;border:1px solid gray" | Operations
! style="padding:0 0.5em;border:1px solid gray" | Menu location
|-
| style="padding:0 0.5em;border:1px solid gray" | Save a static image
| style="padding:0 0.5em;border:1px solid gray" | [File]-[Save]-[PNG/JPEG]
|-
| style="padding:0 0.5em;border:1px solid gray" | Change the expression format
| style="padding:0 0.5em;border:1px solid gray" | [File]-[Display]-[Wireframe/Backbone/Sticks/Spacefill/Ball&amp;amp;Stick/Ribbons/Cartoon]
|-
| style="padding:0 0.5em;border:1px solid gray" | Change the color
| style="padding:0 0.5em;border:1px solid gray" | [File]-[Colors]-[Monochrome/CPK/Shapely/Group/Chain/Temperature/Structure/Charge/Amino]
|}

To execute more complicated operation such as diplaying some piece of the molecule or changing some part of molecule in another style, use command line operation.

See also [[#Other resources]] for details:


== Download ==
You can also download the program and start it up locally.
In this case, installing JOGL is required in advance (see [[Installation_of_jV3 | Installation]] page).
The following links take you to the download pages. (latest version is 4.4.1@2014/11/11)
* [http://ef-site.hgc.jp/eF-site/servlet/DownloadViewerBinary binary (4.4.1)] 
* [http://ef-site.hgc.jp/eF-site/servlet/Registration source code (4.4.1)] (registration will be required)

== Other resources ==
* [http://ef-site.hgc.jp/eF-site/jV/jV_manual.html Manual] (html in English)
* [[How_to_use]] (in this site in English)
* [http://www.pdbj.org/jv/manual/index_ja.html Manual] (html in Japanese)
* [http://www.pdbj.org/jv/manual/jV_manual.pdf Manual] (pdf in English, for ver. 3.3)
* [http://ef-site.hgc.jp/eF-site/jV/jV3_User'sGuide.pdf User's guide] (for ver. 3.8.3 in English)</text>
    <sha1>73ee2eeb9bf13e399ea3ef14509e092f03f98b8e</sha1>
  </revision>
  <revision>
    <id>570</id>
    <parentid>569</parentid>
    <timestamp>2014-12-03T03:04:19Z</timestamp>
    <contributor>
      <username>IMSsato</username>
      <id>4</id>
    </contributor>
    <comment>/* Download */</comment>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="6717" xml:space="preserve">&lt;big&gt;'''Welcome to jV wiki.'''&lt;/big&gt;

jV (formerly known as PDBjViewer) is a program to display molecular graphics of protein and nucleic acids. 
jV supports the following features:
* jV can read and display PDBML files, the canonical XML format for the Protein Data Bank.
* Of course, jV can read and display the traditional PDB format files, too.
* RasMol-like usability.
* jV can process more than one molecules.
* jV can display polygons specified by XML. ([http://www.pdbj.org/jv/polygonSchema XML Schema for polygons] is available.)
* Multiple polygons can be processed simultaneously, and be superimposed onto molecular images.
* Animation can be realized.
* jV runs on the Java Runtime Environment ([http://www.oracle.com/technetwork/java/javase/overview/index.html JRE]) so that it can work as a stand-alone application as well as an applet.
* The graphics of jV is based on OpenGL ([http://jogamp.org/jogl/www/ JOGL]), thereby producing fairly beautiful pictures.


The program 'jV' has been developed by [http://www.hgc.jp/~kinosita/TOP.html Kengo Kinoshita] ([http://www.is.tohoku.ac.jp/index-e.html Graduate School of Information Sciences], [http://www.tohoku.ac.jp/english/ Tohoku University]) and [http://www.protein.osaka-u.ac.jp/rcsfp/pi/ Haruki Nakamura] ([http://www.protein.osaka-u.ac.jp/index_e.php Institute for Protein Research], [http://www.osaka-u.ac.jp/eng/index.html Osaka Univeristy]), with the support from [http://biosciencedbc.jp/ JST-NBDC] and [http://www.protein.osaka-u.ac.jp/index_e.php Institute for Protein Research IPR], [http://www.osaka-u.ac.jp/eng/index.html Osaka Univeristy].
      

&lt;gallery&gt;
File:Spacefill.jpg
File:Cartoon.jpg
File:Surface.jpg
File:edmap.jpg
&lt;/gallery&gt;


== Start up ==
You can start up jV (4.4.2) with Java Web Start technology immediately from here.
* [http://ef-site.hgc.jp/eF-site/servlet/stable/jV.jnlp stable JOGL version] (recommended)
* [http://ef-site.hgc.jp/eF-site/servlet/current/jV.jnlp recent JOGL version]
The current jV requires JRE 1.6 or later.
The previous version, jV version 4.0, can run with JRE 1.4 and 1.5.
* [http://ef-site.hgc.jp/jV/stable/jV_4_0.jnlp jV 4.0]

== Basic Usage ==
You can execute basic operations such as rotation and translation with mouse action. Major actions are described in the following table:
{| style="margin:auto;border:1px solid gray"
! rowspan="2" style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap;font-weight:bold" |Action
! colspan="2" style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap;font-weight:bold" |Mouse Operation
|-
! style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap;font-weight:bold" |Windows, Linux
! style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap;font-weight:bold" |Mac OS X
|-
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |rotate around X (horizontal) axis&lt;br /&gt;rotate around Y (vertical) axis
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |left drag
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |drag
|-
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |translate along X axis (holizontally)&lt;br /&gt;translate along Y axis (vertically)
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |right drag
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |Command + drag
|-
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |translate along Z axis (zoom in/out)
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |Shift + left drag
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |Shift + drag
|}

Operations such as changing display models and colors and saving the image, can be executed with a menu. The location of the menu is at the top of the application window in Windows and at the top of screen in Mac as the stand-alone application. As an applet usage, a popup menu appears by clicking the right mouse button on the display screen, or clicking with a "Command" button in case of Mac.

{| style="margin:auto;border:0"
|-
| [[File:Jv_menu_win.png|The location of menu in jV stand-alone version in Windows.|250px]]
| [[File:Jv_menu_mac.png|The location of menu in jV stand-alone version in Mac.|250px]]
| [[File:popupmenu_en.png|The location of menu in applet version.|250px]]
|-
| style="text-align:center" |Stand-alone (Windows)
| style="text-align:center" |Stand-alone (Mac)
| style="text-align:center" |Applet
|}

Basic menu operations are following (see also [[GUI]] for details):

{| style="margin:auto;border:1px solid gray;border-collapse:collapse"
! style="padding:0 0.5em;border:1px solid gray" | Operations
! style="padding:0 0.5em;border:1px solid gray" | Menu location
|-
| style="padding:0 0.5em;border:1px solid gray" | Save a static image
| style="padding:0 0.5em;border:1px solid gray" | [File]-[Save]-[PNG/JPEG]
|-
| style="padding:0 0.5em;border:1px solid gray" | Change the expression format
| style="padding:0 0.5em;border:1px solid gray" | [File]-[Display]-[Wireframe/Backbone/Sticks/Spacefill/Ball&amp;amp;Stick/Ribbons/Cartoon]
|-
| style="padding:0 0.5em;border:1px solid gray" | Change the color
| style="padding:0 0.5em;border:1px solid gray" | [File]-[Colors]-[Monochrome/CPK/Shapely/Group/Chain/Temperature/Structure/Charge/Amino]
|}

To execute more complicated operation such as diplaying some piece of the molecule or changing some part of molecule in another style, use command line operation.

See also [[#Other resources]] for details:


== Download ==
You can also download the program and start it up locally.
In this case, installing JOGL is required in advance (see [[Installation_of_jV3 | Installation]] page).
The following links take you to the download pages. (latest version is 4.4.2@2014/12/3)
* [http://ef-site.hgc.jp/eF-site/servlet/DownloadViewerBinary binary (4.4.2)] 
* [http://ef-site.hgc.jp/eF-site/servlet/Registration source code (4.4.2)] (registration will be required)

== Other resources ==
* [http://ef-site.hgc.jp/eF-site/jV/jV_manual.html Manual] (html in English)
* [[How_to_use]] (in this site in English)
* [http://www.pdbj.org/jv/manual/index_ja.html Manual] (html in Japanese)
* [http://www.pdbj.org/jv/manual/jV_manual.pdf Manual] (pdf in English, for ver. 3.3)
* [http://ef-site.hgc.jp/eF-site/jV/jV3_User'sGuide.pdf User's guide] (for ver. 3.8.3 in English)</text>
    <sha1>32fa3c2279a946c7342c67240b891c0daf3c4f33</sha1>
  </revision>
  <revision>
    <id>595</id>
    <parentid>570</parentid>
    <timestamp>2015-02-24T06:27:03Z</timestamp>
    <contributor>
      <username>IMSsato</username>
      <id>4</id>
    </contributor>
    <comment>/* Start up */</comment>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="6717" xml:space="preserve">&lt;big&gt;'''Welcome to jV wiki.'''&lt;/big&gt;

jV (formerly known as PDBjViewer) is a program to display molecular graphics of protein and nucleic acids. 
jV supports the following features:
* jV can read and display PDBML files, the canonical XML format for the Protein Data Bank.
* Of course, jV can read and display the traditional PDB format files, too.
* RasMol-like usability.
* jV can process more than one molecules.
* jV can display polygons specified by XML. ([http://www.pdbj.org/jv/polygonSchema XML Schema for polygons] is available.)
* Multiple polygons can be processed simultaneously, and be superimposed onto molecular images.
* Animation can be realized.
* jV runs on the Java Runtime Environment ([http://www.oracle.com/technetwork/java/javase/overview/index.html JRE]) so that it can work as a stand-alone application as well as an applet.
* The graphics of jV is based on OpenGL ([http://jogamp.org/jogl/www/ JOGL]), thereby producing fairly beautiful pictures.


The program 'jV' has been developed by [http://www.hgc.jp/~kinosita/TOP.html Kengo Kinoshita] ([http://www.is.tohoku.ac.jp/index-e.html Graduate School of Information Sciences], [http://www.tohoku.ac.jp/english/ Tohoku University]) and [http://www.protein.osaka-u.ac.jp/rcsfp/pi/ Haruki Nakamura] ([http://www.protein.osaka-u.ac.jp/index_e.php Institute for Protein Research], [http://www.osaka-u.ac.jp/eng/index.html Osaka Univeristy]), with the support from [http://biosciencedbc.jp/ JST-NBDC] and [http://www.protein.osaka-u.ac.jp/index_e.php Institute for Protein Research IPR], [http://www.osaka-u.ac.jp/eng/index.html Osaka Univeristy].
      

&lt;gallery&gt;
File:Spacefill.jpg
File:Cartoon.jpg
File:Surface.jpg
File:edmap.jpg
&lt;/gallery&gt;


== Start up ==
You can start up jV (4.4.3) with Java Web Start technology immediately from here.
* [http://ef-site.hgc.jp/eF-site/servlet/stable/jV.jnlp stable JOGL version] (recommended)
* [http://ef-site.hgc.jp/eF-site/servlet/current/jV.jnlp recent JOGL version]
The current jV requires JRE 1.6 or later.
The previous version, jV version 4.0, can run with JRE 1.4 and 1.5.
* [http://ef-site.hgc.jp/jV/stable/jV_4_0.jnlp jV 4.0]

== Basic Usage ==
You can execute basic operations such as rotation and translation with mouse action. Major actions are described in the following table:
{| style="margin:auto;border:1px solid gray"
! rowspan="2" style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap;font-weight:bold" |Action
! colspan="2" style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap;font-weight:bold" |Mouse Operation
|-
! style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap;font-weight:bold" |Windows, Linux
! style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap;font-weight:bold" |Mac OS X
|-
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |rotate around X (horizontal) axis&lt;br /&gt;rotate around Y (vertical) axis
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |left drag
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |drag
|-
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |translate along X axis (holizontally)&lt;br /&gt;translate along Y axis (vertically)
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |right drag
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |Command + drag
|-
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |translate along Z axis (zoom in/out)
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |Shift + left drag
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |Shift + drag
|}

Operations such as changing display models and colors and saving the image, can be executed with a menu. The location of the menu is at the top of the application window in Windows and at the top of screen in Mac as the stand-alone application. As an applet usage, a popup menu appears by clicking the right mouse button on the display screen, or clicking with a "Command" button in case of Mac.

{| style="margin:auto;border:0"
|-
| [[File:Jv_menu_win.png|The location of menu in jV stand-alone version in Windows.|250px]]
| [[File:Jv_menu_mac.png|The location of menu in jV stand-alone version in Mac.|250px]]
| [[File:popupmenu_en.png|The location of menu in applet version.|250px]]
|-
| style="text-align:center" |Stand-alone (Windows)
| style="text-align:center" |Stand-alone (Mac)
| style="text-align:center" |Applet
|}

Basic menu operations are following (see also [[GUI]] for details):

{| style="margin:auto;border:1px solid gray;border-collapse:collapse"
! style="padding:0 0.5em;border:1px solid gray" | Operations
! style="padding:0 0.5em;border:1px solid gray" | Menu location
|-
| style="padding:0 0.5em;border:1px solid gray" | Save a static image
| style="padding:0 0.5em;border:1px solid gray" | [File]-[Save]-[PNG/JPEG]
|-
| style="padding:0 0.5em;border:1px solid gray" | Change the expression format
| style="padding:0 0.5em;border:1px solid gray" | [File]-[Display]-[Wireframe/Backbone/Sticks/Spacefill/Ball&amp;amp;Stick/Ribbons/Cartoon]
|-
| style="padding:0 0.5em;border:1px solid gray" | Change the color
| style="padding:0 0.5em;border:1px solid gray" | [File]-[Colors]-[Monochrome/CPK/Shapely/Group/Chain/Temperature/Structure/Charge/Amino]
|}

To execute more complicated operation such as diplaying some piece of the molecule or changing some part of molecule in another style, use command line operation.

See also [[#Other resources]] for details:


== Download ==
You can also download the program and start it up locally.
In this case, installing JOGL is required in advance (see [[Installation_of_jV3 | Installation]] page).
The following links take you to the download pages. (latest version is 4.4.2@2014/12/3)
* [http://ef-site.hgc.jp/eF-site/servlet/DownloadViewerBinary binary (4.4.2)] 
* [http://ef-site.hgc.jp/eF-site/servlet/Registration source code (4.4.2)] (registration will be required)

== Other resources ==
* [http://ef-site.hgc.jp/eF-site/jV/jV_manual.html Manual] (html in English)
* [[How_to_use]] (in this site in English)
* [http://www.pdbj.org/jv/manual/index_ja.html Manual] (html in Japanese)
* [http://www.pdbj.org/jv/manual/jV_manual.pdf Manual] (pdf in English, for ver. 3.3)
* [http://ef-site.hgc.jp/eF-site/jV/jV3_User'sGuide.pdf User's guide] (for ver. 3.8.3 in English)</text>
    <sha1>4cdef29bf2e489607b129f1440e8cd986facb749</sha1>
  </revision>
  <revision>
    <id>596</id>
    <parentid>595</parentid>
    <timestamp>2015-02-24T06:27:54Z</timestamp>
    <contributor>
      <username>IMSsato</username>
      <id>4</id>
    </contributor>
    <comment>/* Download */</comment>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="6717" xml:space="preserve">&lt;big&gt;'''Welcome to jV wiki.'''&lt;/big&gt;

jV (formerly known as PDBjViewer) is a program to display molecular graphics of protein and nucleic acids. 
jV supports the following features:
* jV can read and display PDBML files, the canonical XML format for the Protein Data Bank.
* Of course, jV can read and display the traditional PDB format files, too.
* RasMol-like usability.
* jV can process more than one molecules.
* jV can display polygons specified by XML. ([http://www.pdbj.org/jv/polygonSchema XML Schema for polygons] is available.)
* Multiple polygons can be processed simultaneously, and be superimposed onto molecular images.
* Animation can be realized.
* jV runs on the Java Runtime Environment ([http://www.oracle.com/technetwork/java/javase/overview/index.html JRE]) so that it can work as a stand-alone application as well as an applet.
* The graphics of jV is based on OpenGL ([http://jogamp.org/jogl/www/ JOGL]), thereby producing fairly beautiful pictures.


The program 'jV' has been developed by [http://www.hgc.jp/~kinosita/TOP.html Kengo Kinoshita] ([http://www.is.tohoku.ac.jp/index-e.html Graduate School of Information Sciences], [http://www.tohoku.ac.jp/english/ Tohoku University]) and [http://www.protein.osaka-u.ac.jp/rcsfp/pi/ Haruki Nakamura] ([http://www.protein.osaka-u.ac.jp/index_e.php Institute for Protein Research], [http://www.osaka-u.ac.jp/eng/index.html Osaka Univeristy]), with the support from [http://biosciencedbc.jp/ JST-NBDC] and [http://www.protein.osaka-u.ac.jp/index_e.php Institute for Protein Research IPR], [http://www.osaka-u.ac.jp/eng/index.html Osaka Univeristy].
      

&lt;gallery&gt;
File:Spacefill.jpg
File:Cartoon.jpg
File:Surface.jpg
File:edmap.jpg
&lt;/gallery&gt;


== Start up ==
You can start up jV (4.4.3) with Java Web Start technology immediately from here.
* [http://ef-site.hgc.jp/eF-site/servlet/stable/jV.jnlp stable JOGL version] (recommended)
* [http://ef-site.hgc.jp/eF-site/servlet/current/jV.jnlp recent JOGL version]
The current jV requires JRE 1.6 or later.
The previous version, jV version 4.0, can run with JRE 1.4 and 1.5.
* [http://ef-site.hgc.jp/jV/stable/jV_4_0.jnlp jV 4.0]

== Basic Usage ==
You can execute basic operations such as rotation and translation with mouse action. Major actions are described in the following table:
{| style="margin:auto;border:1px solid gray"
! rowspan="2" style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap;font-weight:bold" |Action
! colspan="2" style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap;font-weight:bold" |Mouse Operation
|-
! style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap;font-weight:bold" |Windows, Linux
! style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap;font-weight:bold" |Mac OS X
|-
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |rotate around X (horizontal) axis&lt;br /&gt;rotate around Y (vertical) axis
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |left drag
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |drag
|-
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |translate along X axis (holizontally)&lt;br /&gt;translate along Y axis (vertically)
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |right drag
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |Command + drag
|-
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |translate along Z axis (zoom in/out)
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |Shift + left drag
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |Shift + drag
|}

Operations such as changing display models and colors and saving the image, can be executed with a menu. The location of the menu is at the top of the application window in Windows and at the top of screen in Mac as the stand-alone application. As an applet usage, a popup menu appears by clicking the right mouse button on the display screen, or clicking with a "Command" button in case of Mac.

{| style="margin:auto;border:0"
|-
| [[File:Jv_menu_win.png|The location of menu in jV stand-alone version in Windows.|250px]]
| [[File:Jv_menu_mac.png|The location of menu in jV stand-alone version in Mac.|250px]]
| [[File:popupmenu_en.png|The location of menu in applet version.|250px]]
|-
| style="text-align:center" |Stand-alone (Windows)
| style="text-align:center" |Stand-alone (Mac)
| style="text-align:center" |Applet
|}

Basic menu operations are following (see also [[GUI]] for details):

{| style="margin:auto;border:1px solid gray;border-collapse:collapse"
! style="padding:0 0.5em;border:1px solid gray" | Operations
! style="padding:0 0.5em;border:1px solid gray" | Menu location
|-
| style="padding:0 0.5em;border:1px solid gray" | Save a static image
| style="padding:0 0.5em;border:1px solid gray" | [File]-[Save]-[PNG/JPEG]
|-
| style="padding:0 0.5em;border:1px solid gray" | Change the expression format
| style="padding:0 0.5em;border:1px solid gray" | [File]-[Display]-[Wireframe/Backbone/Sticks/Spacefill/Ball&amp;amp;Stick/Ribbons/Cartoon]
|-
| style="padding:0 0.5em;border:1px solid gray" | Change the color
| style="padding:0 0.5em;border:1px solid gray" | [File]-[Colors]-[Monochrome/CPK/Shapely/Group/Chain/Temperature/Structure/Charge/Amino]
|}

To execute more complicated operation such as diplaying some piece of the molecule or changing some part of molecule in another style, use command line operation.

See also [[#Other resources]] for details:


== Download ==
You can also download the program and start it up locally.
In this case, installing JOGL is required in advance (see [[Installation_of_jV3 | Installation]] page).
The following links take you to the download pages. (latest version is 4.4.3@2015/2/24)
* [http://ef-site.hgc.jp/eF-site/servlet/DownloadViewerBinary binary (4.4.3)] 
* [http://ef-site.hgc.jp/eF-site/servlet/Registration source code (4.4.3)] (registration will be required)

== Other resources ==
* [http://ef-site.hgc.jp/eF-site/jV/jV_manual.html Manual] (html in English)
* [[How_to_use]] (in this site in English)
* [http://www.pdbj.org/jv/manual/index_ja.html Manual] (html in Japanese)
* [http://www.pdbj.org/jv/manual/jV_manual.pdf Manual] (pdf in English, for ver. 3.3)
* [http://ef-site.hgc.jp/eF-site/jV/jV3_User'sGuide.pdf User's guide] (for ver. 3.8.3 in English)</text>
    <sha1>89e2ac31c30b15ad491588d3a1e382de8e3bf60b</sha1>
  </revision>
  <revision>
    <id>597</id>
    <parentid>596</parentid>
    <timestamp>2015-02-24T06:28:51Z</timestamp>
    <contributor>
      <username>IMSsato</username>
      <id>4</id>
    </contributor>
    <comment>/* Download */</comment>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="6613" xml:space="preserve">&lt;big&gt;'''Welcome to jV wiki.'''&lt;/big&gt;

jV (formerly known as PDBjViewer) is a program to display molecular graphics of protein and nucleic acids. 
jV supports the following features:
* jV can read and display PDBML files, the canonical XML format for the Protein Data Bank.
* Of course, jV can read and display the traditional PDB format files, too.
* RasMol-like usability.
* jV can process more than one molecules.
* jV can display polygons specified by XML. ([http://www.pdbj.org/jv/polygonSchema XML Schema for polygons] is available.)
* Multiple polygons can be processed simultaneously, and be superimposed onto molecular images.
* Animation can be realized.
* jV runs on the Java Runtime Environment ([http://www.oracle.com/technetwork/java/javase/overview/index.html JRE]) so that it can work as a stand-alone application as well as an applet.
* The graphics of jV is based on OpenGL ([http://jogamp.org/jogl/www/ JOGL]), thereby producing fairly beautiful pictures.


The program 'jV' has been developed by [http://www.hgc.jp/~kinosita/TOP.html Kengo Kinoshita] ([http://www.is.tohoku.ac.jp/index-e.html Graduate School of Information Sciences], [http://www.tohoku.ac.jp/english/ Tohoku University]) and [http://www.protein.osaka-u.ac.jp/rcsfp/pi/ Haruki Nakamura] ([http://www.protein.osaka-u.ac.jp/index_e.php Institute for Protein Research], [http://www.osaka-u.ac.jp/eng/index.html Osaka Univeristy]), with the support from [http://biosciencedbc.jp/ JST-NBDC] and [http://www.protein.osaka-u.ac.jp/index_e.php Institute for Protein Research IPR], [http://www.osaka-u.ac.jp/eng/index.html Osaka Univeristy].
      

&lt;gallery&gt;
File:Spacefill.jpg
File:Cartoon.jpg
File:Surface.jpg
File:edmap.jpg
&lt;/gallery&gt;


== Start up ==
You can start up jV (4.4.3) with Java Web Start technology immediately from here.
* [http://ef-site.hgc.jp/eF-site/servlet/stable/jV.jnlp stable JOGL version] (recommended)
* [http://ef-site.hgc.jp/eF-site/servlet/current/jV.jnlp recent JOGL version]
The current jV requires JRE 1.6 or later.
The previous version, jV version 4.0, can run with JRE 1.4 and 1.5.
* [http://ef-site.hgc.jp/jV/stable/jV_4_0.jnlp jV 4.0]

== Basic Usage ==
You can execute basic operations such as rotation and translation with mouse action. Major actions are described in the following table:
{| style="margin:auto;border:1px solid gray"
! rowspan="2" style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap;font-weight:bold" |Action
! colspan="2" style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap;font-weight:bold" |Mouse Operation
|-
! style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap;font-weight:bold" |Windows, Linux
! style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap;font-weight:bold" |Mac OS X
|-
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |rotate around X (horizontal) axis&lt;br /&gt;rotate around Y (vertical) axis
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |left drag
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |drag
|-
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |translate along X axis (holizontally)&lt;br /&gt;translate along Y axis (vertically)
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |right drag
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |Command + drag
|-
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |translate along Z axis (zoom in/out)
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |Shift + left drag
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |Shift + drag
|}

Operations such as changing display models and colors and saving the image, can be executed with a menu. The location of the menu is at the top of the application window in Windows and at the top of screen in Mac as the stand-alone application. As an applet usage, a popup menu appears by clicking the right mouse button on the display screen, or clicking with a "Command" button in case of Mac.

{| style="margin:auto;border:0"
|-
| [[File:Jv_menu_win.png|The location of menu in jV stand-alone version in Windows.|250px]]
| [[File:Jv_menu_mac.png|The location of menu in jV stand-alone version in Mac.|250px]]
| [[File:popupmenu_en.png|The location of menu in applet version.|250px]]
|-
| style="text-align:center" |Stand-alone (Windows)
| style="text-align:center" |Stand-alone (Mac)
| style="text-align:center" |Applet
|}

Basic menu operations are following (see also [[GUI]] for details):

{| style="margin:auto;border:1px solid gray;border-collapse:collapse"
! style="padding:0 0.5em;border:1px solid gray" | Operations
! style="padding:0 0.5em;border:1px solid gray" | Menu location
|-
| style="padding:0 0.5em;border:1px solid gray" | Save a static image
| style="padding:0 0.5em;border:1px solid gray" | [File]-[Save]-[PNG/JPEG]
|-
| style="padding:0 0.5em;border:1px solid gray" | Change the expression format
| style="padding:0 0.5em;border:1px solid gray" | [File]-[Display]-[Wireframe/Backbone/Sticks/Spacefill/Ball&amp;amp;Stick/Ribbons/Cartoon]
|-
| style="padding:0 0.5em;border:1px solid gray" | Change the color
| style="padding:0 0.5em;border:1px solid gray" | [File]-[Colors]-[Monochrome/CPK/Shapely/Group/Chain/Temperature/Structure/Charge/Amino]
|}

To execute more complicated operation such as diplaying some piece of the molecule or changing some part of molecule in another style, use command line operation.

See also [[#Other resources]] for details:


== Download ==
You can also download the program and start it up locally.
The following links take you to the download pages. (latest version is 4.4.3@2015/2/24)
* [http://ef-site.hgc.jp/eF-site/servlet/DownloadViewerBinary binary (4.4.3)] 
* [http://ef-site.hgc.jp/eF-site/servlet/Registration source code (4.4.3)] (registration will be required)

== Other resources ==
* [http://ef-site.hgc.jp/eF-site/jV/jV_manual.html Manual] (html in English)
* [[How_to_use]] (in this site in English)
* [http://www.pdbj.org/jv/manual/index_ja.html Manual] (html in Japanese)
* [http://www.pdbj.org/jv/manual/jV_manual.pdf Manual] (pdf in English, for ver. 3.3)
* [http://ef-site.hgc.jp/eF-site/jV/jV3_User'sGuide.pdf User's guide] (for ver. 3.8.3 in English)</text>
    <sha1>6021945801d5952ecf5f385e5928631f249f5383</sha1>
  </revision>
  <revision>
    <id>598</id>
    <parentid>597</parentid>
    <timestamp>2015-02-24T06:30:43Z</timestamp>
    <contributor>
      <username>IMSsato</username>
      <id>4</id>
    </contributor>
    <comment>/* Other resources */</comment>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="6352" xml:space="preserve">&lt;big&gt;'''Welcome to jV wiki.'''&lt;/big&gt;

jV (formerly known as PDBjViewer) is a program to display molecular graphics of protein and nucleic acids. 
jV supports the following features:
* jV can read and display PDBML files, the canonical XML format for the Protein Data Bank.
* Of course, jV can read and display the traditional PDB format files, too.
* RasMol-like usability.
* jV can process more than one molecules.
* jV can display polygons specified by XML. ([http://www.pdbj.org/jv/polygonSchema XML Schema for polygons] is available.)
* Multiple polygons can be processed simultaneously, and be superimposed onto molecular images.
* Animation can be realized.
* jV runs on the Java Runtime Environment ([http://www.oracle.com/technetwork/java/javase/overview/index.html JRE]) so that it can work as a stand-alone application as well as an applet.
* The graphics of jV is based on OpenGL ([http://jogamp.org/jogl/www/ JOGL]), thereby producing fairly beautiful pictures.


The program 'jV' has been developed by [http://www.hgc.jp/~kinosita/TOP.html Kengo Kinoshita] ([http://www.is.tohoku.ac.jp/index-e.html Graduate School of Information Sciences], [http://www.tohoku.ac.jp/english/ Tohoku University]) and [http://www.protein.osaka-u.ac.jp/rcsfp/pi/ Haruki Nakamura] ([http://www.protein.osaka-u.ac.jp/index_e.php Institute for Protein Research], [http://www.osaka-u.ac.jp/eng/index.html Osaka Univeristy]), with the support from [http://biosciencedbc.jp/ JST-NBDC] and [http://www.protein.osaka-u.ac.jp/index_e.php Institute for Protein Research IPR], [http://www.osaka-u.ac.jp/eng/index.html Osaka Univeristy].
      

&lt;gallery&gt;
File:Spacefill.jpg
File:Cartoon.jpg
File:Surface.jpg
File:edmap.jpg
&lt;/gallery&gt;


== Start up ==
You can start up jV (4.4.3) with Java Web Start technology immediately from here.
* [http://ef-site.hgc.jp/eF-site/servlet/stable/jV.jnlp stable JOGL version] (recommended)
* [http://ef-site.hgc.jp/eF-site/servlet/current/jV.jnlp recent JOGL version]
The current jV requires JRE 1.6 or later.
The previous version, jV version 4.0, can run with JRE 1.4 and 1.5.
* [http://ef-site.hgc.jp/jV/stable/jV_4_0.jnlp jV 4.0]

== Basic Usage ==
You can execute basic operations such as rotation and translation with mouse action. Major actions are described in the following table:
{| style="margin:auto;border:1px solid gray"
! rowspan="2" style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap;font-weight:bold" |Action
! colspan="2" style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap;font-weight:bold" |Mouse Operation
|-
! style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap;font-weight:bold" |Windows, Linux
! style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap;font-weight:bold" |Mac OS X
|-
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |rotate around X (horizontal) axis&lt;br /&gt;rotate around Y (vertical) axis
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |left drag
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |drag
|-
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |translate along X axis (holizontally)&lt;br /&gt;translate along Y axis (vertically)
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |right drag
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |Command + drag
|-
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |translate along Z axis (zoom in/out)
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |Shift + left drag
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |Shift + drag
|}

Operations such as changing display models and colors and saving the image, can be executed with a menu. The location of the menu is at the top of the application window in Windows and at the top of screen in Mac as the stand-alone application. As an applet usage, a popup menu appears by clicking the right mouse button on the display screen, or clicking with a "Command" button in case of Mac.

{| style="margin:auto;border:0"
|-
| [[File:Jv_menu_win.png|The location of menu in jV stand-alone version in Windows.|250px]]
| [[File:Jv_menu_mac.png|The location of menu in jV stand-alone version in Mac.|250px]]
| [[File:popupmenu_en.png|The location of menu in applet version.|250px]]
|-
| style="text-align:center" |Stand-alone (Windows)
| style="text-align:center" |Stand-alone (Mac)
| style="text-align:center" |Applet
|}

Basic menu operations are following (see also [[GUI]] for details):

{| style="margin:auto;border:1px solid gray;border-collapse:collapse"
! style="padding:0 0.5em;border:1px solid gray" | Operations
! style="padding:0 0.5em;border:1px solid gray" | Menu location
|-
| style="padding:0 0.5em;border:1px solid gray" | Save a static image
| style="padding:0 0.5em;border:1px solid gray" | [File]-[Save]-[PNG/JPEG]
|-
| style="padding:0 0.5em;border:1px solid gray" | Change the expression format
| style="padding:0 0.5em;border:1px solid gray" | [File]-[Display]-[Wireframe/Backbone/Sticks/Spacefill/Ball&amp;amp;Stick/Ribbons/Cartoon]
|-
| style="padding:0 0.5em;border:1px solid gray" | Change the color
| style="padding:0 0.5em;border:1px solid gray" | [File]-[Colors]-[Monochrome/CPK/Shapely/Group/Chain/Temperature/Structure/Charge/Amino]
|}

To execute more complicated operation such as diplaying some piece of the molecule or changing some part of molecule in another style, use command line operation.

See also [[#Other resources]] for details:


== Download ==
You can also download the program and start it up locally.
The following links take you to the download pages. (latest version is 4.4.3@2015/2/24)
* [http://ef-site.hgc.jp/eF-site/servlet/DownloadViewerBinary binary (4.4.3)] 
* [http://ef-site.hgc.jp/eF-site/servlet/Registration source code (4.4.3)] (registration will be required)

== Other resources ==
* [[How_to_use]] (in this site in English)
* [http://www.pdbj.org/jv/manual/index_ja.html Manual] (html in Japanese)</text>
    <sha1>c0d3b39e285e5a46479201eca615d8f080f9dc16</sha1>
  </revision>
  <revision>
    <id>601</id>
    <parentid>598</parentid>
    <timestamp>2015-10-01T01:41:17Z</timestamp>
    <contributor>
      <username>IMSsato</username>
      <id>4</id>
    </contributor>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="6312" xml:space="preserve">&lt;big&gt;'''Welcome to jV wiki.'''&lt;/big&gt;

jV (formerly known as PDBjViewer) is a program to display molecular graphics of protein and nucleic acids. 
jV supports the following features:
* jV can read and display PDBML files, the canonical XML format for the Protein Data Bank.
* Of course, jV can read and display the traditional PDB format files, too.
* RasMol-like usability.
* jV can process more than one molecules.
* jV can display polygons specified by XML. ([http://www.pdbj.org/jv/polygonSchema XML Schema for polygons] is available.)
* Multiple polygons can be processed simultaneously, and be superimposed onto molecular images.
* Animation can be realized.
* jV runs on the Java Runtime Environment ([http://java.com/download/ JRE]) so that it can work as a stand-alone application as well as an applet.
* The graphics of jV is based on OpenGL ([http://jogamp.org/jogl/www/ JOGL]), thereby producing fairly beautiful pictures.


The program 'jV' has been developed by [http://www.hgc.jp/~kinosita/TOP.html Kengo Kinoshita] ([http://www.is.tohoku.ac.jp/index-e.html Graduate School of Information Sciences], [http://www.tohoku.ac.jp/english/ Tohoku University]) and [http://www.protein.osaka-u.ac.jp/rcsfp/pi/ Haruki Nakamura] ([http://www.protein.osaka-u.ac.jp/index_e.php Institute for Protein Research], [http://www.osaka-u.ac.jp/eng/index.html Osaka Univeristy]), with the support from [http://biosciencedbc.jp/ JST-NBDC] and [http://www.protein.osaka-u.ac.jp/index_e.php Institute for Protein Research IPR], [http://www.osaka-u.ac.jp/eng/index.html Osaka Univeristy].
      

&lt;gallery&gt;
File:Spacefill.jpg
File:Cartoon.jpg
File:Surface.jpg
File:edmap.jpg
&lt;/gallery&gt;


== Start up ==
You can start up jV (4.4.3) with Java Web Start technology immediately from here.
* [http://ef-site.hgc.jp/eF-site/servlet/stable/jV.jnlp stable JOGL version] (recommended)
* [http://ef-site.hgc.jp/eF-site/servlet/current/jV.jnlp recent JOGL version]
The current jV requires JRE 1.6 or later.
The previous version, jV version 4.0, can run with JRE 1.4 and 1.5.
* [http://ef-site.hgc.jp/jV/stable/jV_4_0.jnlp jV 4.0]

== Basic Usage ==
You can execute basic operations such as rotation and translation with mouse action. Major actions are described in the following table:
{| style="margin:auto;border:1px solid gray"
! rowspan="2" style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap;font-weight:bold" |Action
! colspan="2" style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap;font-weight:bold" |Mouse Operation
|-
! style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap;font-weight:bold" |Windows, Linux
! style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap;font-weight:bold" |Mac OS X
|-
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |rotate around X (horizontal) axis&lt;br /&gt;rotate around Y (vertical) axis
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |left drag
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |drag
|-
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |translate along X axis (holizontally)&lt;br /&gt;translate along Y axis (vertically)
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |right drag
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |Command + drag
|-
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |translate along Z axis (zoom in/out)
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |Shift + left drag
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |Shift + drag
|}

Operations such as changing display models and colors and saving the image, can be executed with a menu. The location of the menu is at the top of the application window in Windows and at the top of screen in Mac as the stand-alone application. As an applet usage, a popup menu appears by clicking the right mouse button on the display screen, or clicking with a "Command" button in case of Mac.

{| style="margin:auto;border:0"
|-
| [[File:Jv_menu_win.png|The location of menu in jV stand-alone version in Windows.|250px]]
| [[File:Jv_menu_mac.png|The location of menu in jV stand-alone version in Mac.|250px]]
| [[File:popupmenu_en.png|The location of menu in applet version.|250px]]
|-
| style="text-align:center" |Stand-alone (Windows)
| style="text-align:center" |Stand-alone (Mac)
| style="text-align:center" |Applet
|}

Basic menu operations are following (see also [[GUI]] for details):

{| style="margin:auto;border:1px solid gray;border-collapse:collapse"
! style="padding:0 0.5em;border:1px solid gray" | Operations
! style="padding:0 0.5em;border:1px solid gray" | Menu location
|-
| style="padding:0 0.5em;border:1px solid gray" | Save a static image
| style="padding:0 0.5em;border:1px solid gray" | [File]-[Save]-[PNG/JPEG]
|-
| style="padding:0 0.5em;border:1px solid gray" | Change the expression format
| style="padding:0 0.5em;border:1px solid gray" | [File]-[Display]-[Wireframe/Backbone/Sticks/Spacefill/Ball&amp;amp;Stick/Ribbons/Cartoon]
|-
| style="padding:0 0.5em;border:1px solid gray" | Change the color
| style="padding:0 0.5em;border:1px solid gray" | [File]-[Colors]-[Monochrome/CPK/Shapely/Group/Chain/Temperature/Structure/Charge/Amino]
|}

To execute more complicated operation such as diplaying some piece of the molecule or changing some part of molecule in another style, use command line operation.

See also [[#Other resources]] for details:


== Download ==
You can also download the program and start it up locally.
The following links take you to the download pages. (latest version is 4.4.3@2015/2/24)
* [http://ef-site.hgc.jp/eF-site/servlet/DownloadViewerBinary binary (4.4.3)] 
* [http://ef-site.hgc.jp/eF-site/servlet/Registration source code (4.4.3)] (registration will be required)

== Other resources ==
* [[How_to_use]] (in this site in English)
* [http://www.pdbj.org/jv/manual/index_ja.html Manual] (html in Japanese)</text>
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== System requirements ==
jV runs on the Java Runtime Environment (JRE) with JOGL API. The version requirements are as follows.
* [http://www.oracle.com/technetwork/java/javase/overview/index.html JRE] (includes Java Plug-in) 1.6 or later
* [http://jogamp.org/jogl/www/ JOGL] API 2.2.4 or later 
These softwares are available on typical operation systems such as Windows (XP/Vista/7), Mac OS X 10.6 or later, and Red Hat Linux 7.3 or later.

== Installation ==
From the version 3.8.3, binary distribution of jV contains the JOGL library
and pre-installation of JOGL is not necessary.
Just JRE is required on your computer in advance.
With JRE properly installed, you can download the binary distribution of jV 
and immediately use jV by running a start-up script contained in the distribution.</text>
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== System requirements ==
jV runs on the Java Runtime Environment (JRE) with JOGL API. The version requirements are as follows.
* [http://www.oracle.com/technetwork/java/javase/overview/index.html JRE] (includes Java Plug-in) 1.6 or later
* [http://jogamp.org/jogl/www/ JOGL] API 2.2.4 or later 
These softwares are available on typical operation systems such as Windows (XP/Vista/7/8/8.1), Mac OS X 10.6 or later, and Red Hat Linux 7.3 or later.

== Installation ==
From the version 3.8.3, binary distribution of jV contains the JOGL library
and pre-installation of JOGL is not necessary.
Just JRE is required on your computer in advance.
With JRE properly installed, you can download the binary distribution of jV 
and immediately use jV by running a start-up script contained in the distribution.</text>
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== System requirements ==
jV runs on the Java Runtime Environment (JRE) with JOGL API. The version requirements are as follows.
* [http://java.com/download/ JRE] (includes Java Plug-in) 1.6 or later
* [http://jogamp.org/jogl/www/ JOGL] API 2.2.4 or later 
These softwares are available on typical operation systems such as Windows (XP/Vista/7/8/8.1), Mac OS X 10.6 or later, and Red Hat Linux 7.3 or later.

== Installation ==
From the version 3.8.3, binary distribution of jV contains the JOGL library
and pre-installation of JOGL is not necessary.
Just JRE is required on your computer in advance.
With JRE properly installed, you can download the binary distribution of jV 
and immediately use jV by running a start-up script contained in the distribution.</text>
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 |__TOC__
 |}
== Starting up ==
It is assumed that Java Runtime Environment has been properly installed. You can start up jV by downloading the binary distribution and running a start-up script contained in the distribution. Another way to use jV is to follow [http://ef-site.hgc.jp/eF-site/servlet/stable/jV.jnlp this link], which launch jV via Java Web Start technology.
Figure 1 shows the start-up screen. The window has a 3-panel structure, and the upper-left panel with the black background is a 3D image display area. The status of files that have been loaded to the application is shown in the upper-right panel and the lower panel is a command-input and a message-output area.
[[File:tutorial4_4_fig1.png|thumb|Figure 1: Start-up screen|center|500px]]

== Displaying molecules ==
If you are working in the environment that is getting on the Internet and know the PDB ID of the molecule that you want to display, the simplest way is as follows. A dialog shown in Figure 2 is opened by selecting the [File] – [Open – Remote] – [PDB ID] menu item. Enter a PDB ID '12as', for example, to the text field and click the 'OK' button, then the PDBML file is read through the Internet and the molecule is displayed. A molecule is displayed in a wire frame model with colored by atom type in the initial state.

[[File:Fig2.jpg|thumb|Figure 2: Dialog to open the molecule specified by PDB ID|center|200px]]

Let us next attempt to load an arbitrary file on the Internet. Here we use 'http://ef-site.hgc.jp/eF-site/jV/1yec.pdb' as an example. The file is a conventional PDB file whose PDB ID is 1yec. In this case we choose the [File] – [Open – Remote] – [PDB] menu item. Then the open-remote dialog appears. Enter the above URL to the text field at the top of the dialog and click the 'OK' button and the molecule is read in and displayed. In jV3, each molecule is displayed according to the space coordination described in its file. Therefore, when loading and displaying more than one molecule together, they can be viewed with an appropriate separation in some cases; however, they may be displayed far separately or may be overlapped depending on the combination. In any case, when adding a new file, the position of the viewpoint is automatically controlled for the whole to be displayed.

The coordinate system is the right hand system with the x-y plane being on the screen (the x-axis is a horizontal line with positive values to the right and the y-axis is a vertical line with positive values up). Although, the above examples are about operations for remote files, a PDB file on your local hard disk can also be opened from the [File] – [Open – Local] – [PDB] menu item.

== Operating molecules ==
Interactive mouse operations are possible for 3D images. By left-dragging the mouse on the 3D-display panel, molecules are rotated around the x-axis or y-axis. By left-dragging the mouse while holding the Shift key on the keyboard, molecules are translated along the z-axis. All mouse operations are as follows (as for the Macintosh environment, the Command key + left-drag substitutes for the right-drag).

{| border="1"
 ! Mouse operations !! Actions
 |-
 | Left-drag || The image is rotated around the x (for a vertical motion) and y (for a horizontal motion) axes.
 |-
 | Right-drag || The image is translated on the x-y plane.
 |-
 | [Shift] + left-drag || The image is translated along the z-axis.
 |-
 | [Shift] + right-drag || The image is rotated around the z-axis.
 |-
 | [Alt or Ctrl] + left-drag || The z-clipping plane is shifted when [Option]-[Slab] is checked.
 |-
 | Left-click || An atom of the molecule displayed on the screen is picked.
 |}

In the upper-right panel in the application window (see Figure 3), the file names that have been loaded to the application are listed, where sequential integers are automatically assigned to the individual file. Each integer is a file ID that can be used to specify the file in the command line interface. In addition, three checkboxes are attached to each file. If you change the status of a ‘Disp’ checkbox, the corresponding molecule is switched to be displayed or not to be displayed. If you change the status of a ‘Mouse’ checkbox, the corresponding molecule is switched to be a target of the mouse operations or not. For example, set the both ‘Disp’ checkboxes on, and the both ‘Mouse’ checkboxes off. In this case, either molecule does not move against mouse operations. 

Subsequently set the ‘Mouse’ checkbox of file 1 on. In this case, mouse operations work for the molecule 1. Thus, each file is assigned either selected or not selected, and transform operations, such as rotation or translation, act only on selected files. On the other hand, every atom in a molecule is also assigned either selected or not selected, independently of whether the molecule itself is selected or not. Operations that modify display models or colors work for selected atoms. To see this, choose the [Display] – [Spacefill] menu item. Then the both molecules are displayed with the space fill model because all atoms are initially selected. In the same way, if you choose the [Colors] – [Monochrome] menu item, the both molecules are colored white. A ‘Sel’ checkbox selects or disselects all atoms in each file. 

Let us next try a more detailed operation. Type ‘select *@2’ in the command line area and press Enter key. This command means to select all atoms contained in the file 2 (the usage of the [[Command_List#select|select command]] is summarized in the reference manual). Subsequently, choose the [Display] – [Cartoon] menu item. As a result, only the molecule 2 is displayed in the cartoon model. Furthermore select the [Colors] – [Structure] menu item, and each residue of the molecule 2 is colored according to its secondary structure type (see Figure 3). 

In order to reproduce the same view as that in Figure 3, first execute ‘reset’ command. It restores the position of the viewpoint and the transform of every file to the initial state. Note that the command line interface tries to complement a command word when the Tab key is pressed. If you enter ‘res’ to the command line and subsequently press the Tab key, the command ‘reset’ is automatically entered. Next set the both ‘Mouse’ checkboxes on, and execute ‘translate z 100’ command. This command means to translate the molecules along the z-axis by 100 angstroms.

[[File:Tutorial_fig3.jpg|thumb|Figure 3: An example of molecular images.|center|500px]]

== Displaying polygons ==
In addition to molecules, arbitrary shapes described by polygons can be read in and displayed together, where the polygon file is an XML file, whose document type is described in the section 6. Here, we use ’http://ef-site.hgc.jp/eF-site/jV/1yec.surface.gz’ as an example. This polygon file represents a molecular surface of the molecule 2 (1yec) and the surface is colored according to the electrostatic potential and the hydrophobicity. It is assumed that the current image is the same as that in Figure 3. Then, open the open-remote dialog by choosing the [File] – [Open – Remote] – [Polygon] menu item, enter the above URL to the text field at the top of the dialog, and click the 'OK' button. As a result, the polygon is loaded, displayed and assigned file ID 3. 

Note that the polygon is displayed at the different position from the molecule 2 since the molecule 2 is translated. However, because the polygon and the molecule 2 are described by the same coordinates in their files, their images can be exactly superposed by executing ‘fit 3 2’ from the command line, where the ‘fit’ command performs the copy of the transform matrix. Finally, the image in Figure 4 appears.

[[File:Tutorial_fig4.jpg|thumb|Figure4: An example of polygon images.|center|500px]]

You can control the transparency rate of polygons. Try ’set transparency 0.5’ from the command line, where 0.5 stands for 50% transparency. To restore the image, execute ‘reset transparency’ or ‘set transparency 0’. In the same sense as each atom of a molecule, each vertex of a polygon is assigned either selected or not selected. All vertices are selected in the initial state. Execute a command ’displayvertex off’ and all vertices become invisible. Next execute ’selectvertex within(10.0, 1&amp;*H@2)’, where this means to select vertices that exist within 10 angstroms from each atom that belongs to the first residue of the ‘H’ chain of the molecule 2. Subsequently execute ’displayvertex on’. As a result, only the selected vertices appear. The usage of the [[Command List#selectvertex|selectvertex command]] is summarized in the reference manual.

== Working with PDBMLplus ==
Functional site information on a molecule stored in PDBMLplus is available in jV3. Before trying this, let us close the molecule 2 and the polygon 3 to make the situation simple. Select the [File] – [Close] – [2. 1yec.pdb] and [File] – [Close] – [3. 1yec.surface.gz] menu items sequentially. Then execute a ‘reset’ command and the transform of the molecule 1 and the position of the viewpoint are initialized. 

Next, confirm that the ‘Mouse’ checkbox of the file 1 is checked, and try a ‘show pdbj’ command. The functional site information of the molecule ‘12as’ is read from the PDBMLplus and ‘type’ and ‘subtype’ keywords for each functional site are listed. These keywords can be used to select a set of atoms. For example, if a keyword ‘CATRES’ exists (probably it does), the command ‘select pdbj:CATRES’ selects the corresponding atoms. 

In addition, gene ontology information can be obtained from the PDBMLplus. The gene ontology information for the molecule 12as is displayed by the command ’show godata’. Similar operations can be applied to other external databases on the Internet provided that the external database supports the interface that jV3 requires. See the '[[Functional site information for molecules]]' section for details.

== Animation ==
The animation of molecules can be performed in jV3. The animation file takes the PDB format, where the MODEL line divides each frame. Let us open an animation file ’http://ef-site.hgc.jp/eF-site/jV/anim.pdb.gz’ as an example from the open-remote dialog shown by selecting the [File] – [Open – Remote] – [Animation] menu item. When an animation file is loaded to the application, the first frame is automatically displayed in the wire frame model. You can start the animation by using the animation-control dialog that is shown by choosing the [Options] – [Animation] menu item. The dialog provides operations such as start and stop of the animation, selection of the animation mode, and adjustment of the speed. Some [[GUI#Animation_control_dialog|sample figures]] of the dialog are shown in the GUI section.

== Saving your work ==
While in your work, you can create a script file that contains a set of commands that reproduces the current work by using the [File] – [Save] – [Script] menu item. The script file can be loaded by the [File] – [Open – Local] – [Script] menu item. On the other hand, the [File] – [Save] – [PDB] menu item enables to save a molecule to a PDB format file with the coordinates of the atoms being transformed according to the current image. Here, only one molecule must be selected and only selected atoms in the molecule are saved. The other two menu items in the [File] – [Save] menu, [PNG] and [JPEG], save the current screen image to an image file in the PNG and JPEG format, respectively. The created image file has the same size as that of the 3D-display panel in the application.

== Terminating the application ==
The application is terminated when the [File] – [Exit] menu item is chosen or the application window is closed by the way your operation system provides. You can also quit the application by executing ‘exit’ or ‘quit’ command.</text>
    <sha1>cf6e1ff03e5adf8635aa7e3cf14130aba14646e0</sha1>
  </revision>
  <revision>
    <id>583</id>
    <parentid>582</parentid>
    <timestamp>2015-02-23T07:11:34Z</timestamp>
    <contributor>
      <username>IMSsato</username>
      <id>4</id>
    </contributor>
    <comment>/* Displaying molecules */</comment>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="12039" xml:space="preserve">{| style="float:right"
 |__TOC__
 |}
== Starting up ==
It is assumed that Java Runtime Environment has been properly installed. You can start up jV by downloading the binary distribution and running a start-up script contained in the distribution. Another way to use jV is to follow [http://ef-site.hgc.jp/eF-site/servlet/stable/jV.jnlp this link], which launch jV via Java Web Start technology.
Figure 1 shows the start-up screen. The window has a 3-panel structure, and the upper-left panel with the black background is a 3D image display area. The status of files that have been loaded to the application is shown in the upper-right panel and the lower panel is a command-input and a message-output area.
[[File:tutorial4_4_fig1.png|thumb|Figure 1: Start-up screen|center|500px]]

== Displaying molecules ==
If you are working in the environment that is getting on the Internet and know the PDB ID of the molecule that you want to display, the simplest way is as follows. A dialog shown in Figure 2 is opened by selecting the [File] – [Open – Remote] – [PDB ID] menu item. Enter a PDB ID '12as', for example, to the text field and click the 'OK' button, then the PDBML file is read through the Internet and the molecule is displayed. A molecule is displayed in a wire frame model with colored by atom type in the initial state.

[[File:tutorial4_4_fig2.png|thumb|Figure 2: Dialog to open the molecule specified by PDB ID|center|200px]]

Let us next attempt to load an arbitrary file on the Internet. Here we use 'http://ef-site.hgc.jp/eF-site/jV/1yec.pdb' as an example. The file is a conventional PDB file whose PDB ID is 1yec. In this case we choose the [File] – [Open – Remote] – [PDB] menu item. Then the open-remote dialog appears. Enter the above URL to the text field at the top of the dialog and click the 'OK' button and the molecule is read in and displayed. In jV, each molecule is displayed according to the space coordination described in its file. Therefore, when loading and displaying more than one molecule together, they can be viewed with an appropriate separation in some cases; however, they may be displayed far separately or may be overlapped depending on the combination. In any case, when adding a new file, the position of the viewpoint is automatically controlled for the whole to be displayed.

The coordinate system is the right hand system with the x-y plane being on the screen (the x-axis is a horizontal line with positive values to the right and the y-axis is a vertical line with positive values up). Although, the above examples are about operations for remote files, a PDB file on your local hard disk can also be opened from the [File] – [Open – Local] – [PDB] menu item.

== Operating molecules ==
Interactive mouse operations are possible for 3D images. By left-dragging the mouse on the 3D-display panel, molecules are rotated around the x-axis or y-axis. By left-dragging the mouse while holding the Shift key on the keyboard, molecules are translated along the z-axis. All mouse operations are as follows (as for the Macintosh environment, the Command key + left-drag substitutes for the right-drag).

{| border="1"
 ! Mouse operations !! Actions
 |-
 | Left-drag || The image is rotated around the x (for a vertical motion) and y (for a horizontal motion) axes.
 |-
 | Right-drag || The image is translated on the x-y plane.
 |-
 | [Shift] + left-drag || The image is translated along the z-axis.
 |-
 | [Shift] + right-drag || The image is rotated around the z-axis.
 |-
 | [Alt or Ctrl] + left-drag || The z-clipping plane is shifted when [Option]-[Slab] is checked.
 |-
 | Left-click || An atom of the molecule displayed on the screen is picked.
 |}

In the upper-right panel in the application window (see Figure 3), the file names that have been loaded to the application are listed, where sequential integers are automatically assigned to the individual file. Each integer is a file ID that can be used to specify the file in the command line interface. In addition, three checkboxes are attached to each file. If you change the status of a ‘Disp’ checkbox, the corresponding molecule is switched to be displayed or not to be displayed. If you change the status of a ‘Mouse’ checkbox, the corresponding molecule is switched to be a target of the mouse operations or not. For example, set the both ‘Disp’ checkboxes on, and the both ‘Mouse’ checkboxes off. In this case, either molecule does not move against mouse operations. 

Subsequently set the ‘Mouse’ checkbox of file 1 on. In this case, mouse operations work for the molecule 1. Thus, each file is assigned either selected or not selected, and transform operations, such as rotation or translation, act only on selected files. On the other hand, every atom in a molecule is also assigned either selected or not selected, independently of whether the molecule itself is selected or not. Operations that modify display models or colors work for selected atoms. To see this, choose the [Display] – [Spacefill] menu item. Then the both molecules are displayed with the space fill model because all atoms are initially selected. In the same way, if you choose the [Colors] – [Monochrome] menu item, the both molecules are colored white. A ‘Sel’ checkbox selects or disselects all atoms in each file. 

Let us next try a more detailed operation. Type ‘select *@2’ in the command line area and press Enter key. This command means to select all atoms contained in the file 2 (the usage of the [[Command_List#select|select command]] is summarized in the reference manual). Subsequently, choose the [Display] – [Cartoon] menu item. As a result, only the molecule 2 is displayed in the cartoon model. Furthermore select the [Colors] – [Structure] menu item, and each residue of the molecule 2 is colored according to its secondary structure type (see Figure 3). 

In order to reproduce the same view as that in Figure 3, first execute ‘reset’ command. It restores the position of the viewpoint and the transform of every file to the initial state. Note that the command line interface tries to complement a command word when the Tab key is pressed. If you enter ‘res’ to the command line and subsequently press the Tab key, the command ‘reset’ is automatically entered. Next set the both ‘Mouse’ checkboxes on, and execute ‘translate z 100’ command. This command means to translate the molecules along the z-axis by 100 angstroms.

[[File:Tutorial_fig3.jpg|thumb|Figure 3: An example of molecular images.|center|500px]]

== Displaying polygons ==
In addition to molecules, arbitrary shapes described by polygons can be read in and displayed together, where the polygon file is an XML file, whose document type is described in the section 6. Here, we use ’http://ef-site.hgc.jp/eF-site/jV/1yec.surface.gz’ as an example. This polygon file represents a molecular surface of the molecule 2 (1yec) and the surface is colored according to the electrostatic potential and the hydrophobicity. It is assumed that the current image is the same as that in Figure 3. Then, open the open-remote dialog by choosing the [File] – [Open – Remote] – [Polygon] menu item, enter the above URL to the text field at the top of the dialog, and click the 'OK' button. As a result, the polygon is loaded, displayed and assigned file ID 3. 

Note that the polygon is displayed at the different position from the molecule 2 since the molecule 2 is translated. However, because the polygon and the molecule 2 are described by the same coordinates in their files, their images can be exactly superposed by executing ‘fit 3 2’ from the command line, where the ‘fit’ command performs the copy of the transform matrix. Finally, the image in Figure 4 appears.

[[File:Tutorial_fig4.jpg|thumb|Figure4: An example of polygon images.|center|500px]]

You can control the transparency rate of polygons. Try ’set transparency 0.5’ from the command line, where 0.5 stands for 50% transparency. To restore the image, execute ‘reset transparency’ or ‘set transparency 0’. In the same sense as each atom of a molecule, each vertex of a polygon is assigned either selected or not selected. All vertices are selected in the initial state. Execute a command ’displayvertex off’ and all vertices become invisible. Next execute ’selectvertex within(10.0, 1&amp;*H@2)’, where this means to select vertices that exist within 10 angstroms from each atom that belongs to the first residue of the ‘H’ chain of the molecule 2. Subsequently execute ’displayvertex on’. As a result, only the selected vertices appear. The usage of the [[Command List#selectvertex|selectvertex command]] is summarized in the reference manual.

== Working with PDBMLplus ==
Functional site information on a molecule stored in PDBMLplus is available in jV3. Before trying this, let us close the molecule 2 and the polygon 3 to make the situation simple. Select the [File] – [Close] – [2. 1yec.pdb] and [File] – [Close] – [3. 1yec.surface.gz] menu items sequentially. Then execute a ‘reset’ command and the transform of the molecule 1 and the position of the viewpoint are initialized. 

Next, confirm that the ‘Mouse’ checkbox of the file 1 is checked, and try a ‘show pdbj’ command. The functional site information of the molecule ‘12as’ is read from the PDBMLplus and ‘type’ and ‘subtype’ keywords for each functional site are listed. These keywords can be used to select a set of atoms. For example, if a keyword ‘CATRES’ exists (probably it does), the command ‘select pdbj:CATRES’ selects the corresponding atoms. 

In addition, gene ontology information can be obtained from the PDBMLplus. The gene ontology information for the molecule 12as is displayed by the command ’show godata’. Similar operations can be applied to other external databases on the Internet provided that the external database supports the interface that jV3 requires. See the '[[Functional site information for molecules]]' section for details.

== Animation ==
The animation of molecules can be performed in jV3. The animation file takes the PDB format, where the MODEL line divides each frame. Let us open an animation file ’http://ef-site.hgc.jp/eF-site/jV/anim.pdb.gz’ as an example from the open-remote dialog shown by selecting the [File] – [Open – Remote] – [Animation] menu item. When an animation file is loaded to the application, the first frame is automatically displayed in the wire frame model. You can start the animation by using the animation-control dialog that is shown by choosing the [Options] – [Animation] menu item. The dialog provides operations such as start and stop of the animation, selection of the animation mode, and adjustment of the speed. Some [[GUI#Animation_control_dialog|sample figures]] of the dialog are shown in the GUI section.

== Saving your work ==
While in your work, you can create a script file that contains a set of commands that reproduces the current work by using the [File] – [Save] – [Script] menu item. The script file can be loaded by the [File] – [Open – Local] – [Script] menu item. On the other hand, the [File] – [Save] – [PDB] menu item enables to save a molecule to a PDB format file with the coordinates of the atoms being transformed according to the current image. Here, only one molecule must be selected and only selected atoms in the molecule are saved. The other two menu items in the [File] – [Save] menu, [PNG] and [JPEG], save the current screen image to an image file in the PNG and JPEG format, respectively. The created image file has the same size as that of the 3D-display panel in the application.

== Terminating the application ==
The application is terminated when the [File] – [Exit] menu item is chosen or the application window is closed by the way your operation system provides. You can also quit the application by executing ‘exit’ or ‘quit’ command.</text>
    <sha1>8d053c0ccefe0b0e9f26d8dbce8f5dcb25f96c92</sha1>
  </revision>
  <revision>
    <id>584</id>
    <parentid>583</parentid>
    <timestamp>2015-02-23T07:13:35Z</timestamp>
    <contributor>
      <username>IMSsato</username>
      <id>4</id>
    </contributor>
    <comment>/* Operating molecules */</comment>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="12041" xml:space="preserve">{| style="float:right"
 |__TOC__
 |}
== Starting up ==
It is assumed that Java Runtime Environment has been properly installed. You can start up jV by downloading the binary distribution and running a start-up script contained in the distribution. Another way to use jV is to follow [http://ef-site.hgc.jp/eF-site/servlet/stable/jV.jnlp this link], which launch jV via Java Web Start technology.
Figure 1 shows the start-up screen. The window has a 3-panel structure, and the upper-left panel with the black background is a 3D image display area. The status of files that have been loaded to the application is shown in the upper-right panel and the lower panel is a command-input and a message-output area.
[[File:tutorial4_4_fig1.png|thumb|Figure 1: Start-up screen|center|500px]]

== Displaying molecules ==
If you are working in the environment that is getting on the Internet and know the PDB ID of the molecule that you want to display, the simplest way is as follows. A dialog shown in Figure 2 is opened by selecting the [File] – [Open – Remote] – [PDB ID] menu item. Enter a PDB ID '12as', for example, to the text field and click the 'OK' button, then the PDBML file is read through the Internet and the molecule is displayed. A molecule is displayed in a wire frame model with colored by atom type in the initial state.

[[File:tutorial4_4_fig2.png|thumb|Figure 2: Dialog to open the molecule specified by PDB ID|center|200px]]

Let us next attempt to load an arbitrary file on the Internet. Here we use 'http://ef-site.hgc.jp/eF-site/jV/1yec.pdb' as an example. The file is a conventional PDB file whose PDB ID is 1yec. In this case we choose the [File] – [Open – Remote] – [PDB] menu item. Then the open-remote dialog appears. Enter the above URL to the text field at the top of the dialog and click the 'OK' button and the molecule is read in and displayed. In jV, each molecule is displayed according to the space coordination described in its file. Therefore, when loading and displaying more than one molecule together, they can be viewed with an appropriate separation in some cases; however, they may be displayed far separately or may be overlapped depending on the combination. In any case, when adding a new file, the position of the viewpoint is automatically controlled for the whole to be displayed.

The coordinate system is the right hand system with the x-y plane being on the screen (the x-axis is a horizontal line with positive values to the right and the y-axis is a vertical line with positive values up). Although, the above examples are about operations for remote files, a PDB file on your local hard disk can also be opened from the [File] – [Open – Local] – [PDB] menu item.

== Operating molecules ==
Interactive mouse operations are possible for 3D images. By left-dragging the mouse on the 3D-display panel, molecules are rotated around the x-axis or y-axis. By left-dragging the mouse while holding the Shift key on the keyboard, molecules are translated along the z-axis. All mouse operations are as follows (as for the Mac OS X environment, the Command key + left-drag substitutes for the right-drag).

{| border="1"
 ! Mouse operations !! Actions
 |-
 | Left-drag || The image is rotated around the x (for a vertical motion) and y (for a horizontal motion) axes.
 |-
 | Right-drag || The image is translated on the x-y plane.
 |-
 | [Shift] + left-drag || The image is translated along the z-axis.
 |-
 | [Shift] + right-drag || The image is rotated around the z-axis.
 |-
 | [Alt or Ctrl] + left-drag || The z-clipping plane is shifted when [Option]-[Slab] is checked.
 |-
 | Left-click || An atom of the molecule displayed on the screen is picked.
 |}

In the upper-right panel in the application window (see Figure 3), the file names that have been loaded to the application are listed, where sequential integers are automatically assigned to the individual file. Each integer is a file ID that can be used to specify the file in the command line interface. In addition, three checkboxes are attached to each file. If you change the status of a ‘Disp’ checkbox, the corresponding molecule is switched to be displayed or not to be displayed. If you change the status of a ‘Mouse’ checkbox, the corresponding molecule is switched to be a target of the mouse operations or not. For example, set the both ‘Disp’ checkboxes on, and the both ‘Mouse’ checkboxes off. In this case, either molecule does not move against mouse operations. 

Subsequently set the ‘Mouse’ checkbox of file 1 on. In this case, mouse operations work for the molecule 1. Thus, each file is assigned either selected or not selected, and transform operations, such as rotation or translation, act only on selected files. On the other hand, every atom in a molecule is also assigned either selected or not selected, independently of whether the molecule itself is selected or not. Operations that modify display models or colors work for selected atoms. To see this, choose the [Display] – [Spacefill] menu item. Then the both molecules are displayed with the space fill model because all atoms are initially selected. In the same way, if you choose the [Colors] – [Monochrome] menu item, the both molecules are colored white. A ‘Sel’ checkbox selects or disselects all atoms in each file. 

Let us next try a more detailed operation. Type ‘select *@2’ in the command line area and press Enter key. This command means to select all atoms contained in the file 2 (the usage of the [[Command_List#select|select command]] is summarized in the reference manual). Subsequently, choose the [Display] – [Cartoon] menu item. As a result, only the molecule 2 is displayed in the cartoon model. Furthermore select the [Colors] – [Structure] menu item, and each residue of the molecule 2 is colored according to its secondary structure type (see Figure 3). 

In order to reproduce the same view as that in Figure 3, first execute ‘reset’ command. It restores the position of the viewpoint and the transform of every file to the initial state. Note that the command line interface tries to complement a command word when the Tab key is pressed. If you enter ‘res’ to the command line and subsequently press the Tab key, the command ‘reset’ is automatically entered. Next set the both ‘Mouse’ checkboxes on, and execute ‘translate z 100’ command. This command means to translate the molecules along the z-axis by 100 angstroms.

[[File:tutorial4_4_fig3.png|thumb|Figure 3: An example of molecular images.|center|500px]]

== Displaying polygons ==
In addition to molecules, arbitrary shapes described by polygons can be read in and displayed together, where the polygon file is an XML file, whose document type is described in the section 6. Here, we use ’http://ef-site.hgc.jp/eF-site/jV/1yec.surface.gz’ as an example. This polygon file represents a molecular surface of the molecule 2 (1yec) and the surface is colored according to the electrostatic potential and the hydrophobicity. It is assumed that the current image is the same as that in Figure 3. Then, open the open-remote dialog by choosing the [File] – [Open – Remote] – [Polygon] menu item, enter the above URL to the text field at the top of the dialog, and click the 'OK' button. As a result, the polygon is loaded, displayed and assigned file ID 3. 

Note that the polygon is displayed at the different position from the molecule 2 since the molecule 2 is translated. However, because the polygon and the molecule 2 are described by the same coordinates in their files, their images can be exactly superposed by executing ‘fit 3 2’ from the command line, where the ‘fit’ command performs the copy of the transform matrix. Finally, the image in Figure 4 appears.

[[File:Tutorial_fig4.jpg|thumb|Figure4: An example of polygon images.|center|500px]]

You can control the transparency rate of polygons. Try ’set transparency 0.5’ from the command line, where 0.5 stands for 50% transparency. To restore the image, execute ‘reset transparency’ or ‘set transparency 0’. In the same sense as each atom of a molecule, each vertex of a polygon is assigned either selected or not selected. All vertices are selected in the initial state. Execute a command ’displayvertex off’ and all vertices become invisible. Next execute ’selectvertex within(10.0, 1&amp;*H@2)’, where this means to select vertices that exist within 10 angstroms from each atom that belongs to the first residue of the ‘H’ chain of the molecule 2. Subsequently execute ’displayvertex on’. As a result, only the selected vertices appear. The usage of the [[Command List#selectvertex|selectvertex command]] is summarized in the reference manual.

== Working with PDBMLplus ==
Functional site information on a molecule stored in PDBMLplus is available in jV3. Before trying this, let us close the molecule 2 and the polygon 3 to make the situation simple. Select the [File] – [Close] – [2. 1yec.pdb] and [File] – [Close] – [3. 1yec.surface.gz] menu items sequentially. Then execute a ‘reset’ command and the transform of the molecule 1 and the position of the viewpoint are initialized. 

Next, confirm that the ‘Mouse’ checkbox of the file 1 is checked, and try a ‘show pdbj’ command. The functional site information of the molecule ‘12as’ is read from the PDBMLplus and ‘type’ and ‘subtype’ keywords for each functional site are listed. These keywords can be used to select a set of atoms. For example, if a keyword ‘CATRES’ exists (probably it does), the command ‘select pdbj:CATRES’ selects the corresponding atoms. 

In addition, gene ontology information can be obtained from the PDBMLplus. The gene ontology information for the molecule 12as is displayed by the command ’show godata’. Similar operations can be applied to other external databases on the Internet provided that the external database supports the interface that jV3 requires. See the '[[Functional site information for molecules]]' section for details.

== Animation ==
The animation of molecules can be performed in jV3. The animation file takes the PDB format, where the MODEL line divides each frame. Let us open an animation file ’http://ef-site.hgc.jp/eF-site/jV/anim.pdb.gz’ as an example from the open-remote dialog shown by selecting the [File] – [Open – Remote] – [Animation] menu item. When an animation file is loaded to the application, the first frame is automatically displayed in the wire frame model. You can start the animation by using the animation-control dialog that is shown by choosing the [Options] – [Animation] menu item. The dialog provides operations such as start and stop of the animation, selection of the animation mode, and adjustment of the speed. Some [[GUI#Animation_control_dialog|sample figures]] of the dialog are shown in the GUI section.

== Saving your work ==
While in your work, you can create a script file that contains a set of commands that reproduces the current work by using the [File] – [Save] – [Script] menu item. The script file can be loaded by the [File] – [Open – Local] – [Script] menu item. On the other hand, the [File] – [Save] – [PDB] menu item enables to save a molecule to a PDB format file with the coordinates of the atoms being transformed according to the current image. Here, only one molecule must be selected and only selected atoms in the molecule are saved. The other two menu items in the [File] – [Save] menu, [PNG] and [JPEG], save the current screen image to an image file in the PNG and JPEG format, respectively. The created image file has the same size as that of the 3D-display panel in the application.

== Terminating the application ==
The application is terminated when the [File] – [Exit] menu item is chosen or the application window is closed by the way your operation system provides. You can also quit the application by executing ‘exit’ or ‘quit’ command.</text>
    <sha1>4b551903138986e119bd1d2e0c8a6071cb92af43</sha1>
  </revision>
  <revision>
    <id>585</id>
    <parentid>584</parentid>
    <timestamp>2015-02-23T07:14:35Z</timestamp>
    <contributor>
      <username>IMSsato</username>
      <id>4</id>
    </contributor>
    <comment>/* Displaying polygons */</comment>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="12044" xml:space="preserve">{| style="float:right"
 |__TOC__
 |}
== Starting up ==
It is assumed that Java Runtime Environment has been properly installed. You can start up jV by downloading the binary distribution and running a start-up script contained in the distribution. Another way to use jV is to follow [http://ef-site.hgc.jp/eF-site/servlet/stable/jV.jnlp this link], which launch jV via Java Web Start technology.
Figure 1 shows the start-up screen. The window has a 3-panel structure, and the upper-left panel with the black background is a 3D image display area. The status of files that have been loaded to the application is shown in the upper-right panel and the lower panel is a command-input and a message-output area.
[[File:tutorial4_4_fig1.png|thumb|Figure 1: Start-up screen|center|500px]]

== Displaying molecules ==
If you are working in the environment that is getting on the Internet and know the PDB ID of the molecule that you want to display, the simplest way is as follows. A dialog shown in Figure 2 is opened by selecting the [File] – [Open – Remote] – [PDB ID] menu item. Enter a PDB ID '12as', for example, to the text field and click the 'OK' button, then the PDBML file is read through the Internet and the molecule is displayed. A molecule is displayed in a wire frame model with colored by atom type in the initial state.

[[File:tutorial4_4_fig2.png|thumb|Figure 2: Dialog to open the molecule specified by PDB ID|center|200px]]

Let us next attempt to load an arbitrary file on the Internet. Here we use 'http://ef-site.hgc.jp/eF-site/jV/1yec.pdb' as an example. The file is a conventional PDB file whose PDB ID is 1yec. In this case we choose the [File] – [Open – Remote] – [PDB] menu item. Then the open-remote dialog appears. Enter the above URL to the text field at the top of the dialog and click the 'OK' button and the molecule is read in and displayed. In jV, each molecule is displayed according to the space coordination described in its file. Therefore, when loading and displaying more than one molecule together, they can be viewed with an appropriate separation in some cases; however, they may be displayed far separately or may be overlapped depending on the combination. In any case, when adding a new file, the position of the viewpoint is automatically controlled for the whole to be displayed.

The coordinate system is the right hand system with the x-y plane being on the screen (the x-axis is a horizontal line with positive values to the right and the y-axis is a vertical line with positive values up). Although, the above examples are about operations for remote files, a PDB file on your local hard disk can also be opened from the [File] – [Open – Local] – [PDB] menu item.

== Operating molecules ==
Interactive mouse operations are possible for 3D images. By left-dragging the mouse on the 3D-display panel, molecules are rotated around the x-axis or y-axis. By left-dragging the mouse while holding the Shift key on the keyboard, molecules are translated along the z-axis. All mouse operations are as follows (as for the Mac OS X environment, the Command key + left-drag substitutes for the right-drag).

{| border="1"
 ! Mouse operations !! Actions
 |-
 | Left-drag || The image is rotated around the x (for a vertical motion) and y (for a horizontal motion) axes.
 |-
 | Right-drag || The image is translated on the x-y plane.
 |-
 | [Shift] + left-drag || The image is translated along the z-axis.
 |-
 | [Shift] + right-drag || The image is rotated around the z-axis.
 |-
 | [Alt or Ctrl] + left-drag || The z-clipping plane is shifted when [Option]-[Slab] is checked.
 |-
 | Left-click || An atom of the molecule displayed on the screen is picked.
 |}

In the upper-right panel in the application window (see Figure 3), the file names that have been loaded to the application are listed, where sequential integers are automatically assigned to the individual file. Each integer is a file ID that can be used to specify the file in the command line interface. In addition, three checkboxes are attached to each file. If you change the status of a ‘Disp’ checkbox, the corresponding molecule is switched to be displayed or not to be displayed. If you change the status of a ‘Mouse’ checkbox, the corresponding molecule is switched to be a target of the mouse operations or not. For example, set the both ‘Disp’ checkboxes on, and the both ‘Mouse’ checkboxes off. In this case, either molecule does not move against mouse operations. 

Subsequently set the ‘Mouse’ checkbox of file 1 on. In this case, mouse operations work for the molecule 1. Thus, each file is assigned either selected or not selected, and transform operations, such as rotation or translation, act only on selected files. On the other hand, every atom in a molecule is also assigned either selected or not selected, independently of whether the molecule itself is selected or not. Operations that modify display models or colors work for selected atoms. To see this, choose the [Display] – [Spacefill] menu item. Then the both molecules are displayed with the space fill model because all atoms are initially selected. In the same way, if you choose the [Colors] – [Monochrome] menu item, the both molecules are colored white. A ‘Sel’ checkbox selects or disselects all atoms in each file. 

Let us next try a more detailed operation. Type ‘select *@2’ in the command line area and press Enter key. This command means to select all atoms contained in the file 2 (the usage of the [[Command_List#select|select command]] is summarized in the reference manual). Subsequently, choose the [Display] – [Cartoon] menu item. As a result, only the molecule 2 is displayed in the cartoon model. Furthermore select the [Colors] – [Structure] menu item, and each residue of the molecule 2 is colored according to its secondary structure type (see Figure 3). 

In order to reproduce the same view as that in Figure 3, first execute ‘reset’ command. It restores the position of the viewpoint and the transform of every file to the initial state. Note that the command line interface tries to complement a command word when the Tab key is pressed. If you enter ‘res’ to the command line and subsequently press the Tab key, the command ‘reset’ is automatically entered. Next set the both ‘Mouse’ checkboxes on, and execute ‘translate z 100’ command. This command means to translate the molecules along the z-axis by 100 angstroms.

[[File:tutorial4_4_fig3.png|thumb|Figure 3: An example of molecular images.|center|500px]]

== Displaying polygons ==
In addition to molecules, arbitrary shapes described by polygons can be read in and displayed together, where the polygon file is an XML file, whose document type is described in the section 6. Here, we use ’http://ef-site.hgc.jp/eF-site/jV/1yec.surface.gz’ as an example. This polygon file represents a molecular surface of the molecule 2 (1yec) and the surface is colored according to the electrostatic potential and the hydrophobicity. It is assumed that the current image is the same as that in Figure 3. Then, open the open-remote dialog by choosing the [File] – [Open – Remote] – [Polygon] menu item, enter the above URL to the text field at the top of the dialog, and click the 'OK' button. As a result, the polygon is loaded, displayed and assigned file ID 3. 

Note that the polygon is displayed at the different position from the molecule 2 since the molecule 2 is translated. However, because the polygon and the molecule 2 are described by the same coordinates in their files, their images can be exactly superposed by executing ‘fit 3 2’ from the command line, where the ‘fit’ command performs the copy of the transform matrix. Finally, the image in Figure 4 appears.

[[File:tutorial4_4_fig4.png|thumb|Figure4: An example of polygon images.|center|500px]]

You can control the transparency rate of polygons. Try ’set transparency 0.5’ from the command line, where 0.5 stands for 50% transparency. To restore the image, execute ‘reset transparency’ or ‘set transparency 0’. In the same sense as each atom of a molecule, each vertex of a polygon is assigned either selected or not selected. All vertices are selected in the initial state. Execute a command ’displayvertex off’ and all vertices become invisible. Next execute ’selectvertex within(10.0, 1&amp;*H@2)’, where this means to select vertices that exist within 10 angstroms from each atom that belongs to the first residue of the ‘H’ chain of the molecule 2. Subsequently execute ’displayvertex on’. As a result, only the selected vertices appear. The usage of the [[Command List#selectvertex|selectvertex command]] is summarized in the reference manual.

== Working with PDBMLplus ==
Functional site information on a molecule stored in PDBMLplus is available in jV3. Before trying this, let us close the molecule 2 and the polygon 3 to make the situation simple. Select the [File] – [Close] – [2. 1yec.pdb] and [File] – [Close] – [3. 1yec.surface.gz] menu items sequentially. Then execute a ‘reset’ command and the transform of the molecule 1 and the position of the viewpoint are initialized. 

Next, confirm that the ‘Mouse’ checkbox of the file 1 is checked, and try a ‘show pdbj’ command. The functional site information of the molecule ‘12as’ is read from the PDBMLplus and ‘type’ and ‘subtype’ keywords for each functional site are listed. These keywords can be used to select a set of atoms. For example, if a keyword ‘CATRES’ exists (probably it does), the command ‘select pdbj:CATRES’ selects the corresponding atoms. 

In addition, gene ontology information can be obtained from the PDBMLplus. The gene ontology information for the molecule 12as is displayed by the command ’show godata’. Similar operations can be applied to other external databases on the Internet provided that the external database supports the interface that jV3 requires. See the '[[Functional site information for molecules]]' section for details.

== Animation ==
The animation of molecules can be performed in jV3. The animation file takes the PDB format, where the MODEL line divides each frame. Let us open an animation file ’http://ef-site.hgc.jp/eF-site/jV/anim.pdb.gz’ as an example from the open-remote dialog shown by selecting the [File] – [Open – Remote] – [Animation] menu item. When an animation file is loaded to the application, the first frame is automatically displayed in the wire frame model. You can start the animation by using the animation-control dialog that is shown by choosing the [Options] – [Animation] menu item. The dialog provides operations such as start and stop of the animation, selection of the animation mode, and adjustment of the speed. Some [[GUI#Animation_control_dialog|sample figures]] of the dialog are shown in the GUI section.

== Saving your work ==
While in your work, you can create a script file that contains a set of commands that reproduces the current work by using the [File] – [Save] – [Script] menu item. The script file can be loaded by the [File] – [Open – Local] – [Script] menu item. On the other hand, the [File] – [Save] – [PDB] menu item enables to save a molecule to a PDB format file with the coordinates of the atoms being transformed according to the current image. Here, only one molecule must be selected and only selected atoms in the molecule are saved. The other two menu items in the [File] – [Save] menu, [PNG] and [JPEG], save the current screen image to an image file in the PNG and JPEG format, respectively. The created image file has the same size as that of the 3D-display panel in the application.

== Terminating the application ==
The application is terminated when the [File] – [Exit] menu item is chosen or the application window is closed by the way your operation system provides. You can also quit the application by executing ‘exit’ or ‘quit’ command.</text>
    <sha1>0a69ae1997800f282a08c11590a63bb5749b8f26</sha1>
  </revision>
  <revision>
    <id>586</id>
    <parentid>585</parentid>
    <timestamp>2015-02-23T07:15:32Z</timestamp>
    <contributor>
      <username>IMSsato</username>
      <id>4</id>
    </contributor>
    <comment>/* Working with PDBMLplus */</comment>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="12042" xml:space="preserve">{| style="float:right"
 |__TOC__
 |}
== Starting up ==
It is assumed that Java Runtime Environment has been properly installed. You can start up jV by downloading the binary distribution and running a start-up script contained in the distribution. Another way to use jV is to follow [http://ef-site.hgc.jp/eF-site/servlet/stable/jV.jnlp this link], which launch jV via Java Web Start technology.
Figure 1 shows the start-up screen. The window has a 3-panel structure, and the upper-left panel with the black background is a 3D image display area. The status of files that have been loaded to the application is shown in the upper-right panel and the lower panel is a command-input and a message-output area.
[[File:tutorial4_4_fig1.png|thumb|Figure 1: Start-up screen|center|500px]]

== Displaying molecules ==
If you are working in the environment that is getting on the Internet and know the PDB ID of the molecule that you want to display, the simplest way is as follows. A dialog shown in Figure 2 is opened by selecting the [File] – [Open – Remote] – [PDB ID] menu item. Enter a PDB ID '12as', for example, to the text field and click the 'OK' button, then the PDBML file is read through the Internet and the molecule is displayed. A molecule is displayed in a wire frame model with colored by atom type in the initial state.

[[File:tutorial4_4_fig2.png|thumb|Figure 2: Dialog to open the molecule specified by PDB ID|center|200px]]

Let us next attempt to load an arbitrary file on the Internet. Here we use 'http://ef-site.hgc.jp/eF-site/jV/1yec.pdb' as an example. The file is a conventional PDB file whose PDB ID is 1yec. In this case we choose the [File] – [Open – Remote] – [PDB] menu item. Then the open-remote dialog appears. Enter the above URL to the text field at the top of the dialog and click the 'OK' button and the molecule is read in and displayed. In jV, each molecule is displayed according to the space coordination described in its file. Therefore, when loading and displaying more than one molecule together, they can be viewed with an appropriate separation in some cases; however, they may be displayed far separately or may be overlapped depending on the combination. In any case, when adding a new file, the position of the viewpoint is automatically controlled for the whole to be displayed.

The coordinate system is the right hand system with the x-y plane being on the screen (the x-axis is a horizontal line with positive values to the right and the y-axis is a vertical line with positive values up). Although, the above examples are about operations for remote files, a PDB file on your local hard disk can also be opened from the [File] – [Open – Local] – [PDB] menu item.

== Operating molecules ==
Interactive mouse operations are possible for 3D images. By left-dragging the mouse on the 3D-display panel, molecules are rotated around the x-axis or y-axis. By left-dragging the mouse while holding the Shift key on the keyboard, molecules are translated along the z-axis. All mouse operations are as follows (as for the Mac OS X environment, the Command key + left-drag substitutes for the right-drag).

{| border="1"
 ! Mouse operations !! Actions
 |-
 | Left-drag || The image is rotated around the x (for a vertical motion) and y (for a horizontal motion) axes.
 |-
 | Right-drag || The image is translated on the x-y plane.
 |-
 | [Shift] + left-drag || The image is translated along the z-axis.
 |-
 | [Shift] + right-drag || The image is rotated around the z-axis.
 |-
 | [Alt or Ctrl] + left-drag || The z-clipping plane is shifted when [Option]-[Slab] is checked.
 |-
 | Left-click || An atom of the molecule displayed on the screen is picked.
 |}

In the upper-right panel in the application window (see Figure 3), the file names that have been loaded to the application are listed, where sequential integers are automatically assigned to the individual file. Each integer is a file ID that can be used to specify the file in the command line interface. In addition, three checkboxes are attached to each file. If you change the status of a ‘Disp’ checkbox, the corresponding molecule is switched to be displayed or not to be displayed. If you change the status of a ‘Mouse’ checkbox, the corresponding molecule is switched to be a target of the mouse operations or not. For example, set the both ‘Disp’ checkboxes on, and the both ‘Mouse’ checkboxes off. In this case, either molecule does not move against mouse operations. 

Subsequently set the ‘Mouse’ checkbox of file 1 on. In this case, mouse operations work for the molecule 1. Thus, each file is assigned either selected or not selected, and transform operations, such as rotation or translation, act only on selected files. On the other hand, every atom in a molecule is also assigned either selected or not selected, independently of whether the molecule itself is selected or not. Operations that modify display models or colors work for selected atoms. To see this, choose the [Display] – [Spacefill] menu item. Then the both molecules are displayed with the space fill model because all atoms are initially selected. In the same way, if you choose the [Colors] – [Monochrome] menu item, the both molecules are colored white. A ‘Sel’ checkbox selects or disselects all atoms in each file. 

Let us next try a more detailed operation. Type ‘select *@2’ in the command line area and press Enter key. This command means to select all atoms contained in the file 2 (the usage of the [[Command_List#select|select command]] is summarized in the reference manual). Subsequently, choose the [Display] – [Cartoon] menu item. As a result, only the molecule 2 is displayed in the cartoon model. Furthermore select the [Colors] – [Structure] menu item, and each residue of the molecule 2 is colored according to its secondary structure type (see Figure 3). 

In order to reproduce the same view as that in Figure 3, first execute ‘reset’ command. It restores the position of the viewpoint and the transform of every file to the initial state. Note that the command line interface tries to complement a command word when the Tab key is pressed. If you enter ‘res’ to the command line and subsequently press the Tab key, the command ‘reset’ is automatically entered. Next set the both ‘Mouse’ checkboxes on, and execute ‘translate z 100’ command. This command means to translate the molecules along the z-axis by 100 angstroms.

[[File:tutorial4_4_fig3.png|thumb|Figure 3: An example of molecular images.|center|500px]]

== Displaying polygons ==
In addition to molecules, arbitrary shapes described by polygons can be read in and displayed together, where the polygon file is an XML file, whose document type is described in the section 6. Here, we use ’http://ef-site.hgc.jp/eF-site/jV/1yec.surface.gz’ as an example. This polygon file represents a molecular surface of the molecule 2 (1yec) and the surface is colored according to the electrostatic potential and the hydrophobicity. It is assumed that the current image is the same as that in Figure 3. Then, open the open-remote dialog by choosing the [File] – [Open – Remote] – [Polygon] menu item, enter the above URL to the text field at the top of the dialog, and click the 'OK' button. As a result, the polygon is loaded, displayed and assigned file ID 3. 

Note that the polygon is displayed at the different position from the molecule 2 since the molecule 2 is translated. However, because the polygon and the molecule 2 are described by the same coordinates in their files, their images can be exactly superposed by executing ‘fit 3 2’ from the command line, where the ‘fit’ command performs the copy of the transform matrix. Finally, the image in Figure 4 appears.

[[File:tutorial4_4_fig4.png|thumb|Figure4: An example of polygon images.|center|500px]]

You can control the transparency rate of polygons. Try ’set transparency 0.5’ from the command line, where 0.5 stands for 50% transparency. To restore the image, execute ‘reset transparency’ or ‘set transparency 0’. In the same sense as each atom of a molecule, each vertex of a polygon is assigned either selected or not selected. All vertices are selected in the initial state. Execute a command ’displayvertex off’ and all vertices become invisible. Next execute ’selectvertex within(10.0, 1&amp;*H@2)’, where this means to select vertices that exist within 10 angstroms from each atom that belongs to the first residue of the ‘H’ chain of the molecule 2. Subsequently execute ’displayvertex on’. As a result, only the selected vertices appear. The usage of the [[Command List#selectvertex|selectvertex command]] is summarized in the reference manual.

== Working with PDBMLplus ==
Functional site information on a molecule stored in PDBMLplus is available in jV. Before trying this, let us close the molecule 2 and the polygon 3 to make the situation simple. Select the [File] – [Close] – [2. 1yec.pdb] and [File] – [Close] – [3. 1yec.surface.gz] menu items sequentially. Then execute a ‘reset’ command and the transform of the molecule 1 and the position of the viewpoint are initialized. 

Next, confirm that the ‘Mouse’ checkbox of the file 1 is checked, and try a ‘show pdbj’ command. The functional site information of the molecule ‘12as’ is read from the PDBMLplus and ‘type’ and ‘subtype’ keywords for each functional site are listed. These keywords can be used to select a set of atoms. For example, if a keyword ‘CATRES’ exists (probably it does), the command ‘select pdbj:CATRES’ selects the corresponding atoms. 

In addition, gene ontology information can be obtained from the PDBMLplus. The gene ontology information for the molecule 12as is displayed by the command ’show godata’. Similar operations can be applied to other external databases on the Internet provided that the external database supports the interface that jV requires. See the '[[Functional site information for molecules]]' section for details.

== Animation ==
The animation of molecules can be performed in jV3. The animation file takes the PDB format, where the MODEL line divides each frame. Let us open an animation file ’http://ef-site.hgc.jp/eF-site/jV/anim.pdb.gz’ as an example from the open-remote dialog shown by selecting the [File] – [Open – Remote] – [Animation] menu item. When an animation file is loaded to the application, the first frame is automatically displayed in the wire frame model. You can start the animation by using the animation-control dialog that is shown by choosing the [Options] – [Animation] menu item. The dialog provides operations such as start and stop of the animation, selection of the animation mode, and adjustment of the speed. Some [[GUI#Animation_control_dialog|sample figures]] of the dialog are shown in the GUI section.

== Saving your work ==
While in your work, you can create a script file that contains a set of commands that reproduces the current work by using the [File] – [Save] – [Script] menu item. The script file can be loaded by the [File] – [Open – Local] – [Script] menu item. On the other hand, the [File] – [Save] – [PDB] menu item enables to save a molecule to a PDB format file with the coordinates of the atoms being transformed according to the current image. Here, only one molecule must be selected and only selected atoms in the molecule are saved. The other two menu items in the [File] – [Save] menu, [PNG] and [JPEG], save the current screen image to an image file in the PNG and JPEG format, respectively. The created image file has the same size as that of the 3D-display panel in the application.

== Terminating the application ==
The application is terminated when the [File] – [Exit] menu item is chosen or the application window is closed by the way your operation system provides. You can also quit the application by executing ‘exit’ or ‘quit’ command.</text>
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  </revision>
  <revision>
    <id>587</id>
    <parentid>586</parentid>
    <timestamp>2015-02-23T07:15:55Z</timestamp>
    <contributor>
      <username>IMSsato</username>
      <id>4</id>
    </contributor>
    <comment>/* Animation */</comment>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="12041" xml:space="preserve">{| style="float:right"
 |__TOC__
 |}
== Starting up ==
It is assumed that Java Runtime Environment has been properly installed. You can start up jV by downloading the binary distribution and running a start-up script contained in the distribution. Another way to use jV is to follow [http://ef-site.hgc.jp/eF-site/servlet/stable/jV.jnlp this link], which launch jV via Java Web Start technology.
Figure 1 shows the start-up screen. The window has a 3-panel structure, and the upper-left panel with the black background is a 3D image display area. The status of files that have been loaded to the application is shown in the upper-right panel and the lower panel is a command-input and a message-output area.
[[File:tutorial4_4_fig1.png|thumb|Figure 1: Start-up screen|center|500px]]

== Displaying molecules ==
If you are working in the environment that is getting on the Internet and know the PDB ID of the molecule that you want to display, the simplest way is as follows. A dialog shown in Figure 2 is opened by selecting the [File] – [Open – Remote] – [PDB ID] menu item. Enter a PDB ID '12as', for example, to the text field and click the 'OK' button, then the PDBML file is read through the Internet and the molecule is displayed. A molecule is displayed in a wire frame model with colored by atom type in the initial state.

[[File:tutorial4_4_fig2.png|thumb|Figure 2: Dialog to open the molecule specified by PDB ID|center|200px]]

Let us next attempt to load an arbitrary file on the Internet. Here we use 'http://ef-site.hgc.jp/eF-site/jV/1yec.pdb' as an example. The file is a conventional PDB file whose PDB ID is 1yec. In this case we choose the [File] – [Open – Remote] – [PDB] menu item. Then the open-remote dialog appears. Enter the above URL to the text field at the top of the dialog and click the 'OK' button and the molecule is read in and displayed. In jV, each molecule is displayed according to the space coordination described in its file. Therefore, when loading and displaying more than one molecule together, they can be viewed with an appropriate separation in some cases; however, they may be displayed far separately or may be overlapped depending on the combination. In any case, when adding a new file, the position of the viewpoint is automatically controlled for the whole to be displayed.

The coordinate system is the right hand system with the x-y plane being on the screen (the x-axis is a horizontal line with positive values to the right and the y-axis is a vertical line with positive values up). Although, the above examples are about operations for remote files, a PDB file on your local hard disk can also be opened from the [File] – [Open – Local] – [PDB] menu item.

== Operating molecules ==
Interactive mouse operations are possible for 3D images. By left-dragging the mouse on the 3D-display panel, molecules are rotated around the x-axis or y-axis. By left-dragging the mouse while holding the Shift key on the keyboard, molecules are translated along the z-axis. All mouse operations are as follows (as for the Mac OS X environment, the Command key + left-drag substitutes for the right-drag).

{| border="1"
 ! Mouse operations !! Actions
 |-
 | Left-drag || The image is rotated around the x (for a vertical motion) and y (for a horizontal motion) axes.
 |-
 | Right-drag || The image is translated on the x-y plane.
 |-
 | [Shift] + left-drag || The image is translated along the z-axis.
 |-
 | [Shift] + right-drag || The image is rotated around the z-axis.
 |-
 | [Alt or Ctrl] + left-drag || The z-clipping plane is shifted when [Option]-[Slab] is checked.
 |-
 | Left-click || An atom of the molecule displayed on the screen is picked.
 |}

In the upper-right panel in the application window (see Figure 3), the file names that have been loaded to the application are listed, where sequential integers are automatically assigned to the individual file. Each integer is a file ID that can be used to specify the file in the command line interface. In addition, three checkboxes are attached to each file. If you change the status of a ‘Disp’ checkbox, the corresponding molecule is switched to be displayed or not to be displayed. If you change the status of a ‘Mouse’ checkbox, the corresponding molecule is switched to be a target of the mouse operations or not. For example, set the both ‘Disp’ checkboxes on, and the both ‘Mouse’ checkboxes off. In this case, either molecule does not move against mouse operations. 

Subsequently set the ‘Mouse’ checkbox of file 1 on. In this case, mouse operations work for the molecule 1. Thus, each file is assigned either selected or not selected, and transform operations, such as rotation or translation, act only on selected files. On the other hand, every atom in a molecule is also assigned either selected or not selected, independently of whether the molecule itself is selected or not. Operations that modify display models or colors work for selected atoms. To see this, choose the [Display] – [Spacefill] menu item. Then the both molecules are displayed with the space fill model because all atoms are initially selected. In the same way, if you choose the [Colors] – [Monochrome] menu item, the both molecules are colored white. A ‘Sel’ checkbox selects or disselects all atoms in each file. 

Let us next try a more detailed operation. Type ‘select *@2’ in the command line area and press Enter key. This command means to select all atoms contained in the file 2 (the usage of the [[Command_List#select|select command]] is summarized in the reference manual). Subsequently, choose the [Display] – [Cartoon] menu item. As a result, only the molecule 2 is displayed in the cartoon model. Furthermore select the [Colors] – [Structure] menu item, and each residue of the molecule 2 is colored according to its secondary structure type (see Figure 3). 

In order to reproduce the same view as that in Figure 3, first execute ‘reset’ command. It restores the position of the viewpoint and the transform of every file to the initial state. Note that the command line interface tries to complement a command word when the Tab key is pressed. If you enter ‘res’ to the command line and subsequently press the Tab key, the command ‘reset’ is automatically entered. Next set the both ‘Mouse’ checkboxes on, and execute ‘translate z 100’ command. This command means to translate the molecules along the z-axis by 100 angstroms.

[[File:tutorial4_4_fig3.png|thumb|Figure 3: An example of molecular images.|center|500px]]

== Displaying polygons ==
In addition to molecules, arbitrary shapes described by polygons can be read in and displayed together, where the polygon file is an XML file, whose document type is described in the section 6. Here, we use ’http://ef-site.hgc.jp/eF-site/jV/1yec.surface.gz’ as an example. This polygon file represents a molecular surface of the molecule 2 (1yec) and the surface is colored according to the electrostatic potential and the hydrophobicity. It is assumed that the current image is the same as that in Figure 3. Then, open the open-remote dialog by choosing the [File] – [Open – Remote] – [Polygon] menu item, enter the above URL to the text field at the top of the dialog, and click the 'OK' button. As a result, the polygon is loaded, displayed and assigned file ID 3. 

Note that the polygon is displayed at the different position from the molecule 2 since the molecule 2 is translated. However, because the polygon and the molecule 2 are described by the same coordinates in their files, their images can be exactly superposed by executing ‘fit 3 2’ from the command line, where the ‘fit’ command performs the copy of the transform matrix. Finally, the image in Figure 4 appears.

[[File:tutorial4_4_fig4.png|thumb|Figure4: An example of polygon images.|center|500px]]

You can control the transparency rate of polygons. Try ’set transparency 0.5’ from the command line, where 0.5 stands for 50% transparency. To restore the image, execute ‘reset transparency’ or ‘set transparency 0’. In the same sense as each atom of a molecule, each vertex of a polygon is assigned either selected or not selected. All vertices are selected in the initial state. Execute a command ’displayvertex off’ and all vertices become invisible. Next execute ’selectvertex within(10.0, 1&amp;*H@2)’, where this means to select vertices that exist within 10 angstroms from each atom that belongs to the first residue of the ‘H’ chain of the molecule 2. Subsequently execute ’displayvertex on’. As a result, only the selected vertices appear. The usage of the [[Command List#selectvertex|selectvertex command]] is summarized in the reference manual.

== Working with PDBMLplus ==
Functional site information on a molecule stored in PDBMLplus is available in jV. Before trying this, let us close the molecule 2 and the polygon 3 to make the situation simple. Select the [File] – [Close] – [2. 1yec.pdb] and [File] – [Close] – [3. 1yec.surface.gz] menu items sequentially. Then execute a ‘reset’ command and the transform of the molecule 1 and the position of the viewpoint are initialized. 

Next, confirm that the ‘Mouse’ checkbox of the file 1 is checked, and try a ‘show pdbj’ command. The functional site information of the molecule ‘12as’ is read from the PDBMLplus and ‘type’ and ‘subtype’ keywords for each functional site are listed. These keywords can be used to select a set of atoms. For example, if a keyword ‘CATRES’ exists (probably it does), the command ‘select pdbj:CATRES’ selects the corresponding atoms. 

In addition, gene ontology information can be obtained from the PDBMLplus. The gene ontology information for the molecule 12as is displayed by the command ’show godata’. Similar operations can be applied to other external databases on the Internet provided that the external database supports the interface that jV requires. See the '[[Functional site information for molecules]]' section for details.

== Animation ==
The animation of molecules can be performed in jV. The animation file takes the PDB format, where the MODEL line divides each frame. Let us open an animation file ’http://ef-site.hgc.jp/eF-site/jV/anim.pdb.gz’ as an example from the open-remote dialog shown by selecting the [File] – [Open – Remote] – [Animation] menu item. When an animation file is loaded to the application, the first frame is automatically displayed in the wire frame model. You can start the animation by using the animation-control dialog that is shown by choosing the [Options] – [Animation] menu item. The dialog provides operations such as start and stop of the animation, selection of the animation mode, and adjustment of the speed. Some [[GUI#Animation_control_dialog|sample figures]] of the dialog are shown in the GUI section.

== Saving your work ==
While in your work, you can create a script file that contains a set of commands that reproduces the current work by using the [File] – [Save] – [Script] menu item. The script file can be loaded by the [File] – [Open – Local] – [Script] menu item. On the other hand, the [File] – [Save] – [PDB] menu item enables to save a molecule to a PDB format file with the coordinates of the atoms being transformed according to the current image. Here, only one molecule must be selected and only selected atoms in the molecule are saved. The other two menu items in the [File] – [Save] menu, [PNG] and [JPEG], save the current screen image to an image file in the PNG and JPEG format, respectively. The created image file has the same size as that of the 3D-display panel in the application.

== Terminating the application ==
The application is terminated when the [File] – [Exit] menu item is chosen or the application window is closed by the way your operation system provides. You can also quit the application by executing ‘exit’ or ‘quit’ command.</text>
    <sha1>d8ca43b317aa791ed02976eef9e6c2c00c824684</sha1>
  </revision>
  <revision>
    <id>588</id>
    <parentid>587</parentid>
    <timestamp>2015-02-23T07:17:22Z</timestamp>
    <contributor>
      <username>IMSsato</username>
      <id>4</id>
    </contributor>
    <comment>/* Saving your work */</comment>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="12109" xml:space="preserve">{| style="float:right"
 |__TOC__
 |}
== Starting up ==
It is assumed that Java Runtime Environment has been properly installed. You can start up jV by downloading the binary distribution and running a start-up script contained in the distribution. Another way to use jV is to follow [http://ef-site.hgc.jp/eF-site/servlet/stable/jV.jnlp this link], which launch jV via Java Web Start technology.
Figure 1 shows the start-up screen. The window has a 3-panel structure, and the upper-left panel with the black background is a 3D image display area. The status of files that have been loaded to the application is shown in the upper-right panel and the lower panel is a command-input and a message-output area.
[[File:tutorial4_4_fig1.png|thumb|Figure 1: Start-up screen|center|500px]]

== Displaying molecules ==
If you are working in the environment that is getting on the Internet and know the PDB ID of the molecule that you want to display, the simplest way is as follows. A dialog shown in Figure 2 is opened by selecting the [File] – [Open – Remote] – [PDB ID] menu item. Enter a PDB ID '12as', for example, to the text field and click the 'OK' button, then the PDBML file is read through the Internet and the molecule is displayed. A molecule is displayed in a wire frame model with colored by atom type in the initial state.

[[File:tutorial4_4_fig2.png|thumb|Figure 2: Dialog to open the molecule specified by PDB ID|center|200px]]

Let us next attempt to load an arbitrary file on the Internet. Here we use 'http://ef-site.hgc.jp/eF-site/jV/1yec.pdb' as an example. The file is a conventional PDB file whose PDB ID is 1yec. In this case we choose the [File] – [Open – Remote] – [PDB] menu item. Then the open-remote dialog appears. Enter the above URL to the text field at the top of the dialog and click the 'OK' button and the molecule is read in and displayed. In jV, each molecule is displayed according to the space coordination described in its file. Therefore, when loading and displaying more than one molecule together, they can be viewed with an appropriate separation in some cases; however, they may be displayed far separately or may be overlapped depending on the combination. In any case, when adding a new file, the position of the viewpoint is automatically controlled for the whole to be displayed.

The coordinate system is the right hand system with the x-y plane being on the screen (the x-axis is a horizontal line with positive values to the right and the y-axis is a vertical line with positive values up). Although, the above examples are about operations for remote files, a PDB file on your local hard disk can also be opened from the [File] – [Open – Local] – [PDB] menu item.

== Operating molecules ==
Interactive mouse operations are possible for 3D images. By left-dragging the mouse on the 3D-display panel, molecules are rotated around the x-axis or y-axis. By left-dragging the mouse while holding the Shift key on the keyboard, molecules are translated along the z-axis. All mouse operations are as follows (as for the Mac OS X environment, the Command key + left-drag substitutes for the right-drag).

{| border="1"
 ! Mouse operations !! Actions
 |-
 | Left-drag || The image is rotated around the x (for a vertical motion) and y (for a horizontal motion) axes.
 |-
 | Right-drag || The image is translated on the x-y plane.
 |-
 | [Shift] + left-drag || The image is translated along the z-axis.
 |-
 | [Shift] + right-drag || The image is rotated around the z-axis.
 |-
 | [Alt or Ctrl] + left-drag || The z-clipping plane is shifted when [Option]-[Slab] is checked.
 |-
 | Left-click || An atom of the molecule displayed on the screen is picked.
 |}

In the upper-right panel in the application window (see Figure 3), the file names that have been loaded to the application are listed, where sequential integers are automatically assigned to the individual file. Each integer is a file ID that can be used to specify the file in the command line interface. In addition, three checkboxes are attached to each file. If you change the status of a ‘Disp’ checkbox, the corresponding molecule is switched to be displayed or not to be displayed. If you change the status of a ‘Mouse’ checkbox, the corresponding molecule is switched to be a target of the mouse operations or not. For example, set the both ‘Disp’ checkboxes on, and the both ‘Mouse’ checkboxes off. In this case, either molecule does not move against mouse operations. 

Subsequently set the ‘Mouse’ checkbox of file 1 on. In this case, mouse operations work for the molecule 1. Thus, each file is assigned either selected or not selected, and transform operations, such as rotation or translation, act only on selected files. On the other hand, every atom in a molecule is also assigned either selected or not selected, independently of whether the molecule itself is selected or not. Operations that modify display models or colors work for selected atoms. To see this, choose the [Display] – [Spacefill] menu item. Then the both molecules are displayed with the space fill model because all atoms are initially selected. In the same way, if you choose the [Colors] – [Monochrome] menu item, the both molecules are colored white. A ‘Sel’ checkbox selects or disselects all atoms in each file. 

Let us next try a more detailed operation. Type ‘select *@2’ in the command line area and press Enter key. This command means to select all atoms contained in the file 2 (the usage of the [[Command_List#select|select command]] is summarized in the reference manual). Subsequently, choose the [Display] – [Cartoon] menu item. As a result, only the molecule 2 is displayed in the cartoon model. Furthermore select the [Colors] – [Structure] menu item, and each residue of the molecule 2 is colored according to its secondary structure type (see Figure 3). 

In order to reproduce the same view as that in Figure 3, first execute ‘reset’ command. It restores the position of the viewpoint and the transform of every file to the initial state. Note that the command line interface tries to complement a command word when the Tab key is pressed. If you enter ‘res’ to the command line and subsequently press the Tab key, the command ‘reset’ is automatically entered. Next set the both ‘Mouse’ checkboxes on, and execute ‘translate z 100’ command. This command means to translate the molecules along the z-axis by 100 angstroms.

[[File:tutorial4_4_fig3.png|thumb|Figure 3: An example of molecular images.|center|500px]]

== Displaying polygons ==
In addition to molecules, arbitrary shapes described by polygons can be read in and displayed together, where the polygon file is an XML file, whose document type is described in the section 6. Here, we use ’http://ef-site.hgc.jp/eF-site/jV/1yec.surface.gz’ as an example. This polygon file represents a molecular surface of the molecule 2 (1yec) and the surface is colored according to the electrostatic potential and the hydrophobicity. It is assumed that the current image is the same as that in Figure 3. Then, open the open-remote dialog by choosing the [File] – [Open – Remote] – [Polygon] menu item, enter the above URL to the text field at the top of the dialog, and click the 'OK' button. As a result, the polygon is loaded, displayed and assigned file ID 3. 

Note that the polygon is displayed at the different position from the molecule 2 since the molecule 2 is translated. However, because the polygon and the molecule 2 are described by the same coordinates in their files, their images can be exactly superposed by executing ‘fit 3 2’ from the command line, where the ‘fit’ command performs the copy of the transform matrix. Finally, the image in Figure 4 appears.

[[File:tutorial4_4_fig4.png|thumb|Figure4: An example of polygon images.|center|500px]]

You can control the transparency rate of polygons. Try ’set transparency 0.5’ from the command line, where 0.5 stands for 50% transparency. To restore the image, execute ‘reset transparency’ or ‘set transparency 0’. In the same sense as each atom of a molecule, each vertex of a polygon is assigned either selected or not selected. All vertices are selected in the initial state. Execute a command ’displayvertex off’ and all vertices become invisible. Next execute ’selectvertex within(10.0, 1&amp;*H@2)’, where this means to select vertices that exist within 10 angstroms from each atom that belongs to the first residue of the ‘H’ chain of the molecule 2. Subsequently execute ’displayvertex on’. As a result, only the selected vertices appear. The usage of the [[Command List#selectvertex|selectvertex command]] is summarized in the reference manual.

== Working with PDBMLplus ==
Functional site information on a molecule stored in PDBMLplus is available in jV. Before trying this, let us close the molecule 2 and the polygon 3 to make the situation simple. Select the [File] – [Close] – [2. 1yec.pdb] and [File] – [Close] – [3. 1yec.surface.gz] menu items sequentially. Then execute a ‘reset’ command and the transform of the molecule 1 and the position of the viewpoint are initialized. 

Next, confirm that the ‘Mouse’ checkbox of the file 1 is checked, and try a ‘show pdbj’ command. The functional site information of the molecule ‘12as’ is read from the PDBMLplus and ‘type’ and ‘subtype’ keywords for each functional site are listed. These keywords can be used to select a set of atoms. For example, if a keyword ‘CATRES’ exists (probably it does), the command ‘select pdbj:CATRES’ selects the corresponding atoms. 

In addition, gene ontology information can be obtained from the PDBMLplus. The gene ontology information for the molecule 12as is displayed by the command ’show godata’. Similar operations can be applied to other external databases on the Internet provided that the external database supports the interface that jV requires. See the '[[Functional site information for molecules]]' section for details.

== Animation ==
The animation of molecules can be performed in jV. The animation file takes the PDB format, where the MODEL line divides each frame. Let us open an animation file ’http://ef-site.hgc.jp/eF-site/jV/anim.pdb.gz’ as an example from the open-remote dialog shown by selecting the [File] – [Open – Remote] – [Animation] menu item. When an animation file is loaded to the application, the first frame is automatically displayed in the wire frame model. You can start the animation by using the animation-control dialog that is shown by choosing the [Options] – [Animation] menu item. The dialog provides operations such as start and stop of the animation, selection of the animation mode, and adjustment of the speed. Some [[GUI#Animation_control_dialog|sample figures]] of the dialog are shown in the GUI section.

== Saving your work ==
While in your work, you can create a script file that contains a set of commands that reproduces the current work by using the [File] – [Save] – [Script] menu item. The script file can be loaded by the [File] – [Open – Local] – [Script] menu item. On the other hand, the [File] – [Save] – [mmCIF] menu item and [File] – [Save] – [PDB] menu item enable to save a molecule to a mmCIF and PDB format file, respectively, with the coordinates of the atoms being transformed according to the current image. Here, only one molecule must be selected and only selected atoms in the molecule are saved. The other two menu items in the [File] – [Save] menu, [PNG] and [JPEG], save the current screen image to an image file in the PNG and JPEG format, respectively. The created image file has the same size as that of the 3D-display panel in the application.

== Terminating the application ==
The application is terminated when the [File] – [Exit] menu item is chosen or the application window is closed by the way your operation system provides. You can also quit the application by executing ‘exit’ or ‘quit’ command.</text>
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  </revision>
  <revision>
    <id>589</id>
    <parentid>588</parentid>
    <timestamp>2015-02-23T07:17:54Z</timestamp>
    <contributor>
      <username>IMSsato</username>
      <id>4</id>
    </contributor>
    <comment>/* Terminating the application */</comment>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="12109" xml:space="preserve">{| style="float:right"
 |__TOC__
 |}
== Starting up ==
It is assumed that Java Runtime Environment has been properly installed. You can start up jV by downloading the binary distribution and running a start-up script contained in the distribution. Another way to use jV is to follow [http://ef-site.hgc.jp/eF-site/servlet/stable/jV.jnlp this link], which launch jV via Java Web Start technology.
Figure 1 shows the start-up screen. The window has a 3-panel structure, and the upper-left panel with the black background is a 3D image display area. The status of files that have been loaded to the application is shown in the upper-right panel and the lower panel is a command-input and a message-output area.
[[File:tutorial4_4_fig1.png|thumb|Figure 1: Start-up screen|center|500px]]

== Displaying molecules ==
If you are working in the environment that is getting on the Internet and know the PDB ID of the molecule that you want to display, the simplest way is as follows. A dialog shown in Figure 2 is opened by selecting the [File] – [Open – Remote] – [PDB ID] menu item. Enter a PDB ID '12as', for example, to the text field and click the 'OK' button, then the PDBML file is read through the Internet and the molecule is displayed. A molecule is displayed in a wire frame model with colored by atom type in the initial state.

[[File:tutorial4_4_fig2.png|thumb|Figure 2: Dialog to open the molecule specified by PDB ID|center|200px]]

Let us next attempt to load an arbitrary file on the Internet. Here we use 'http://ef-site.hgc.jp/eF-site/jV/1yec.pdb' as an example. The file is a conventional PDB file whose PDB ID is 1yec. In this case we choose the [File] – [Open – Remote] – [PDB] menu item. Then the open-remote dialog appears. Enter the above URL to the text field at the top of the dialog and click the 'OK' button and the molecule is read in and displayed. In jV, each molecule is displayed according to the space coordination described in its file. Therefore, when loading and displaying more than one molecule together, they can be viewed with an appropriate separation in some cases; however, they may be displayed far separately or may be overlapped depending on the combination. In any case, when adding a new file, the position of the viewpoint is automatically controlled for the whole to be displayed.

The coordinate system is the right hand system with the x-y plane being on the screen (the x-axis is a horizontal line with positive values to the right and the y-axis is a vertical line with positive values up). Although, the above examples are about operations for remote files, a PDB file on your local hard disk can also be opened from the [File] – [Open – Local] – [PDB] menu item.

== Operating molecules ==
Interactive mouse operations are possible for 3D images. By left-dragging the mouse on the 3D-display panel, molecules are rotated around the x-axis or y-axis. By left-dragging the mouse while holding the Shift key on the keyboard, molecules are translated along the z-axis. All mouse operations are as follows (as for the Mac OS X environment, the Command key + left-drag substitutes for the right-drag).

{| border="1"
 ! Mouse operations !! Actions
 |-
 | Left-drag || The image is rotated around the x (for a vertical motion) and y (for a horizontal motion) axes.
 |-
 | Right-drag || The image is translated on the x-y plane.
 |-
 | [Shift] + left-drag || The image is translated along the z-axis.
 |-
 | [Shift] + right-drag || The image is rotated around the z-axis.
 |-
 | [Alt or Ctrl] + left-drag || The z-clipping plane is shifted when [Option]-[Slab] is checked.
 |-
 | Left-click || An atom of the molecule displayed on the screen is picked.
 |}

In the upper-right panel in the application window (see Figure 3), the file names that have been loaded to the application are listed, where sequential integers are automatically assigned to the individual file. Each integer is a file ID that can be used to specify the file in the command line interface. In addition, three checkboxes are attached to each file. If you change the status of a ‘Disp’ checkbox, the corresponding molecule is switched to be displayed or not to be displayed. If you change the status of a ‘Mouse’ checkbox, the corresponding molecule is switched to be a target of the mouse operations or not. For example, set the both ‘Disp’ checkboxes on, and the both ‘Mouse’ checkboxes off. In this case, either molecule does not move against mouse operations. 

Subsequently set the ‘Mouse’ checkbox of file 1 on. In this case, mouse operations work for the molecule 1. Thus, each file is assigned either selected or not selected, and transform operations, such as rotation or translation, act only on selected files. On the other hand, every atom in a molecule is also assigned either selected or not selected, independently of whether the molecule itself is selected or not. Operations that modify display models or colors work for selected atoms. To see this, choose the [Display] – [Spacefill] menu item. Then the both molecules are displayed with the space fill model because all atoms are initially selected. In the same way, if you choose the [Colors] – [Monochrome] menu item, the both molecules are colored white. A ‘Sel’ checkbox selects or disselects all atoms in each file. 

Let us next try a more detailed operation. Type ‘select *@2’ in the command line area and press Enter key. This command means to select all atoms contained in the file 2 (the usage of the [[Command_List#select|select command]] is summarized in the reference manual). Subsequently, choose the [Display] – [Cartoon] menu item. As a result, only the molecule 2 is displayed in the cartoon model. Furthermore select the [Colors] – [Structure] menu item, and each residue of the molecule 2 is colored according to its secondary structure type (see Figure 3). 

In order to reproduce the same view as that in Figure 3, first execute ‘reset’ command. It restores the position of the viewpoint and the transform of every file to the initial state. Note that the command line interface tries to complement a command word when the Tab key is pressed. If you enter ‘res’ to the command line and subsequently press the Tab key, the command ‘reset’ is automatically entered. Next set the both ‘Mouse’ checkboxes on, and execute ‘translate z 100’ command. This command means to translate the molecules along the z-axis by 100 angstroms.

[[File:tutorial4_4_fig3.png|thumb|Figure 3: An example of molecular images.|center|500px]]

== Displaying polygons ==
In addition to molecules, arbitrary shapes described by polygons can be read in and displayed together, where the polygon file is an XML file, whose document type is described in the section 6. Here, we use ’http://ef-site.hgc.jp/eF-site/jV/1yec.surface.gz’ as an example. This polygon file represents a molecular surface of the molecule 2 (1yec) and the surface is colored according to the electrostatic potential and the hydrophobicity. It is assumed that the current image is the same as that in Figure 3. Then, open the open-remote dialog by choosing the [File] – [Open – Remote] – [Polygon] menu item, enter the above URL to the text field at the top of the dialog, and click the 'OK' button. As a result, the polygon is loaded, displayed and assigned file ID 3. 

Note that the polygon is displayed at the different position from the molecule 2 since the molecule 2 is translated. However, because the polygon and the molecule 2 are described by the same coordinates in their files, their images can be exactly superposed by executing ‘fit 3 2’ from the command line, where the ‘fit’ command performs the copy of the transform matrix. Finally, the image in Figure 4 appears.

[[File:tutorial4_4_fig4.png|thumb|Figure4: An example of polygon images.|center|500px]]

You can control the transparency rate of polygons. Try ’set transparency 0.5’ from the command line, where 0.5 stands for 50% transparency. To restore the image, execute ‘reset transparency’ or ‘set transparency 0’. In the same sense as each atom of a molecule, each vertex of a polygon is assigned either selected or not selected. All vertices are selected in the initial state. Execute a command ’displayvertex off’ and all vertices become invisible. Next execute ’selectvertex within(10.0, 1&amp;*H@2)’, where this means to select vertices that exist within 10 angstroms from each atom that belongs to the first residue of the ‘H’ chain of the molecule 2. Subsequently execute ’displayvertex on’. As a result, only the selected vertices appear. The usage of the [[Command List#selectvertex|selectvertex command]] is summarized in the reference manual.

== Working with PDBMLplus ==
Functional site information on a molecule stored in PDBMLplus is available in jV. Before trying this, let us close the molecule 2 and the polygon 3 to make the situation simple. Select the [File] – [Close] – [2. 1yec.pdb] and [File] – [Close] – [3. 1yec.surface.gz] menu items sequentially. Then execute a ‘reset’ command and the transform of the molecule 1 and the position of the viewpoint are initialized. 

Next, confirm that the ‘Mouse’ checkbox of the file 1 is checked, and try a ‘show pdbj’ command. The functional site information of the molecule ‘12as’ is read from the PDBMLplus and ‘type’ and ‘subtype’ keywords for each functional site are listed. These keywords can be used to select a set of atoms. For example, if a keyword ‘CATRES’ exists (probably it does), the command ‘select pdbj:CATRES’ selects the corresponding atoms. 

In addition, gene ontology information can be obtained from the PDBMLplus. The gene ontology information for the molecule 12as is displayed by the command ’show godata’. Similar operations can be applied to other external databases on the Internet provided that the external database supports the interface that jV requires. See the '[[Functional site information for molecules]]' section for details.

== Animation ==
The animation of molecules can be performed in jV. The animation file takes the PDB format, where the MODEL line divides each frame. Let us open an animation file ’http://ef-site.hgc.jp/eF-site/jV/anim.pdb.gz’ as an example from the open-remote dialog shown by selecting the [File] – [Open – Remote] – [Animation] menu item. When an animation file is loaded to the application, the first frame is automatically displayed in the wire frame model. You can start the animation by using the animation-control dialog that is shown by choosing the [Options] – [Animation] menu item. The dialog provides operations such as start and stop of the animation, selection of the animation mode, and adjustment of the speed. Some [[GUI#Animation_control_dialog|sample figures]] of the dialog are shown in the GUI section.

== Saving your work ==
While in your work, you can create a script file that contains a set of commands that reproduces the current work by using the [File] – [Save] – [Script] menu item. The script file can be loaded by the [File] – [Open – Local] – [Script] menu item. On the other hand, the [File] – [Save] – [mmCIF] menu item and [File] – [Save] – [PDB] menu item enable to save a molecule to a mmCIF and PDB format file, respectively, with the coordinates of the atoms being transformed according to the current image. Here, only one molecule must be selected and only selected atoms in the molecule are saved. The other two menu items in the [File] – [Save] menu, [PNG] and [JPEG], save the current screen image to an image file in the PNG and JPEG format, respectively. The created image file has the same size as that of the 3D-display panel in the application.

== Terminating the application ==
The application is terminated when the [File] – [Exit] menu item is chosen or the application window is closed by the way your operating system provides. You can also quit the application by executing ‘exit’ or ‘quit’ command.</text>
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<page arvcontinue="20140430014530|554">
  <title>GUI</title>
  <ns>0</ns>
  <id>30</id>
  <revision>
    <id>590</id>
    <parentid>437</parentid>
    <timestamp>2015-02-23T07:29:22Z</timestamp>
    <contributor>
      <username>IMSsato</username>
      <id>4</id>
    </contributor>
    <comment>/* Menu bar */</comment>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="9421" xml:space="preserve">{| style="float:right"
 |__TOC__
 |}
== Menu bar ==
The organization of the menu bar and the function of its components are shown below.

;1) File menu
{| class="wikitable" border="1"
 |-
 | style="background-color:gainsboro" colspan="2" | Component
 | style="background-color:gainsboro" | Function
 |-
 | rowspan="7" | Open - Local
 | mmCIF
 | A local mmCIF file is opened.
 |-
 | PDBML
 | A local PDBML file is opened.
 |-
 | PDB
 | A local PDB file is opened.
 |-
 | Polygon
 | A local polygon file is opened.
 |-
 | Polygon CGO
 | A local polygon CGO file is opened.
 |-
 | Script 
 | A local script file is opened.
 |-
 | Animation
 | A local animation file is opened.
 |-
 | rowspan="9" | Open-Remote
 | PDB ID
 | A PDBML file at the PDBML FTP site is opened.
 |-
 | eF-site ID
 | A set of molecular and polygon files stored in eF-site database are opened.
 |-
 | mmCIF
 | A remote mmCIF file is opened.
 |-
 | PDBML
 | A remote PDBML file is opened.
 |-
 | PDB
 | A remote PDB file is opened.
 |-
 | Polygon
 | A remote polygon file is opened.
 |- 
 | Polygon CGO
 | A remote polygon CGO file is opened.
 |- 
 | Script
 | A remote script file is opened.
 |-
 | Animation
 | A remote animation file is opened.
 |-
 | colspan="2" | Information
 | Information about the selected files are shown.
 |-
 | colspan="2" | Close
 | The specified file is closed.
 |-
 | rowspan="5" | Save
 | mmCIF
 | A mmCIF format file that contains the current atom coordinates is created.
 |-
 | PDB
 | A PDB format file that contains the current atom coordinates is created.
 |-
 | Script
 | A script by which the present condition is reproduced is created.
 |-
 | PNG
 | The current image is saved as PNG.
 |-
 | JPEG
 | The current image is saved as JPEG.
 |-
 | colspan="2" | Exit
 | The application is terminated.
 |}

;2) Display menu
{| class="wikitable" border="1"
 |-
 | style="background-color:gainsboro" | Component
 | style="background-color:gainsboro" | Function
 |-
 | Wireframe
 | The selected atoms are displayed in a wire frame model.
 |-
 | Backbone
 | The selected atoms are displayed in a backbone model.
 |-
 | Sticks
 | The selected atoms are displayed in a stick model.
 |-
 | Spacefill
 | The selected atoms are displayed in a space-fill model.
 |-
 | Ball&amp;Stick
 | The selected atoms are displayed in a ball &amp; stick model.
 |-
 | Ribbons
 | The selected atoms are displayed in a ribbon model.
 |-
 | Cartoon
 | The selected atoms are displayed in a cartoon model.
 |}

;3) Colors menu
{| class="wikitable" border="1"
 |-
 | style="background-color:gainsboro" | Component
 | style="background-color:gainsboro" | Function
 |-
 | Monochrome
 | The selected atoms are colored in white.
 |-
 | CPK
 | The selected atoms are colored by CPK color scheme.
 |-
 | Shapely
 | The selected atoms are colored by the color scheme in which each amino acid and nucleic acid is assigned a unique color according to the amino acid and nucleic acid properties.
 |-
 | Group
 | The atoms of every chain are drawn as a smooth spectrum from red (N-terminal of the molecule) to blue (C-terminal).
 |-
 | Chain
 | The selected atoms are colored by the color scheme in which each chain is assigned a unique color.
 |-
 | Temperature
 | The selected atoms are drawn as a smooth spectrum from red (high value) to blue (low value) according to the value of the temperature factor.
 |-
 | Structure
 | The secondary structures are colored by the color scheme in which each secondary structure is assigned a unique color.
 |-
 | Charge
 | The selected atoms are drawn as a smooth spectrum from blue (positive) to red (negative) according to the charge.
 |-
 | Amino
 | The selected atoms are colored by the color scheme in which each amino acid is assigned a unique color.
 |}

;4) Options menu
{| class="wikitable" border="1"
 |-
 | style="background-color:gainsboro" colspan="2" | Component
 | style="background-color:gainsboro" | Function
 |-
 | colspan="2" | Hetero Atoms
 | Users can choose whether the heterogeneous atoms described by ‘HETATM’ in PDB files are selected or not.
 |-
 | colspan="2" | Hydrogens
 | Users can choose whether the hydrogen atoms are selected or not.
 |-
 | colspan="2" | Slab
 | Users can choose whether the z-clipping plane is located on the default position or is shifted.
 |-
 | rowspan="6" | Stereo
 | Off
 | Disables stereo display.
 |-
 | Wall-Eyed
 | Enables side-by-side wall-eyed stereo viewing.
 |-
 | Cross-Eyed
 | Enables side-by-side cross-eyed stereo viewing.
 |-
 | Red-Blue
 | Enables red-blue anaglyph 3D rendering.
 |-
 | Red-Cyan
 | Enables red-cyan anaglyph 3D rendering.
 |-
 | Red-Green
 | Enables red-green anaglyph 3D rendering.
 |-
 | colspan="2" | Load To Center
 | Users can choose whether a new image is added to the center of screen or not when a new file is opened.
 |-
 | rowspan="6" | Pick
 | Off
 | The mouse-pick is disabled. 
 |-
 | Ident
 | The atom and residue names, their serial numbers, chain identifier and file ID of the object picked by mouse-click are represented.
 |-
 | Coordinates
 | The atom and residue names, their serial numbers, chain identifier, file ID and coordinate of the object picked by mouse-click are represented.
 |-
 | Distance
 | The distance between the first and second clicked atoms is calculated and shown.
 |-
 | Center
 | The center of rotation and window are transferred to the clicked position.
 |-
 | Select
 | Only clicked files are operated.
 |- 
 | colspan="2" | Animation
 | The animation control dialog is opened.
 |}

;5) Help menu
{| class="wikitable" border="1"
 |-
 | style="background-color:gainsboro" | Component
 | style="background-color:gainsboro" | Function
 |-
 | About jV || Information about this application is shown.
 |-
 | Open Manual || A manual page is opened with a web browser.
 |}

== Open-Remode dialog ==
;1) URL with parameters
Selecting [PDBML], [PDB], [Polygon], [Script] or [Animation] menu item in the [File] – [Open – Remote] menu opens the open-remote dialog that can handle a URL with parameters. For example, Figure 5 shows a dialog opened by the [File] – [Open – Remote] – [PDBML] menu item.

[[File:Fig5.jpg|thumb|Figure5: The open-remote dialog|center|400px]]

When ‘Add’ button is clicked, a new parameter line is appended in the table at the center of the dialog. Figure 6 shows an example of a URL with one parameter. By clicking the ‘Add’ button the necessary number of times, you can attach multiple parameters. When ‘Remove’ button is clicked, a highlighted line in the parameter table is removed. When ‘Clear’ button is clicked, all parameters are removed.

[[File:Fig6.jpg|thumb|Figure6: Example of a URL with a parameter|center|400px]]

;2)'type' column and mouse pick
The ‘type’ column in the parameter table is selected from the follows.

{| class="wikitable" border="1"
 |-
 | style="background-color:gainsboro" | type
 | style="background-color:gainsboro" | values
 | style="background-color:gainsboro" | mouse pick
 |-
 | text || arbitrary value || does not work
 |-
 | atom ID || atom ID || work
 |-
 | atom || set of chain ID, residue ID and atom ID || work
 |-
 | residue || set of chain ID and residue ID || work
 |-
 | orig_coords || atom coordinates written in the molecule file || work
 |-
 | curr_coords || atom coordinates currently displayed || work
 |}

For the case of a type to which mouse pick works, selecting an atom in the screen by mouse pick sets the corresponding value to the ‘value’ column in a highlighted line in the parameter table. The value of the ‘delimiter’ field is used to delimit atom’s x, y, and z coordinate.

;3) Saving and loading the configuration
By clicking the ‘save’ button, a file chooser dialog appears and the current configuration can be saved to a file. In the same way, a configuration can be loaded by clicking the ‘load’ button. The contents of a configuration file are in XML format as follows.

 &lt;?xml version="1.0"?&gt;
 &amp;nbsp;
 &amp;nbsp;
 &lt;remote_file url="http://example.com"&gt;
  &lt;params attach="true" coordinates_delimiter=","&gt;
    &lt;param name="param1" value="value1" type="text"/&gt;
  &lt;/params&gt;
 &lt;/remote_file&gt;

;4) Copy of the transform
When a file ID that currently exists is entered to the ‘fit to’ field, the transform of the newly opened file is set identical to that of the specified file.

;5) Execution
When the ‘OK’ button is clicked, a new file is loaded and the dialog is closed. When you use ‘Submit’ button, on the other hand, the dialog remains visible even after a new file is loaded.

== Animation control dialog ==
The animation control dialog is visible only if [Options] - [Animation] menu is checked. When there is no animation file loaded, the animation control dialog is as Figure 7. If some animation files are opened, the animation control dialog is altered according to the number of the files. Figure 8 indicates the dialog in the presence of two files.

[[File:Tutorial_fig7.jpg|thumb|Figure7: The animation control dialog in the absence of files.|center|400px]]

[[File:Tutorial_fig8.jpg|thumb|Figure8: The animation control dialog in the presence of two files.|center|400px]]

Users can select which files are controlled by their checkbox. The frame position and playback and stop of the animation can be controlled individually to each file. The playback-speed and the selection of ‘loop’ and ‘swing’ modes are common for all files.</text>
    <sha1>3dec866a54cf1f5a06a636cedb45574f2675f9c2</sha1>
  </revision>
  <revision>
    <id>591</id>
    <parentid>590</parentid>
    <timestamp>2015-02-23T07:39:01Z</timestamp>
    <contributor>
      <username>IMSsato</username>
      <id>4</id>
    </contributor>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="10721" xml:space="preserve">{| style="float:right"
 |__TOC__
 |}
== Menu bar ==
The organization of the menu bar and the function of its components are shown below.

;1) File menu
{| class="wikitable" border="1"
 |-
 | style="background-color:gainsboro" colspan="2" | Component
 | style="background-color:gainsboro" | Function
 |-
 | rowspan="7" | Open - Local
 | mmCIF
 | A local mmCIF file is opened.
 |-
 | PDBML
 | A local PDBML file is opened.
 |-
 | PDB
 | A local PDB file is opened.
 |-
 | Polygon
 | A local polygon file is opened.
 |-
 | Polygon CGO
 | A local polygon CGO file is opened.
 |-
 | Script 
 | A local script file is opened.
 |-
 | Animation
 | A local animation file is opened.
 |-
 | rowspan="9" | Open-Remote
 | PDB ID
 | A PDBML file at the PDBML FTP site is opened.
 |-
 | eF-site ID
 | A set of molecular and polygon files stored in eF-site database are opened.
 |-
 | mmCIF
 | A remote mmCIF file is opened.
 |-
 | PDBML
 | A remote PDBML file is opened.
 |-
 | PDB
 | A remote PDB file is opened.
 |-
 | Polygon
 | A remote polygon file is opened.
 |- 
 | Polygon CGO
 | A remote polygon CGO file is opened.
 |- 
 | Script
 | A remote script file is opened.
 |-
 | Animation
 | A remote animation file is opened.
 |-
 | colspan="2" | Information
 | Information about the selected files are shown.
 |-
 | colspan="2" | Close
 | The specified file is closed.
 |-
 | rowspan="5" | Save
 | mmCIF
 | A mmCIF format file that contains the current atom coordinates is created.
 |-
 | PDB
 | A PDB format file that contains the current atom coordinates is created.
 |-
 | Script
 | A script by which the present condition is reproduced is created.
 |-
 | PNG
 | The current image is saved as PNG.
 |-
 | JPEG
 | The current image is saved as JPEG.
 |-
 | colspan="2" | Exit
 | The application is terminated.
 |}

;2) Display menu
{| class="wikitable" border="1"
 |-
 | style="background-color:gainsboro" | Component
 | style="background-color:gainsboro" | Function
 |-
 | Wireframe
 | The selected atoms are displayed in a wire frame model.
 |-
 | Backbone
 | The selected atoms are displayed in a backbone model.
 |-
 | Sticks
 | The selected atoms are displayed in a stick model.
 |-
 | Spacefill
 | The selected atoms are displayed in a space-fill model.
 |-
 | Ball&amp;Stick
 | The selected atoms are displayed in a ball &amp; stick model.
 |-
 | Ribbons
 | The selected atoms are displayed in a ribbon model.
 |-
 | Cartoon
 | The selected atoms are displayed in a cartoon model.
 |}

;3) Colors menu
{| class="wikitable" border="1"
 |-
 | style="background-color:gainsboro" | Component
 | style="background-color:gainsboro" | Function
 |-
 | Monochrome
 | The selected atoms are colored in white.
 |-
 | CPK
 | The selected atoms are colored by CPK color scheme.
 |-
 | Shapely
 | The selected atoms are colored by the color scheme in which each amino acid and nucleic acid is assigned a unique color according to the amino acid and nucleic acid properties.
 |-
 | Group
 | The atoms of every chain are drawn as a smooth spectrum from red (N-terminal of the molecule) to blue (C-terminal).
 |-
 | Chain
 | The selected atoms are colored by the color scheme in which each chain is assigned a unique color.
 |-
 | Temperature
 | The selected atoms are drawn as a smooth spectrum from red (high value) to blue (low value) according to the value of the temperature factor.
 |-
 | Structure
 | The secondary structures are colored by the color scheme in which each secondary structure is assigned a unique color.
 |-
 | Charge
 | The selected atoms are drawn as a smooth spectrum from blue (positive) to red (negative) according to the charge.
 |-
 | Amino
 | The selected atoms are colored by the color scheme in which each amino acid is assigned a unique color.
 |}

;4) Options menu
{| class="wikitable" border="1"
 |-
 | style="background-color:gainsboro" colspan="2" | Component
 | style="background-color:gainsboro" | Function
 |-
 | colspan="2" | Hetero Atoms
 | Users can choose whether the heterogeneous atoms described by ‘HETATM’ in PDB files are selected or not.
 |-
 | colspan="2" | Hydrogens
 | Users can choose whether the hydrogen atoms are selected or not.
 |-
 | colspan="2" | Slab
 | Users can choose whether the z-clipping plane is located on the default position or is shifted.
 |-
 | rowspan="6" | Stereo
 | Off
 | Disables stereo display.
 |-
 | Wall-Eyed
 | Enables side-by-side wall-eyed stereo viewing.
 |-
 | Cross-Eyed
 | Enables side-by-side cross-eyed stereo viewing.
 |-
 | Red-Blue
 | Enables red-blue anaglyph 3D rendering.
 |-
 | Red-Cyan
 | Enables red-cyan anaglyph 3D rendering.
 |-
 | Red-Green
 | Enables red-green anaglyph 3D rendering.
 |-
 | colspan="2" | Load To Center
 | Users can choose whether a new image is added to the center of screen or not when a new file is opened.
 |-
 | rowspan="6" | Pick
 | Off
 | The mouse-pick is disabled. 
 |-
 | Ident
 | The atom and residue names, their serial numbers, chain identifier and file ID of the object picked by mouse-click are represented.
 |-
 | Coordinates
 | The atom and residue names, their serial numbers, chain identifier, file ID and coordinate of the object picked by mouse-click are represented.
 |-
 | Distance
 | The distance between the first and second clicked atoms is calculated and shown.
 |-
 | Center
 | The center of rotation and window are transferred to the clicked position.
 |-
 | Select
 | Only clicked files are operated.
 |- 
 | colspan="2" | Animation
 | The animation control dialog is opened.
 |}

;5) Help menu
{| class="wikitable" border="1"
 |-
 | style="background-color:gainsboro" | Component
 | style="background-color:gainsboro" | Function
 |-
 | About jV || Information about this application is shown.
 |-
 | Open Manual || A manual page is opened with a web browser.
 |}

== Open-Local dialog ==

Selecting each menu item in the [File] – [Open – Local] menu opens the open-local dialog. For example, Figure 5 shows a dialog opened by the [File] – [Open – Local] – [mmCIF] menu item.

[[File:tutorial4_4_fig5.png|thumb|Figure5: The open-local dialog|center|400px]]

Users can enter a local file path at the ‘Enter file’ text filed, or select a file by using a file chooser dialog that your operating system provides by clicking the ‘Browse…’ button. If a file ID that is already opened in the application is specified at the ‘fit’ text field, the transform of the newly opened file is set identical to that of the specified file. A biomolecule structure can be specified by entering assembly ID at the 'biomolecule' text field. For a biomolecule structure, a distinct model ID is assigned to each transform operation, which is listed by 'show information' command. When a filter expression is entered at the ‘filter’ text field, only atoms that matches a given filter are loaded. The filter takes any atom expressions except some keywords (bonded, helix, sheet, turn, within and pdbj:). The atom expression should be double-quoted or enclosed in a parenthesis when it contains spaces.

== Open-Remode dialog ==
;1) URL with parameters
Selecting [mmCIF], [PDBML], [PDB], [Polygon], [Script] or [Animation] menu item in the [File] – [Open – Remote] menu opens the open-remote dialog that can handle a URL with parameters. For example, Figure 6 shows a dialog opened by the [File] – [Open – Remote] – [mmCIF] menu item.

[[File:tutorial4_4_fig6.png|thumb|Figure6: The open-remote dialog|center|400px]]

When ‘Add’ button is clicked, a new parameter line is appended in the table at the center of the dialog. Figure 6 shows an example of a URL with one parameter. By clicking the ‘Add’ button the necessary number of times, you can attach multiple parameters. When ‘Remove’ button is clicked, a highlighted line in the parameter table is removed. When ‘Clear’ button is clicked, all parameters are removed.

[[File:tutorial4_4_fig7.png|thumb|Figure7: Example of a URL with a parameter|center|400px]]

;2)'type' column and mouse pick
The ‘type’ column in the parameter table is selected from the follows.

{| class="wikitable" border="1"
 |-
 | style="background-color:gainsboro" | type
 | style="background-color:gainsboro" | values
 | style="background-color:gainsboro" | mouse pick
 |-
 | text || arbitrary value || does not work
 |-
 | atom ID || atom ID || work
 |-
 | atom || set of chain ID, residue ID and atom ID || work
 |-
 | residue || set of chain ID and residue ID || work
 |-
 | orig_coords || atom coordinates written in the molecule file || work
 |-
 | curr_coords || atom coordinates currently displayed || work
 |}

For the case of a type to which mouse pick works, selecting an atom in the screen by mouse pick sets the corresponding value to the ‘value’ column in a highlighted line in the parameter table. The value of the ‘delimiter’ field is used to delimit atom’s x, y, and z coordinate.

;3) Saving and loading the configuration
By clicking the ‘save’ button, a file chooser dialog appears and the current configuration can be saved to a file. In the same way, a configuration can be loaded by clicking the ‘load’ button. The contents of a configuration file are in XML format as follows.

 &lt;?xml version="1.0"?&gt;
 &amp;nbsp;
 &amp;nbsp;
 &lt;remote_file url="http://example.com"&gt;
  &lt;params attach="true" coordinates_delimiter=","&gt;
    &lt;param name="param1" value="value1" type="text"/&gt;
  &lt;/params&gt;
 &lt;/remote_file&gt;

;4) fit, biomolecule and filter
Three text fields entitled fit, biomolecule and filter work the same way as opening a local file. How to use them is described at the previous ‘Open-Local dialog’ section.

;5) Execution
When the ‘OK’ button is clicked, a new file is loaded and the dialog is closed. When you use ‘Submit’ button, on the other hand, the dialog remains visible even after a new file is loaded.

== Animation control dialog ==
The animation control dialog is visible only if [Options] - [Animation] menu is checked. When there is no animation file loaded, the animation control dialog is as Figure 7. If some animation files are opened, the animation control dialog is altered according to the number of the files. Figure 8 indicates the dialog in the presence of two files.

[[File:tutorial4_4_fig8.png|thumb|Figure8: The animation control dialog in the absence of files.|center|400px]]

[[File:tutorial4_4_fig9.png|thumb|Figure9: The animation control dialog in the presence of two files.|center|400px]]

Users can select which files are controlled by their checkbox. The frame position and playback and stop of the animation can be controlled individually to each file. The playback-speed and the selection of ‘loop’ and ‘swing’ modes are common for all files.</text>
    <sha1>9f102b23bde6431f8fff10c300ec9f67ba19e822</sha1>
  </revision>
  <revision>
    <id>594</id>
    <parentid>591</parentid>
    <timestamp>2015-02-24T02:49:51Z</timestamp>
    <contributor>
      <username>IMSsato</username>
      <id>4</id>
    </contributor>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="10794" xml:space="preserve">{| style="float:right"
 |__TOC__
 |}
== Menu bar ==
The organization of the menu bar and the function of its components are shown below.

;1) File menu
{| class="wikitable" border="1"
 |-
 | style="background-color:gainsboro" colspan="2" | Component
 | style="background-color:gainsboro" | Function
 |-
 | rowspan="7" | Open - Local
 | mmCIF
 | A local mmCIF file is opened.
 |-
 | PDBML
 | A local PDBML file is opened.
 |-
 | PDB
 | A local PDB file is opened.
 |-
 | Polygon
 | A local polygon file is opened.
 |-
 | Polygon CGO
 | A local polygon CGO file is opened.
 |-
 | Script 
 | A local script file is opened.
 |-
 | Animation
 | A local animation file is opened.
 |-
 | rowspan="9" | Open-Remote
 | PDB ID
 | A PDBML file at the PDBML FTP site is opened.
 |-
 | eF-site ID
 | A set of molecular and polygon files stored in eF-site database are opened.
 |-
 | mmCIF
 | A remote mmCIF file is opened.
 |-
 | PDBML
 | A remote PDBML file is opened.
 |-
 | PDB
 | A remote PDB file is opened.
 |-
 | Polygon
 | A remote polygon file is opened.
 |- 
 | Polygon CGO
 | A remote polygon CGO file is opened.
 |- 
 | Script
 | A remote script file is opened.
 |-
 | Animation
 | A remote animation file is opened.
 |-
 | colspan="2" | Information
 | Information about the selected files are shown.
 |-
 | colspan="2" | Close
 | The specified file is closed.
 |-
 | rowspan="5" | Save
 | mmCIF
 | A mmCIF format file that contains the current atom coordinates is created.
 |-
 | PDB
 | A PDB format file that contains the current atom coordinates is created.
 |-
 | Script
 | A script by which the present condition is reproduced is created.
 |-
 | PNG
 | The current image is saved as PNG.
 |-
 | JPEG
 | The current image is saved as JPEG.
 |-
 | colspan="2" | Exit
 | The application is terminated.
 |}

;2) Display menu
{| class="wikitable" border="1"
 |-
 | style="background-color:gainsboro" | Component
 | style="background-color:gainsboro" | Function
 |-
 | Wireframe
 | The selected atoms are displayed in a wire frame model.
 |-
 | Backbone
 | The selected atoms are displayed in a backbone model.
 |-
 | Sticks
 | The selected atoms are displayed in a stick model.
 |-
 | Spacefill
 | The selected atoms are displayed in a space-fill model.
 |-
 | Ball&amp;Stick
 | The selected atoms are displayed in a ball &amp; stick model.
 |-
 | Ribbons
 | The selected atoms are displayed in a ribbon model.
 |-
 | Cartoon
 | The selected atoms are displayed in a cartoon model.
 |}

;3) Colors menu
{| class="wikitable" border="1"
 |-
 | style="background-color:gainsboro" | Component
 | style="background-color:gainsboro" | Function
 |-
 | Monochrome
 | The selected atoms are colored in white.
 |-
 | CPK
 | The selected atoms are colored by CPK color scheme.
 |-
 | Shapely
 | The selected atoms are colored by the color scheme in which each amino acid and nucleic acid is assigned a unique color according to the amino acid and nucleic acid properties.
 |-
 | Group
 | The atoms of every chain are drawn as a smooth spectrum from red (N-terminal of the molecule) to blue (C-terminal).
 |-
 | Chain
 | The selected atoms are colored by the color scheme in which each chain is assigned a unique color.
 |-
 | Temperature
 | The selected atoms are drawn as a smooth spectrum from red (high value) to blue (low value) according to the value of the temperature factor.
 |-
 | Structure
 | The secondary structures are colored by the color scheme in which each secondary structure is assigned a unique color.
 |-
 | Charge
 | The selected atoms are drawn as a smooth spectrum from blue (positive) to red (negative) according to the charge.
 |-
 | Amino
 | The selected atoms are colored by the color scheme in which each amino acid is assigned a unique color.
 |}

;4) Options menu
{| class="wikitable" border="1"
 |-
 | style="background-color:gainsboro" colspan="2" | Component
 | style="background-color:gainsboro" | Function
 |-
 | colspan="2" | Hetero Atoms
 | Users can choose whether the heterogeneous atoms described by ‘HETATM’ in PDB files are selected or not.
 |-
 | colspan="2" | Hydrogens
 | Users can choose whether the hydrogen atoms are selected or not.
 |-
 | colspan="2" | Slab
 | Users can choose whether the z-clipping plane is located on the default position or is shifted.
 |-
 | rowspan="6" | Stereo
 | Off
 | Disables stereo display.
 |-
 | Wall-Eyed
 | Enables side-by-side wall-eyed stereo viewing.
 |-
 | Cross-Eyed
 | Enables side-by-side cross-eyed stereo viewing.
 |-
 | Red-Blue
 | Enables red-blue anaglyph 3D rendering.
 |-
 | Red-Cyan
 | Enables red-cyan anaglyph 3D rendering.
 |-
 | Red-Green
 | Enables red-green anaglyph 3D rendering.
 |-
 | colspan="2" | Load To Center
 | Users can choose whether a new image is added to the center of screen or not when a new file is opened.
 |-
 | rowspan="6" | Pick
 | Off
 | The mouse-pick is disabled. 
 |-
 | Ident
 | The atom and residue names, their serial numbers, chain identifier and file ID of the object picked by mouse-click are represented.
 |-
 | Coordinates
 | The atom and residue names, their serial numbers, chain identifier, file ID and coordinate of the object picked by mouse-click are represented.
 |-
 | Distance
 | The distance between the first and second clicked atoms is calculated and shown.
 |-
 | Center
 | The center of rotation and window are transferred to the clicked position.
 |-
 | Select
 | Only clicked files are operated.
 |- 
 | colspan="2" | Animation
 | The animation control dialog is opened.
 |}

;5) Help menu
{| class="wikitable" border="1"
 |-
 | style="background-color:gainsboro" | Component
 | style="background-color:gainsboro" | Function
 |-
 | About jV || Information about this application is shown.
 |-
 | Open Manual || A manual page is opened with a web browser.
 |}

== Open-Local dialog ==

Selecting each menu item in the [File] – [Open – Local] menu opens the open-local dialog. For example, Figure 5 shows a dialog opened by the [File] – [Open – Local] – [mmCIF] menu item.

[[File:tutorial4_4_fig5.png|thumb|Figure5: The open-local dialog|center|400px]]

Users can enter a local file path at the ‘Enter file’ text filed, or select a file by using a file chooser dialog that your operating system provides by clicking the ‘Browse…’ button. If a file ID that is already opened in the application is specified at the ‘fit’ text field, the transform of the newly opened file is set identical to that of the specified file. A biomolecule structure can be specified by entering assembly ID at the 'biomolecule' text field. For a biomolecule structure, a distinct model ID is assigned to each transform operation, which is listed by 'show information' command. Note that the biomolecule parameter is not available for flat PDB files. When a filter expression is entered at the ‘filter’ text field, only atoms that matches a given filter are loaded. The filter takes any atom expressions except some keywords (bonded, helix, sheet, turn, within and pdbj:). The atom expression should be double-quoted or enclosed in a parenthesis when it contains spaces.

== Open-Remode dialog ==
;1) URL with parameters
Selecting [mmCIF], [PDBML], [PDB], [Polygon], [Script] or [Animation] menu item in the [File] – [Open – Remote] menu opens the open-remote dialog that can handle a URL with parameters. For example, Figure 6 shows a dialog opened by the [File] – [Open – Remote] – [mmCIF] menu item.

[[File:tutorial4_4_fig6.png|thumb|Figure6: The open-remote dialog|center|400px]]

When ‘Add’ button is clicked, a new parameter line is appended in the table at the center of the dialog. Figure 6 shows an example of a URL with one parameter. By clicking the ‘Add’ button the necessary number of times, you can attach multiple parameters. When ‘Remove’ button is clicked, a highlighted line in the parameter table is removed. When ‘Clear’ button is clicked, all parameters are removed.

[[File:tutorial4_4_fig7.png|thumb|Figure7: Example of a URL with a parameter|center|400px]]

;2)'type' column and mouse pick
The ‘type’ column in the parameter table is selected from the follows.

{| class="wikitable" border="1"
 |-
 | style="background-color:gainsboro" | type
 | style="background-color:gainsboro" | values
 | style="background-color:gainsboro" | mouse pick
 |-
 | text || arbitrary value || does not work
 |-
 | atom ID || atom ID || work
 |-
 | atom || set of chain ID, residue ID and atom ID || work
 |-
 | residue || set of chain ID and residue ID || work
 |-
 | orig_coords || atom coordinates written in the molecule file || work
 |-
 | curr_coords || atom coordinates currently displayed || work
 |}

For the case of a type to which mouse pick works, selecting an atom in the screen by mouse pick sets the corresponding value to the ‘value’ column in a highlighted line in the parameter table. The value of the ‘delimiter’ field is used to delimit atom’s x, y, and z coordinate.

;3) Saving and loading the configuration
By clicking the ‘save’ button, a file chooser dialog appears and the current configuration can be saved to a file. In the same way, a configuration can be loaded by clicking the ‘load’ button. The contents of a configuration file are in XML format as follows.

 &lt;?xml version="1.0"?&gt;
 &amp;nbsp;
 &amp;nbsp;
 &lt;remote_file url="http://example.com"&gt;
  &lt;params attach="true" coordinates_delimiter=","&gt;
    &lt;param name="param1" value="value1" type="text"/&gt;
  &lt;/params&gt;
 &lt;/remote_file&gt;

;4) fit, biomolecule and filter
Three text fields entitled fit, biomolecule and filter work the same way as opening a local file. How to use them is described at the previous ‘Open-Local dialog’ section.

;5) Execution
When the ‘OK’ button is clicked, a new file is loaded and the dialog is closed. When you use ‘Submit’ button, on the other hand, the dialog remains visible even after a new file is loaded.

== Animation control dialog ==
The animation control dialog is visible only if [Options] - [Animation] menu is checked. When there is no animation file loaded, the animation control dialog is as Figure 7. If some animation files are opened, the animation control dialog is altered according to the number of the files. Figure 8 indicates the dialog in the presence of two files.

[[File:tutorial4_4_fig8.png|thumb|Figure8: The animation control dialog in the absence of files.|center|400px]]

[[File:tutorial4_4_fig9.png|thumb|Figure9: The animation control dialog in the presence of two files.|center|400px]]

Users can select which files are controlled by their checkbox. The frame position and playback and stop of the animation can be controlled individually to each file. The playback-speed and the selection of ‘loop’ and ‘swing’ modes are common for all files.</text>
    <sha1>36eae653ddc50c0a09adfa7f7b2f99bf70b6b71e</sha1>
  </revision>
</page>
<page arvcontinue="20140430014530|554">
  <title>Functional site information for molecules</title>
  <ns>0</ns>
  <id>36</id>
  <revision>
    <id>592</id>
    <parentid>439</parentid>
    <timestamp>2015-02-23T07:42:57Z</timestamp>
    <contributor>
      <username>IMSsato</username>
      <id>4</id>
    </contributor>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="5592" xml:space="preserve">A simple XML file is defined in jV in order to describe functional sites of a molecule. If an external database server that returns this type of XML file is prepared, you can let jV read the file through the network and obtain the functional site information. An example of the XML file is as follows.

 &lt;?xml version=”1.0” ?&gt;
 &amp;nbsp;
 &lt;site_list&gt;
  &lt;site id=”CATRES1” db=”CATRES” category=”catalytic”
        description=”a catalytic site defined by CATRES, Medline 98100076”&gt;
    &lt;region chain_id=”A” beg_seq_id=”100” end_seq_id=”100”/&gt;
    &lt;region chain_id=”A” beg_seq_id=”46” end_seq_id=”46”/&gt;
    &lt;region chain_id=”A” beg_seq_id=”116” end_seq_id=”116”/&gt;
  &lt;/site&gt;
  &lt;site id=”ASN” db=”pdb_hetatom” category=”binding”
        description=”ASPARAGINE binding site”&gt;
    &lt;region chain_id=”A” beg_seq_id=”48” end_seq_id=”48”/&gt;
    &lt;region chain_id=”A” beg_seq_id=”72” end_seq_id=”74”/&gt;
  &lt;/site&gt;
  &lt;site id=”0006529” db=”godata” category=”biological_process”
        description=”asparagine biosynthesis”&gt;
    &lt;region chain_id=”A”/&gt;
  &lt;/site&gt;
  &lt;site id=”0016874” db=”godata” category=”molecular_function”
        description=”ligase activity”&gt;
    &lt;region chain_id=”A”/&gt;
  &lt;/site&gt;
 &lt;/site_list&gt;

The XML schema file that defines the document type of the above XML file is published at http://ef-site.hgc.jp/eF-site/schema/sitelist10.xsd. When a text file ‘properties.txt’ exists in the same directory as the application jar file, jV reads the file as a configuration file for the application. The current configuration file, which is attached to the binary distribution, contains a set of URL necessary to connect to the PDBMLplus and eF-site system as follows.

 # PDBML files are retrieved from the following site.
 pdbml_noatom=ftp://ftp.pdbj.org/XML/all-noatom/
 pdbml_extatom=ftp://ftp.pdbj.org/XML/all-extatom/
 pdbml_plus=http://service.pdbj.org/mine/pdbmlplus/noatom/
 &amp;nbsp;
 # eF-site data are retrieved from the following site.
 efsite=http://ef-site.hgc.jp/eF-site/

If a database server that returns the functional site file is prepared, its URL should be appended to the configuration file. Because one functional site file is assumed to exist for one PDB ID, the URL written in the configuration file depends on the PDB ID. Therefore, the URL is represented with the use of substitute characters {0}, {1}, {2} and {3} that are substituted by each column of the PDB ID sequentially. An example is as follows.

 # works with my database.
 mydb=http://myhost.jp/mydb/jv3/{0}{1}{2}{3}_jv.xml

Here, the property name, ‘mydb’ in the above example, is arbitrary. Note that a PDB ID {0}{1}{2}{3} is substituted as lowercases and available protocols are http:, ftp: and file:. For simplicity, it is assumed that only one molecule file that corresponds to the above example XML file is opened in the application. Then functional site information can be displayed by the ‘show’ command as follows.

 jV&gt; show site mydb
 File 1:
  db           category
  -------------------------------
  CATRES       catalytic
  pdb_hetatom  binding
  godata       biological_process
  godata       molcular_function
 jV&gt; show site mydb:CATRES
 File 1:
  id=CATRES1  category=catalytic  region=A:100-100,A:46-46,A:116-116
      description=a catalytic site defined by CATRES, Medline 98100076
 jV&gt; show site mydb:pdb_hetatom:binding
 File 1:
  id=ASN  category=binding  region=A:48-48,A:72-74 
      description=ASPARAGINE binding site
 jV&gt; show site mydb:godata
 File 1:
  id=0006529  category=biological_process  region=A
      description=asparagine biosynthesis
  id=0016874  category=molecular_function  region=A
      description=ligase activity
 jV&gt; show site mydb:godata:molecular_function
 File 1:
  id=0016874  category=molecular_function  region=A
      description=ligase activity
 jV&gt;

With a similar syntax, the ‘select’ command can be used to select the relevant set of atoms. To demonstrate the operations described in this section, let us add a following line to the configuration file ‘properties.txt’.

 ex=http://ef-site.hgc.jp/jv3site/servlet/Site?pdb={0}{1}{2}{3}

The above URL provides functional site information whose contents are equivalent to those of PDBMLplus for all PDB. To reload the configuration file, quit the application (if it runs) and restart it. Then open the molecule ‘1yec’ as an example. To do this, you can use [File] – [Open – Remote] – [PDB ID] menu item as in the '[[Tutorials#Displaying_molecules|Displaying molecules]]' section, or equivalently execute ‘load ftp 1yec’ in the command line. Subsequently, execute ‘show site ex’ and the following keywords will be listed (the contents may change in the future).

 jV&gt; show site ex
 File 1:
  db           category
  ---------------------
  prosite      prosite
  pdb_hetatom  binding

Detail site information can be shown as follows.

 jV&gt; show site ex:prosite
 File 1:
  id=PS00290  db=prosite  category=prosite  region=L:192-198
    description=Immunoglobulins and major histocompatibility complex proteins signature. [FY]-{L}-C-x-[VA]-{LC}-H

Atoms in the region ‘L:192-198’ can be selected with a similar syntax.

 jV&gt; select ex:prosite
 56 Atoms Selected.

In the same way, the following atom selections are possible.

 jV&gt; select ex:pdb_hetatom
 298 Atoms Selected.
 jV&gt; select ex:
 354 Atoms Selected.

Here the last command selects both regions specified by ‘prosite’ and ‘pdb_hetatom’ keywords, respectively.</text>
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</page>
<page arvcontinue="20140430014530|554">
  <title>Trouble shooting</title>
  <ns>0</ns>
  <id>48</id>
  <revision>
    <id>600</id>
    <parentid>546</parentid>
    <timestamp>2015-08-26T01:34:19Z</timestamp>
    <contributor>
      <username>Cudo29</username>
      <id>5</id>
    </contributor>
    <comment>/* The key modifier for mouse drag action is not available in Mac 10.10 + Firefox */ added.</comment>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="6878" xml:space="preserve">{| style="left"
 |__TOC__
 |}

== Latest environment is recommended ==

Using latest version of Java and jV is recommended to avoid problems.
Following issues are known for older versions of them.

* jV applet fails to start on JRE 1.6.0_15 and 1.6.0_16 by a certificate error.
* Java's file-cache functionality causes a problem on JRE 1.6.0_15 and 1.6.0_16.
* jV applet fails to start on JRE 1.6.0_21 because of a conflict with next-generation Java Plug-in.
* jV of versions eariler than 4.1 do not run as an applet on recent Mac OS.

=== JRE 1.7 is required on Mac OS 10.7 or later ===

Apple-provided Java SE 6 does not support Java applets now.
The following changes were made at Java 1.6.0_37[http://support.apple.com/kb/HT5493]:

# All the java plug-ins for every web browser provided from Apple Inc. will be removed.
# The "Java Preferences" application will be removed.

If you access a web page containing a Java applet and click on the region labeled "Missing plug-in",
you can go to a download page of JRE 1.7.
When JRE 1.7 is installed, you can use Java applets.
It is reported, however, that Java Web Start fails to start with JRE 1.7 in some cases,
and the issue is not resolved yet.

== JOGL library conflict ==

If you cannot start jV as a standalone program or view jV applets due to a failure of locating the JOGL library, try the followings.

===clear cached files===

Previously cached JOGL files may be the cause of a problem
(on JRE 1.6.0_15 and 1.6.0_16, cached JOGL files conflict with newer files placed on the server).
The following steps show how to clear cached files. 

;1) Open Java Control Panel
:In Windows, double-click the [Java] icon located at Control Panel. In Mac OS, click the [Java] icon in System Preferences.

;2) Open Java Cache Viewer
:On the Java Control Panel, select [General] tab and click [View...] button at the section of Temporary Internet Files, then Java Cache Viewer window appears.
:[[File:Java_cache_viewer.png|600px]]

;3) Remove cache files
:In Java Cache Viewer, you can switch categories with [Show:] pull-down list. Remove all cache files in [Applications] and [Resources] categories.

In old versions of Mac OS, Java Preferences utility is offered instead of Java Control Panel.
In such cases, use Java Preferences as follows.
;1) Open the Java Preferences window
:Double-click the [Java Preferences] icon, then the Java Preferences window appears. The place of [Java Preferences] depends on the version of Mac OS as following:
:{|style="border:1px solid gray;border-collapse:collapse"
!style="border:1px solid gray;padding:0 0.5em;background-color:lightyellow"|Mac OS X version
!style="border:1px solid gray;padding:0 0.5em;background-color:lightyellow"|place
|-
|style="border:1px solid gray;padding:0 0.5em"|10.4
|style="border:1px solid gray;padding:0 0.5em"|[Applications]-[Utilities]-[Java]-[J2SE 5.0]
|-
|style="border:1px solid gray;padding:0 0.5em"|10.5 (before installing Java for Mac OS X 10.5 Update 4)
|style="border:1px solid gray;padding:0 0.5em"|[Applications]-[Utilities]-[Java]
|-
|style="border:1px solid gray;padding:0 0.5em"|10.5 (after installing Java for Mac OS X 10.5 Update 4 or later)
|style="border:1px solid gray;padding:0 0.5em"|[Applications]-[Utilities]
|-
|style="border:1px solid gray;padding:0 0.5em"|10.6
|style="border:1px solid gray;padding:0 0.5em"|[Applications]-[Utilities]
|}
:The contents of the [Java Preferences] differ for the version of Mac OS. In case 10.4, use the [General] tab, which is default displayed. In case 10.5 or later, click to display [Network] tab.

;2) Press 'Delete Files...' button
:The [Delete Temporary Files] window, which asks which items are to remove, will be opened.

:[[File:Javacache_del_en.png]]

;3) Leave all the checkboxs on and click 'OK' button.

;4) In some case, restoring the Java environment to the default may be also required. 
:To do it, click "Restore Defaults" button in the [General] tab.

===remove local JOGL library===

Older versions of jV asked users to install JOGL libraries locally;
however, manual installation of JOGL is not necessary for recent jV.
Locally-installed JOGL libraries of different version cause conflicts with
recent distributions of jV and should be removed.
JOGL library files are different between operating systems.

'''Mac OS X'''

Open the [Macintosh HD]-[Library]-[Java]-[Extensions] folder.
If some of the following files

* jogl.jar
* gluegen-rt.jar
* libjogl.jnilib
* libjogl_awt.jnilib
* libjogl_cg.jnilib
* libgluegen-rt.jnilib

exist in the folder, remove them.
Here, this operation requires root privilege.

'''Windows'''

Files that should be removed are as follows.

* &lt;JRE&gt;\lib\ext\jogl.jar
* &lt;JRE&gt;\lib\ext\gluegen-rt.jar
* &lt;JRE&gt;\bin\jogl.dll
* &lt;JRE&gt;\bin\jogl_cg.dll
* &lt;JRE&gt;\bin\jogl_awt.dll
* &lt;JRE&gt;\bin\gluegen-rt.dll

Here, &lt;JRE&gt; denotes the folder that JRE has been installed; typically &lt;JRE&gt;=C:\Program Files\Java\jre6.

'''Linux'''

Files that should be removed are as follows.

* &lt;JRE&gt;/lib/ext/jogl.jar
* &lt;JRE&gt;/lib/ext/gluegen-rt.jar
* &lt;JRE&gt;/lib/&lt;arch&gt;/libjogl.so
* &lt;JRE&gt;/lib/&lt;arch&gt;/libjogl_cg.so
* &lt;JRE&gt;/lib/&lt;arch&gt;/libjogl_awt.so
* &lt;JRE&gt;/lib/&lt;arch&gt;/libjogl_drihack.so
* &lt;JRE&gt;/lib/&lt;arch&gt;/libgluegen-rt.so

Here, &lt;JRE&gt; denotes the directory that JRE has been installed; typically &lt;JRE&gt;=/usr/java/jdk1.6.0_17/jre,
and &lt;arch&gt; the processor architecture such as &lt;arch&gt;=i386.

==Check the environment variable==
In some environment, especially Windows, you can't launch the stand alone jar version of jV.
If you fell on such trouble, please check the environment variant includes the path of java.

;The name of environment variant
* PATH
* JAVA_HOME
;The value that should be added
:The path of java(.exe). e.g: C:¥Program Files (x86)¥java¥jre7¥bin

==Radio button/Pull down menu to switch displaying manner doesn't work==
When you browse jV applet pages such as in PDBj Mine and the radio button or pull down menu doesn't work,
please try following procedures.

# Close the jV applet page.
# Terminate all running Java Applet application.
# Open the page again.

==The key modifier for mouse drag action is not available in Mac 10.10 + Firefox==
;Environment
:Mac 10.10 + Firefox 37.0b1-40.0.3 
;Phenomenon
:The modifier is ignored for mouse actions with key modifier such as Shift+drag (zoom in/out) and Command+drag (translate), so the behaviors of these actions are same as simple drag (rotate).
;Solution
At the date of 26 August 2015, we are waiting for the correction of Firefox. The alternative way to such action with command is available. You can zoom in/out by zoom command and translate by translate command. Or you can use another web browser such as Safari and Opera. The stand alone version is also available.
;References
* [https://bugzilla.mozilla.org/show_bug.cgi?id=1197709 1197709 – MouseEvent's key-modifier flags are always false in Java applets on Mac]</text>
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  </revision>
</page>
<page arvcontinue="20151001071243|604">
  <title>Main Page</title>
  <ns>0</ns>
  <id>1</id>
  <revision>
    <id>604</id>
    <parentid>601</parentid>
    <timestamp>2015-10-01T07:12:43Z</timestamp>
    <contributor>
      <username>IMSsato</username>
      <id>4</id>
    </contributor>
    <comment>/* Start up */</comment>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="6312" xml:space="preserve">&lt;big&gt;'''Welcome to jV wiki.'''&lt;/big&gt;

jV (formerly known as PDBjViewer) is a program to display molecular graphics of protein and nucleic acids. 
jV supports the following features:
* jV can read and display PDBML files, the canonical XML format for the Protein Data Bank.
* Of course, jV can read and display the traditional PDB format files, too.
* RasMol-like usability.
* jV can process more than one molecules.
* jV can display polygons specified by XML. ([http://www.pdbj.org/jv/polygonSchema XML Schema for polygons] is available.)
* Multiple polygons can be processed simultaneously, and be superimposed onto molecular images.
* Animation can be realized.
* jV runs on the Java Runtime Environment ([http://java.com/download/ JRE]) so that it can work as a stand-alone application as well as an applet.
* The graphics of jV is based on OpenGL ([http://jogamp.org/jogl/www/ JOGL]), thereby producing fairly beautiful pictures.


The program 'jV' has been developed by [http://www.hgc.jp/~kinosita/TOP.html Kengo Kinoshita] ([http://www.is.tohoku.ac.jp/index-e.html Graduate School of Information Sciences], [http://www.tohoku.ac.jp/english/ Tohoku University]) and [http://www.protein.osaka-u.ac.jp/rcsfp/pi/ Haruki Nakamura] ([http://www.protein.osaka-u.ac.jp/index_e.php Institute for Protein Research], [http://www.osaka-u.ac.jp/eng/index.html Osaka Univeristy]), with the support from [http://biosciencedbc.jp/ JST-NBDC] and [http://www.protein.osaka-u.ac.jp/index_e.php Institute for Protein Research IPR], [http://www.osaka-u.ac.jp/eng/index.html Osaka Univeristy].
      

&lt;gallery&gt;
File:Spacefill.jpg
File:Cartoon.jpg
File:Surface.jpg
File:edmap.jpg
&lt;/gallery&gt;


== Start up ==
You can start up jV (4.4.4) with Java Web Start technology immediately from here.
* [http://ef-site.hgc.jp/eF-site/servlet/stable/jV.jnlp stable JOGL version] (recommended)
* [http://ef-site.hgc.jp/eF-site/servlet/current/jV.jnlp recent JOGL version]
The current jV requires JRE 1.6 or later.
The previous version, jV version 4.0, can run with JRE 1.4 and 1.5.
* [http://ef-site.hgc.jp/jV/stable/jV_4_0.jnlp jV 4.0]

== Basic Usage ==
You can execute basic operations such as rotation and translation with mouse action. Major actions are described in the following table:
{| style="margin:auto;border:1px solid gray"
! rowspan="2" style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap;font-weight:bold" |Action
! colspan="2" style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap;font-weight:bold" |Mouse Operation
|-
! style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap;font-weight:bold" |Windows, Linux
! style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap;font-weight:bold" |Mac OS X
|-
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |rotate around X (horizontal) axis&lt;br /&gt;rotate around Y (vertical) axis
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |left drag
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |drag
|-
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |translate along X axis (holizontally)&lt;br /&gt;translate along Y axis (vertically)
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |right drag
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |Command + drag
|-
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |translate along Z axis (zoom in/out)
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |Shift + left drag
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |Shift + drag
|}

Operations such as changing display models and colors and saving the image, can be executed with a menu. The location of the menu is at the top of the application window in Windows and at the top of screen in Mac as the stand-alone application. As an applet usage, a popup menu appears by clicking the right mouse button on the display screen, or clicking with a "Command" button in case of Mac.

{| style="margin:auto;border:0"
|-
| [[File:Jv_menu_win.png|The location of menu in jV stand-alone version in Windows.|250px]]
| [[File:Jv_menu_mac.png|The location of menu in jV stand-alone version in Mac.|250px]]
| [[File:popupmenu_en.png|The location of menu in applet version.|250px]]
|-
| style="text-align:center" |Stand-alone (Windows)
| style="text-align:center" |Stand-alone (Mac)
| style="text-align:center" |Applet
|}

Basic menu operations are following (see also [[GUI]] for details):

{| style="margin:auto;border:1px solid gray;border-collapse:collapse"
! style="padding:0 0.5em;border:1px solid gray" | Operations
! style="padding:0 0.5em;border:1px solid gray" | Menu location
|-
| style="padding:0 0.5em;border:1px solid gray" | Save a static image
| style="padding:0 0.5em;border:1px solid gray" | [File]-[Save]-[PNG/JPEG]
|-
| style="padding:0 0.5em;border:1px solid gray" | Change the expression format
| style="padding:0 0.5em;border:1px solid gray" | [File]-[Display]-[Wireframe/Backbone/Sticks/Spacefill/Ball&amp;amp;Stick/Ribbons/Cartoon]
|-
| style="padding:0 0.5em;border:1px solid gray" | Change the color
| style="padding:0 0.5em;border:1px solid gray" | [File]-[Colors]-[Monochrome/CPK/Shapely/Group/Chain/Temperature/Structure/Charge/Amino]
|}

To execute more complicated operation such as diplaying some piece of the molecule or changing some part of molecule in another style, use command line operation.

See also [[#Other resources]] for details:


== Download ==
You can also download the program and start it up locally.
The following links take you to the download pages. (latest version is 4.4.3@2015/2/24)
* [http://ef-site.hgc.jp/eF-site/servlet/DownloadViewerBinary binary (4.4.3)] 
* [http://ef-site.hgc.jp/eF-site/servlet/Registration source code (4.4.3)] (registration will be required)

== Other resources ==
* [[How_to_use]] (in this site in English)
* [http://www.pdbj.org/jv/manual/index_ja.html Manual] (html in Japanese)</text>
    <sha1>baaff99491049a1a9631d9959252f0c686038ff6</sha1>
  </revision>
  <revision>
    <id>605</id>
    <parentid>604</parentid>
    <timestamp>2015-10-01T07:13:27Z</timestamp>
    <contributor>
      <username>IMSsato</username>
      <id>4</id>
    </contributor>
    <comment>/* Download */</comment>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="6312" xml:space="preserve">&lt;big&gt;'''Welcome to jV wiki.'''&lt;/big&gt;

jV (formerly known as PDBjViewer) is a program to display molecular graphics of protein and nucleic acids. 
jV supports the following features:
* jV can read and display PDBML files, the canonical XML format for the Protein Data Bank.
* Of course, jV can read and display the traditional PDB format files, too.
* RasMol-like usability.
* jV can process more than one molecules.
* jV can display polygons specified by XML. ([http://www.pdbj.org/jv/polygonSchema XML Schema for polygons] is available.)
* Multiple polygons can be processed simultaneously, and be superimposed onto molecular images.
* Animation can be realized.
* jV runs on the Java Runtime Environment ([http://java.com/download/ JRE]) so that it can work as a stand-alone application as well as an applet.
* The graphics of jV is based on OpenGL ([http://jogamp.org/jogl/www/ JOGL]), thereby producing fairly beautiful pictures.


The program 'jV' has been developed by [http://www.hgc.jp/~kinosita/TOP.html Kengo Kinoshita] ([http://www.is.tohoku.ac.jp/index-e.html Graduate School of Information Sciences], [http://www.tohoku.ac.jp/english/ Tohoku University]) and [http://www.protein.osaka-u.ac.jp/rcsfp/pi/ Haruki Nakamura] ([http://www.protein.osaka-u.ac.jp/index_e.php Institute for Protein Research], [http://www.osaka-u.ac.jp/eng/index.html Osaka Univeristy]), with the support from [http://biosciencedbc.jp/ JST-NBDC] and [http://www.protein.osaka-u.ac.jp/index_e.php Institute for Protein Research IPR], [http://www.osaka-u.ac.jp/eng/index.html Osaka Univeristy].
      

&lt;gallery&gt;
File:Spacefill.jpg
File:Cartoon.jpg
File:Surface.jpg
File:edmap.jpg
&lt;/gallery&gt;


== Start up ==
You can start up jV (4.4.4) with Java Web Start technology immediately from here.
* [http://ef-site.hgc.jp/eF-site/servlet/stable/jV.jnlp stable JOGL version] (recommended)
* [http://ef-site.hgc.jp/eF-site/servlet/current/jV.jnlp recent JOGL version]
The current jV requires JRE 1.6 or later.
The previous version, jV version 4.0, can run with JRE 1.4 and 1.5.
* [http://ef-site.hgc.jp/jV/stable/jV_4_0.jnlp jV 4.0]

== Basic Usage ==
You can execute basic operations such as rotation and translation with mouse action. Major actions are described in the following table:
{| style="margin:auto;border:1px solid gray"
! rowspan="2" style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap;font-weight:bold" |Action
! colspan="2" style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap;font-weight:bold" |Mouse Operation
|-
! style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap;font-weight:bold" |Windows, Linux
! style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap;font-weight:bold" |Mac OS X
|-
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |rotate around X (horizontal) axis&lt;br /&gt;rotate around Y (vertical) axis
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |left drag
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |drag
|-
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |translate along X axis (holizontally)&lt;br /&gt;translate along Y axis (vertically)
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |right drag
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |Command + drag
|-
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |translate along Z axis (zoom in/out)
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |Shift + left drag
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |Shift + drag
|}

Operations such as changing display models and colors and saving the image, can be executed with a menu. The location of the menu is at the top of the application window in Windows and at the top of screen in Mac as the stand-alone application. As an applet usage, a popup menu appears by clicking the right mouse button on the display screen, or clicking with a "Command" button in case of Mac.

{| style="margin:auto;border:0"
|-
| [[File:Jv_menu_win.png|The location of menu in jV stand-alone version in Windows.|250px]]
| [[File:Jv_menu_mac.png|The location of menu in jV stand-alone version in Mac.|250px]]
| [[File:popupmenu_en.png|The location of menu in applet version.|250px]]
|-
| style="text-align:center" |Stand-alone (Windows)
| style="text-align:center" |Stand-alone (Mac)
| style="text-align:center" |Applet
|}

Basic menu operations are following (see also [[GUI]] for details):

{| style="margin:auto;border:1px solid gray;border-collapse:collapse"
! style="padding:0 0.5em;border:1px solid gray" | Operations
! style="padding:0 0.5em;border:1px solid gray" | Menu location
|-
| style="padding:0 0.5em;border:1px solid gray" | Save a static image
| style="padding:0 0.5em;border:1px solid gray" | [File]-[Save]-[PNG/JPEG]
|-
| style="padding:0 0.5em;border:1px solid gray" | Change the expression format
| style="padding:0 0.5em;border:1px solid gray" | [File]-[Display]-[Wireframe/Backbone/Sticks/Spacefill/Ball&amp;amp;Stick/Ribbons/Cartoon]
|-
| style="padding:0 0.5em;border:1px solid gray" | Change the color
| style="padding:0 0.5em;border:1px solid gray" | [File]-[Colors]-[Monochrome/CPK/Shapely/Group/Chain/Temperature/Structure/Charge/Amino]
|}

To execute more complicated operation such as diplaying some piece of the molecule or changing some part of molecule in another style, use command line operation.

See also [[#Other resources]] for details:


== Download ==
You can also download the program and start it up locally.
The following links take you to the download pages. (latest version is 4.4.4@2015/10/1)
* [http://ef-site.hgc.jp/eF-site/servlet/DownloadViewerBinary binary (4.4.4)] 
* [http://ef-site.hgc.jp/eF-site/servlet/Registration source code (4.4.4)] (registration will be required)

== Other resources ==
* [[How_to_use]] (in this site in English)
* [http://www.pdbj.org/jv/manual/index_ja.html Manual] (html in Japanese)</text>
    <sha1>b813eece68de110ac36a75df0ae426ebdf3bcce9</sha1>
  </revision>
  <revision>
    <id>609</id>
    <parentid>605</parentid>
    <timestamp>2016-01-08T07:20:21Z</timestamp>
    <contributor>
      <username>IMSsato</username>
      <id>4</id>
    </contributor>
    <comment>/* Start up */</comment>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="6312" xml:space="preserve">&lt;big&gt;'''Welcome to jV wiki.'''&lt;/big&gt;

jV (formerly known as PDBjViewer) is a program to display molecular graphics of protein and nucleic acids. 
jV supports the following features:
* jV can read and display PDBML files, the canonical XML format for the Protein Data Bank.
* Of course, jV can read and display the traditional PDB format files, too.
* RasMol-like usability.
* jV can process more than one molecules.
* jV can display polygons specified by XML. ([http://www.pdbj.org/jv/polygonSchema XML Schema for polygons] is available.)
* Multiple polygons can be processed simultaneously, and be superimposed onto molecular images.
* Animation can be realized.
* jV runs on the Java Runtime Environment ([http://java.com/download/ JRE]) so that it can work as a stand-alone application as well as an applet.
* The graphics of jV is based on OpenGL ([http://jogamp.org/jogl/www/ JOGL]), thereby producing fairly beautiful pictures.


The program 'jV' has been developed by [http://www.hgc.jp/~kinosita/TOP.html Kengo Kinoshita] ([http://www.is.tohoku.ac.jp/index-e.html Graduate School of Information Sciences], [http://www.tohoku.ac.jp/english/ Tohoku University]) and [http://www.protein.osaka-u.ac.jp/rcsfp/pi/ Haruki Nakamura] ([http://www.protein.osaka-u.ac.jp/index_e.php Institute for Protein Research], [http://www.osaka-u.ac.jp/eng/index.html Osaka Univeristy]), with the support from [http://biosciencedbc.jp/ JST-NBDC] and [http://www.protein.osaka-u.ac.jp/index_e.php Institute for Protein Research IPR], [http://www.osaka-u.ac.jp/eng/index.html Osaka Univeristy].
      

&lt;gallery&gt;
File:Spacefill.jpg
File:Cartoon.jpg
File:Surface.jpg
File:edmap.jpg
&lt;/gallery&gt;


== Start up ==
You can start up jV (4.4.5) with Java Web Start technology immediately from here.
* [http://ef-site.hgc.jp/eF-site/servlet/stable/jV.jnlp stable JOGL version] (recommended)
* [http://ef-site.hgc.jp/eF-site/servlet/current/jV.jnlp recent JOGL version]
The current jV requires JRE 1.6 or later.
The previous version, jV version 4.0, can run with JRE 1.4 and 1.5.
* [http://ef-site.hgc.jp/jV/stable/jV_4_0.jnlp jV 4.0]

== Basic Usage ==
You can execute basic operations such as rotation and translation with mouse action. Major actions are described in the following table:
{| style="margin:auto;border:1px solid gray"
! rowspan="2" style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap;font-weight:bold" |Action
! colspan="2" style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap;font-weight:bold" |Mouse Operation
|-
! style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap;font-weight:bold" |Windows, Linux
! style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap;font-weight:bold" |Mac OS X
|-
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |rotate around X (horizontal) axis&lt;br /&gt;rotate around Y (vertical) axis
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |left drag
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |drag
|-
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |translate along X axis (holizontally)&lt;br /&gt;translate along Y axis (vertically)
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |right drag
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |Command + drag
|-
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |translate along Z axis (zoom in/out)
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |Shift + left drag
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |Shift + drag
|}

Operations such as changing display models and colors and saving the image, can be executed with a menu. The location of the menu is at the top of the application window in Windows and at the top of screen in Mac as the stand-alone application. As an applet usage, a popup menu appears by clicking the right mouse button on the display screen, or clicking with a "Command" button in case of Mac.

{| style="margin:auto;border:0"
|-
| [[File:Jv_menu_win.png|The location of menu in jV stand-alone version in Windows.|250px]]
| [[File:Jv_menu_mac.png|The location of menu in jV stand-alone version in Mac.|250px]]
| [[File:popupmenu_en.png|The location of menu in applet version.|250px]]
|-
| style="text-align:center" |Stand-alone (Windows)
| style="text-align:center" |Stand-alone (Mac)
| style="text-align:center" |Applet
|}

Basic menu operations are following (see also [[GUI]] for details):

{| style="margin:auto;border:1px solid gray;border-collapse:collapse"
! style="padding:0 0.5em;border:1px solid gray" | Operations
! style="padding:0 0.5em;border:1px solid gray" | Menu location
|-
| style="padding:0 0.5em;border:1px solid gray" | Save a static image
| style="padding:0 0.5em;border:1px solid gray" | [File]-[Save]-[PNG/JPEG]
|-
| style="padding:0 0.5em;border:1px solid gray" | Change the expression format
| style="padding:0 0.5em;border:1px solid gray" | [File]-[Display]-[Wireframe/Backbone/Sticks/Spacefill/Ball&amp;amp;Stick/Ribbons/Cartoon]
|-
| style="padding:0 0.5em;border:1px solid gray" | Change the color
| style="padding:0 0.5em;border:1px solid gray" | [File]-[Colors]-[Monochrome/CPK/Shapely/Group/Chain/Temperature/Structure/Charge/Amino]
|}

To execute more complicated operation such as diplaying some piece of the molecule or changing some part of molecule in another style, use command line operation.

See also [[#Other resources]] for details:


== Download ==
You can also download the program and start it up locally.
The following links take you to the download pages. (latest version is 4.4.4@2015/10/1)
* [http://ef-site.hgc.jp/eF-site/servlet/DownloadViewerBinary binary (4.4.4)] 
* [http://ef-site.hgc.jp/eF-site/servlet/Registration source code (4.4.4)] (registration will be required)

== Other resources ==
* [[How_to_use]] (in this site in English)
* [http://www.pdbj.org/jv/manual/index_ja.html Manual] (html in Japanese)</text>
    <sha1>a5f26f8ce3feb7c5b5d31b744905eaa93b7909c1</sha1>
  </revision>
  <revision>
    <id>610</id>
    <parentid>609</parentid>
    <timestamp>2016-01-08T07:20:42Z</timestamp>
    <contributor>
      <username>IMSsato</username>
      <id>4</id>
    </contributor>
    <comment>/* Download */</comment>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="6311" xml:space="preserve">&lt;big&gt;'''Welcome to jV wiki.'''&lt;/big&gt;

jV (formerly known as PDBjViewer) is a program to display molecular graphics of protein and nucleic acids. 
jV supports the following features:
* jV can read and display PDBML files, the canonical XML format for the Protein Data Bank.
* Of course, jV can read and display the traditional PDB format files, too.
* RasMol-like usability.
* jV can process more than one molecules.
* jV can display polygons specified by XML. ([http://www.pdbj.org/jv/polygonSchema XML Schema for polygons] is available.)
* Multiple polygons can be processed simultaneously, and be superimposed onto molecular images.
* Animation can be realized.
* jV runs on the Java Runtime Environment ([http://java.com/download/ JRE]) so that it can work as a stand-alone application as well as an applet.
* The graphics of jV is based on OpenGL ([http://jogamp.org/jogl/www/ JOGL]), thereby producing fairly beautiful pictures.


The program 'jV' has been developed by [http://www.hgc.jp/~kinosita/TOP.html Kengo Kinoshita] ([http://www.is.tohoku.ac.jp/index-e.html Graduate School of Information Sciences], [http://www.tohoku.ac.jp/english/ Tohoku University]) and [http://www.protein.osaka-u.ac.jp/rcsfp/pi/ Haruki Nakamura] ([http://www.protein.osaka-u.ac.jp/index_e.php Institute for Protein Research], [http://www.osaka-u.ac.jp/eng/index.html Osaka Univeristy]), with the support from [http://biosciencedbc.jp/ JST-NBDC] and [http://www.protein.osaka-u.ac.jp/index_e.php Institute for Protein Research IPR], [http://www.osaka-u.ac.jp/eng/index.html Osaka Univeristy].
      

&lt;gallery&gt;
File:Spacefill.jpg
File:Cartoon.jpg
File:Surface.jpg
File:edmap.jpg
&lt;/gallery&gt;


== Start up ==
You can start up jV (4.4.5) with Java Web Start technology immediately from here.
* [http://ef-site.hgc.jp/eF-site/servlet/stable/jV.jnlp stable JOGL version] (recommended)
* [http://ef-site.hgc.jp/eF-site/servlet/current/jV.jnlp recent JOGL version]
The current jV requires JRE 1.6 or later.
The previous version, jV version 4.0, can run with JRE 1.4 and 1.5.
* [http://ef-site.hgc.jp/jV/stable/jV_4_0.jnlp jV 4.0]

== Basic Usage ==
You can execute basic operations such as rotation and translation with mouse action. Major actions are described in the following table:
{| style="margin:auto;border:1px solid gray"
! rowspan="2" style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap;font-weight:bold" |Action
! colspan="2" style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap;font-weight:bold" |Mouse Operation
|-
! style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap;font-weight:bold" |Windows, Linux
! style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap;font-weight:bold" |Mac OS X
|-
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |rotate around X (horizontal) axis&lt;br /&gt;rotate around Y (vertical) axis
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |left drag
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |drag
|-
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |translate along X axis (holizontally)&lt;br /&gt;translate along Y axis (vertically)
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |right drag
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |Command + drag
|-
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |translate along Z axis (zoom in/out)
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |Shift + left drag
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |Shift + drag
|}

Operations such as changing display models and colors and saving the image, can be executed with a menu. The location of the menu is at the top of the application window in Windows and at the top of screen in Mac as the stand-alone application. As an applet usage, a popup menu appears by clicking the right mouse button on the display screen, or clicking with a "Command" button in case of Mac.

{| style="margin:auto;border:0"
|-
| [[File:Jv_menu_win.png|The location of menu in jV stand-alone version in Windows.|250px]]
| [[File:Jv_menu_mac.png|The location of menu in jV stand-alone version in Mac.|250px]]
| [[File:popupmenu_en.png|The location of menu in applet version.|250px]]
|-
| style="text-align:center" |Stand-alone (Windows)
| style="text-align:center" |Stand-alone (Mac)
| style="text-align:center" |Applet
|}

Basic menu operations are following (see also [[GUI]] for details):

{| style="margin:auto;border:1px solid gray;border-collapse:collapse"
! style="padding:0 0.5em;border:1px solid gray" | Operations
! style="padding:0 0.5em;border:1px solid gray" | Menu location
|-
| style="padding:0 0.5em;border:1px solid gray" | Save a static image
| style="padding:0 0.5em;border:1px solid gray" | [File]-[Save]-[PNG/JPEG]
|-
| style="padding:0 0.5em;border:1px solid gray" | Change the expression format
| style="padding:0 0.5em;border:1px solid gray" | [File]-[Display]-[Wireframe/Backbone/Sticks/Spacefill/Ball&amp;amp;Stick/Ribbons/Cartoon]
|-
| style="padding:0 0.5em;border:1px solid gray" | Change the color
| style="padding:0 0.5em;border:1px solid gray" | [File]-[Colors]-[Monochrome/CPK/Shapely/Group/Chain/Temperature/Structure/Charge/Amino]
|}

To execute more complicated operation such as diplaying some piece of the molecule or changing some part of molecule in another style, use command line operation.

See also [[#Other resources]] for details:


== Download ==
You can also download the program and start it up locally.
The following links take you to the download pages. (latest version is 4.4.5@2016/1/8)
* [http://ef-site.hgc.jp/eF-site/servlet/DownloadViewerBinary binary (4.4.5)] 
* [http://ef-site.hgc.jp/eF-site/servlet/Registration source code (4.4.5)] (registration will be required)

== Other resources ==
* [[How_to_use]] (in this site in English)
* [http://www.pdbj.org/jv/manual/index_ja.html Manual] (html in Japanese)</text>
    <sha1>90d6f96a256269eaab06fc86616ff90b5dabde99</sha1>
  </revision>
  <revision>
    <id>611</id>
    <parentid>610</parentid>
    <timestamp>2016-01-08T07:21:30Z</timestamp>
    <contributor>
      <username>IMSsato</username>
      <id>4</id>
    </contributor>
    <comment>/* Download */</comment>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="6323" xml:space="preserve">&lt;big&gt;'''Welcome to jV wiki.'''&lt;/big&gt;

jV (formerly known as PDBjViewer) is a program to display molecular graphics of protein and nucleic acids. 
jV supports the following features:
* jV can read and display PDBML files, the canonical XML format for the Protein Data Bank.
* Of course, jV can read and display the traditional PDB format files, too.
* RasMol-like usability.
* jV can process more than one molecules.
* jV can display polygons specified by XML. ([http://www.pdbj.org/jv/polygonSchema XML Schema for polygons] is available.)
* Multiple polygons can be processed simultaneously, and be superimposed onto molecular images.
* Animation can be realized.
* jV runs on the Java Runtime Environment ([http://java.com/download/ JRE]) so that it can work as a stand-alone application as well as an applet.
* The graphics of jV is based on OpenGL ([http://jogamp.org/jogl/www/ JOGL]), thereby producing fairly beautiful pictures.


The program 'jV' has been developed by [http://www.hgc.jp/~kinosita/TOP.html Kengo Kinoshita] ([http://www.is.tohoku.ac.jp/index-e.html Graduate School of Information Sciences], [http://www.tohoku.ac.jp/english/ Tohoku University]) and [http://www.protein.osaka-u.ac.jp/rcsfp/pi/ Haruki Nakamura] ([http://www.protein.osaka-u.ac.jp/index_e.php Institute for Protein Research], [http://www.osaka-u.ac.jp/eng/index.html Osaka Univeristy]), with the support from [http://biosciencedbc.jp/ JST-NBDC] and [http://www.protein.osaka-u.ac.jp/index_e.php Institute for Protein Research IPR], [http://www.osaka-u.ac.jp/eng/index.html Osaka Univeristy].
      

&lt;gallery&gt;
File:Spacefill.jpg
File:Cartoon.jpg
File:Surface.jpg
File:edmap.jpg
&lt;/gallery&gt;


== Start up ==
You can start up jV (4.4.5) with Java Web Start technology immediately from here.
* [http://ef-site.hgc.jp/eF-site/servlet/stable/jV.jnlp stable JOGL version] (recommended)
* [http://ef-site.hgc.jp/eF-site/servlet/current/jV.jnlp recent JOGL version]
The current jV requires JRE 1.6 or later.
The previous version, jV version 4.0, can run with JRE 1.4 and 1.5.
* [http://ef-site.hgc.jp/jV/stable/jV_4_0.jnlp jV 4.0]

== Basic Usage ==
You can execute basic operations such as rotation and translation with mouse action. Major actions are described in the following table:
{| style="margin:auto;border:1px solid gray"
! rowspan="2" style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap;font-weight:bold" |Action
! colspan="2" style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap;font-weight:bold" |Mouse Operation
|-
! style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap;font-weight:bold" |Windows, Linux
! style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap;font-weight:bold" |Mac OS X
|-
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |rotate around X (horizontal) axis&lt;br /&gt;rotate around Y (vertical) axis
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |left drag
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |drag
|-
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |translate along X axis (holizontally)&lt;br /&gt;translate along Y axis (vertically)
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |right drag
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |Command + drag
|-
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |translate along Z axis (zoom in/out)
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |Shift + left drag
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |Shift + drag
|}

Operations such as changing display models and colors and saving the image, can be executed with a menu. The location of the menu is at the top of the application window in Windows and at the top of screen in Mac as the stand-alone application. As an applet usage, a popup menu appears by clicking the right mouse button on the display screen, or clicking with a "Command" button in case of Mac.

{| style="margin:auto;border:0"
|-
| [[File:Jv_menu_win.png|The location of menu in jV stand-alone version in Windows.|250px]]
| [[File:Jv_menu_mac.png|The location of menu in jV stand-alone version in Mac.|250px]]
| [[File:popupmenu_en.png|The location of menu in applet version.|250px]]
|-
| style="text-align:center" |Stand-alone (Windows)
| style="text-align:center" |Stand-alone (Mac)
| style="text-align:center" |Applet
|}

Basic menu operations are following (see also [[GUI]] for details):

{| style="margin:auto;border:1px solid gray;border-collapse:collapse"
! style="padding:0 0.5em;border:1px solid gray" | Operations
! style="padding:0 0.5em;border:1px solid gray" | Menu location
|-
| style="padding:0 0.5em;border:1px solid gray" | Save a static image
| style="padding:0 0.5em;border:1px solid gray" | [File]-[Save]-[PNG/JPEG]
|-
| style="padding:0 0.5em;border:1px solid gray" | Change the expression format
| style="padding:0 0.5em;border:1px solid gray" | [File]-[Display]-[Wireframe/Backbone/Sticks/Spacefill/Ball&amp;amp;Stick/Ribbons/Cartoon]
|-
| style="padding:0 0.5em;border:1px solid gray" | Change the color
| style="padding:0 0.5em;border:1px solid gray" | [File]-[Colors]-[Monochrome/CPK/Shapely/Group/Chain/Temperature/Structure/Charge/Amino]
|}

To execute more complicated operation such as diplaying some piece of the molecule or changing some part of molecule in another style, use command line operation.

See also [[#Other resources]] for details:


== Download ==
You can also download the program and start it up locally.
The following links take you to the download pages. (latest version is 4.4.5@2016/1/8)
* [http://service.ipr.pdbj.org/eF-site/servlet/DownloadViewerBinary binary (4.4.5)] 
* [http://service.ipr.pdbj.org/eF-site/servlet/Registration source code (4.4.5)] (registration will be required)

== Other resources ==
* [[How_to_use]] (in this site in English)
* [http://www.pdbj.org/jv/manual/index_ja.html Manual] (html in Japanese)</text>
    <sha1>1fafad578068e76f5e45d8c8f0d55e835d1c1191</sha1>
  </revision>
  <revision>
    <id>614</id>
    <parentid>611</parentid>
    <timestamp>2016-03-02T04:48:52Z</timestamp>
    <contributor>
      <username>IMSsato</username>
      <id>4</id>
    </contributor>
    <comment>/* Start up */</comment>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="6321" xml:space="preserve">&lt;big&gt;'''Welcome to jV wiki.'''&lt;/big&gt;

jV (formerly known as PDBjViewer) is a program to display molecular graphics of protein and nucleic acids. 
jV supports the following features:
* jV can read and display PDBML files, the canonical XML format for the Protein Data Bank.
* Of course, jV can read and display the traditional PDB format files, too.
* RasMol-like usability.
* jV can process more than one molecules.
* jV can display polygons specified by XML. ([http://www.pdbj.org/jv/polygonSchema XML Schema for polygons] is available.)
* Multiple polygons can be processed simultaneously, and be superimposed onto molecular images.
* Animation can be realized.
* jV runs on the Java Runtime Environment ([http://java.com/download/ JRE]) so that it can work as a stand-alone application as well as an applet.
* The graphics of jV is based on OpenGL ([http://jogamp.org/jogl/www/ JOGL]), thereby producing fairly beautiful pictures.


The program 'jV' has been developed by [http://www.hgc.jp/~kinosita/TOP.html Kengo Kinoshita] ([http://www.is.tohoku.ac.jp/index-e.html Graduate School of Information Sciences], [http://www.tohoku.ac.jp/english/ Tohoku University]) and [http://www.protein.osaka-u.ac.jp/rcsfp/pi/ Haruki Nakamura] ([http://www.protein.osaka-u.ac.jp/index_e.php Institute for Protein Research], [http://www.osaka-u.ac.jp/eng/index.html Osaka Univeristy]), with the support from [http://biosciencedbc.jp/ JST-NBDC] and [http://www.protein.osaka-u.ac.jp/index_e.php Institute for Protein Research IPR], [http://www.osaka-u.ac.jp/eng/index.html Osaka Univeristy].
      

&lt;gallery&gt;
File:Spacefill.jpg
File:Cartoon.jpg
File:Surface.jpg
File:edmap.jpg
&lt;/gallery&gt;


== Start up ==
You can start up jV (4.5) with Java Web Start technology immediately from here.
* [http://ef-site.hgc.jp/eF-site/servlet/stable/jV.jnlp stable JOGL version] (recommended)
* [http://ef-site.hgc.jp/eF-site/servlet/current/jV.jnlp recent JOGL version]
The current jV requires JRE 1.6 or later.
The previous version, jV version 4.0, can run with JRE 1.4 and 1.5.
* [http://ef-site.hgc.jp/jV/stable/jV_4_0.jnlp jV 4.0]

== Basic Usage ==
You can execute basic operations such as rotation and translation with mouse action. Major actions are described in the following table:
{| style="margin:auto;border:1px solid gray"
! rowspan="2" style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap;font-weight:bold" |Action
! colspan="2" style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap;font-weight:bold" |Mouse Operation
|-
! style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap;font-weight:bold" |Windows, Linux
! style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap;font-weight:bold" |Mac OS X
|-
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |rotate around X (horizontal) axis&lt;br /&gt;rotate around Y (vertical) axis
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |left drag
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |drag
|-
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |translate along X axis (holizontally)&lt;br /&gt;translate along Y axis (vertically)
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |right drag
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |Command + drag
|-
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |translate along Z axis (zoom in/out)
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |Shift + left drag
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |Shift + drag
|}

Operations such as changing display models and colors and saving the image, can be executed with a menu. The location of the menu is at the top of the application window in Windows and at the top of screen in Mac as the stand-alone application. As an applet usage, a popup menu appears by clicking the right mouse button on the display screen, or clicking with a "Command" button in case of Mac.

{| style="margin:auto;border:0"
|-
| [[File:Jv_menu_win.png|The location of menu in jV stand-alone version in Windows.|250px]]
| [[File:Jv_menu_mac.png|The location of menu in jV stand-alone version in Mac.|250px]]
| [[File:popupmenu_en.png|The location of menu in applet version.|250px]]
|-
| style="text-align:center" |Stand-alone (Windows)
| style="text-align:center" |Stand-alone (Mac)
| style="text-align:center" |Applet
|}

Basic menu operations are following (see also [[GUI]] for details):

{| style="margin:auto;border:1px solid gray;border-collapse:collapse"
! style="padding:0 0.5em;border:1px solid gray" | Operations
! style="padding:0 0.5em;border:1px solid gray" | Menu location
|-
| style="padding:0 0.5em;border:1px solid gray" | Save a static image
| style="padding:0 0.5em;border:1px solid gray" | [File]-[Save]-[PNG/JPEG]
|-
| style="padding:0 0.5em;border:1px solid gray" | Change the expression format
| style="padding:0 0.5em;border:1px solid gray" | [File]-[Display]-[Wireframe/Backbone/Sticks/Spacefill/Ball&amp;amp;Stick/Ribbons/Cartoon]
|-
| style="padding:0 0.5em;border:1px solid gray" | Change the color
| style="padding:0 0.5em;border:1px solid gray" | [File]-[Colors]-[Monochrome/CPK/Shapely/Group/Chain/Temperature/Structure/Charge/Amino]
|}

To execute more complicated operation such as diplaying some piece of the molecule or changing some part of molecule in another style, use command line operation.

See also [[#Other resources]] for details:


== Download ==
You can also download the program and start it up locally.
The following links take you to the download pages. (latest version is 4.4.5@2016/1/8)
* [http://service.ipr.pdbj.org/eF-site/servlet/DownloadViewerBinary binary (4.4.5)] 
* [http://service.ipr.pdbj.org/eF-site/servlet/Registration source code (4.4.5)] (registration will be required)

== Other resources ==
* [[How_to_use]] (in this site in English)
* [http://www.pdbj.org/jv/manual/index_ja.html Manual] (html in Japanese)</text>
    <sha1>e024cb2aa3ffd9eb7d96f95b0cd3206092c627d5</sha1>
  </revision>
  <revision>
    <id>615</id>
    <parentid>614</parentid>
    <timestamp>2016-03-02T04:49:11Z</timestamp>
    <contributor>
      <username>IMSsato</username>
      <id>4</id>
    </contributor>
    <comment>/* Download */</comment>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="6315" xml:space="preserve">&lt;big&gt;'''Welcome to jV wiki.'''&lt;/big&gt;

jV (formerly known as PDBjViewer) is a program to display molecular graphics of protein and nucleic acids. 
jV supports the following features:
* jV can read and display PDBML files, the canonical XML format for the Protein Data Bank.
* Of course, jV can read and display the traditional PDB format files, too.
* RasMol-like usability.
* jV can process more than one molecules.
* jV can display polygons specified by XML. ([http://www.pdbj.org/jv/polygonSchema XML Schema for polygons] is available.)
* Multiple polygons can be processed simultaneously, and be superimposed onto molecular images.
* Animation can be realized.
* jV runs on the Java Runtime Environment ([http://java.com/download/ JRE]) so that it can work as a stand-alone application as well as an applet.
* The graphics of jV is based on OpenGL ([http://jogamp.org/jogl/www/ JOGL]), thereby producing fairly beautiful pictures.


The program 'jV' has been developed by [http://www.hgc.jp/~kinosita/TOP.html Kengo Kinoshita] ([http://www.is.tohoku.ac.jp/index-e.html Graduate School of Information Sciences], [http://www.tohoku.ac.jp/english/ Tohoku University]) and [http://www.protein.osaka-u.ac.jp/rcsfp/pi/ Haruki Nakamura] ([http://www.protein.osaka-u.ac.jp/index_e.php Institute for Protein Research], [http://www.osaka-u.ac.jp/eng/index.html Osaka Univeristy]), with the support from [http://biosciencedbc.jp/ JST-NBDC] and [http://www.protein.osaka-u.ac.jp/index_e.php Institute for Protein Research IPR], [http://www.osaka-u.ac.jp/eng/index.html Osaka Univeristy].
      

&lt;gallery&gt;
File:Spacefill.jpg
File:Cartoon.jpg
File:Surface.jpg
File:edmap.jpg
&lt;/gallery&gt;


== Start up ==
You can start up jV (4.5) with Java Web Start technology immediately from here.
* [http://ef-site.hgc.jp/eF-site/servlet/stable/jV.jnlp stable JOGL version] (recommended)
* [http://ef-site.hgc.jp/eF-site/servlet/current/jV.jnlp recent JOGL version]
The current jV requires JRE 1.6 or later.
The previous version, jV version 4.0, can run with JRE 1.4 and 1.5.
* [http://ef-site.hgc.jp/jV/stable/jV_4_0.jnlp jV 4.0]

== Basic Usage ==
You can execute basic operations such as rotation and translation with mouse action. Major actions are described in the following table:
{| style="margin:auto;border:1px solid gray"
! rowspan="2" style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap;font-weight:bold" |Action
! colspan="2" style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap;font-weight:bold" |Mouse Operation
|-
! style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap;font-weight:bold" |Windows, Linux
! style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap;font-weight:bold" |Mac OS X
|-
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |rotate around X (horizontal) axis&lt;br /&gt;rotate around Y (vertical) axis
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |left drag
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |drag
|-
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |translate along X axis (holizontally)&lt;br /&gt;translate along Y axis (vertically)
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |right drag
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |Command + drag
|-
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |translate along Z axis (zoom in/out)
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |Shift + left drag
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |Shift + drag
|}

Operations such as changing display models and colors and saving the image, can be executed with a menu. The location of the menu is at the top of the application window in Windows and at the top of screen in Mac as the stand-alone application. As an applet usage, a popup menu appears by clicking the right mouse button on the display screen, or clicking with a "Command" button in case of Mac.

{| style="margin:auto;border:0"
|-
| [[File:Jv_menu_win.png|The location of menu in jV stand-alone version in Windows.|250px]]
| [[File:Jv_menu_mac.png|The location of menu in jV stand-alone version in Mac.|250px]]
| [[File:popupmenu_en.png|The location of menu in applet version.|250px]]
|-
| style="text-align:center" |Stand-alone (Windows)
| style="text-align:center" |Stand-alone (Mac)
| style="text-align:center" |Applet
|}

Basic menu operations are following (see also [[GUI]] for details):

{| style="margin:auto;border:1px solid gray;border-collapse:collapse"
! style="padding:0 0.5em;border:1px solid gray" | Operations
! style="padding:0 0.5em;border:1px solid gray" | Menu location
|-
| style="padding:0 0.5em;border:1px solid gray" | Save a static image
| style="padding:0 0.5em;border:1px solid gray" | [File]-[Save]-[PNG/JPEG]
|-
| style="padding:0 0.5em;border:1px solid gray" | Change the expression format
| style="padding:0 0.5em;border:1px solid gray" | [File]-[Display]-[Wireframe/Backbone/Sticks/Spacefill/Ball&amp;amp;Stick/Ribbons/Cartoon]
|-
| style="padding:0 0.5em;border:1px solid gray" | Change the color
| style="padding:0 0.5em;border:1px solid gray" | [File]-[Colors]-[Monochrome/CPK/Shapely/Group/Chain/Temperature/Structure/Charge/Amino]
|}

To execute more complicated operation such as diplaying some piece of the molecule or changing some part of molecule in another style, use command line operation.

See also [[#Other resources]] for details:


== Download ==
You can also download the program and start it up locally.
The following links take you to the download pages. (latest version is 4.5@2016/3/2)
* [http://service.ipr.pdbj.org/eF-site/servlet/DownloadViewerBinary binary (4.5)] 
* [http://service.ipr.pdbj.org/eF-site/servlet/Registration source code (4.5)] (registration will be required)

== Other resources ==
* [[How_to_use]] (in this site in English)
* [http://www.pdbj.org/jv/manual/index_ja.html Manual] (html in Japanese)</text>
    <sha1>870eac68749cca1aec0699971cfae881d37b29f2</sha1>
  </revision>
  <revision>
    <id>617</id>
    <parentid>615</parentid>
    <timestamp>2016-05-10T05:12:32Z</timestamp>
    <contributor>
      <username>IMSsato</username>
      <id>4</id>
    </contributor>
    <comment>/* Start up */</comment>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="6317" xml:space="preserve">&lt;big&gt;'''Welcome to jV wiki.'''&lt;/big&gt;

jV (formerly known as PDBjViewer) is a program to display molecular graphics of protein and nucleic acids. 
jV supports the following features:
* jV can read and display PDBML files, the canonical XML format for the Protein Data Bank.
* Of course, jV can read and display the traditional PDB format files, too.
* RasMol-like usability.
* jV can process more than one molecules.
* jV can display polygons specified by XML. ([http://www.pdbj.org/jv/polygonSchema XML Schema for polygons] is available.)
* Multiple polygons can be processed simultaneously, and be superimposed onto molecular images.
* Animation can be realized.
* jV runs on the Java Runtime Environment ([http://java.com/download/ JRE]) so that it can work as a stand-alone application as well as an applet.
* The graphics of jV is based on OpenGL ([http://jogamp.org/jogl/www/ JOGL]), thereby producing fairly beautiful pictures.


The program 'jV' has been developed by [http://www.hgc.jp/~kinosita/TOP.html Kengo Kinoshita] ([http://www.is.tohoku.ac.jp/index-e.html Graduate School of Information Sciences], [http://www.tohoku.ac.jp/english/ Tohoku University]) and [http://www.protein.osaka-u.ac.jp/rcsfp/pi/ Haruki Nakamura] ([http://www.protein.osaka-u.ac.jp/index_e.php Institute for Protein Research], [http://www.osaka-u.ac.jp/eng/index.html Osaka Univeristy]), with the support from [http://biosciencedbc.jp/ JST-NBDC] and [http://www.protein.osaka-u.ac.jp/index_e.php Institute for Protein Research IPR], [http://www.osaka-u.ac.jp/eng/index.html Osaka Univeristy].
      

&lt;gallery&gt;
File:Spacefill.jpg
File:Cartoon.jpg
File:Surface.jpg
File:edmap.jpg
&lt;/gallery&gt;


== Start up ==
You can start up jV (4.5.1) with Java Web Start technology immediately from here.
* [http://ef-site.hgc.jp/eF-site/servlet/stable/jV.jnlp stable JOGL version] (recommended)
* [http://ef-site.hgc.jp/eF-site/servlet/current/jV.jnlp recent JOGL version]
The current jV requires JRE 1.6 or later.
The previous version, jV version 4.0, can run with JRE 1.4 and 1.5.
* [http://ef-site.hgc.jp/jV/stable/jV_4_0.jnlp jV 4.0]

== Basic Usage ==
You can execute basic operations such as rotation and translation with mouse action. Major actions are described in the following table:
{| style="margin:auto;border:1px solid gray"
! rowspan="2" style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap;font-weight:bold" |Action
! colspan="2" style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap;font-weight:bold" |Mouse Operation
|-
! style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap;font-weight:bold" |Windows, Linux
! style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap;font-weight:bold" |Mac OS X
|-
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |rotate around X (horizontal) axis&lt;br /&gt;rotate around Y (vertical) axis
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |left drag
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |drag
|-
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |translate along X axis (holizontally)&lt;br /&gt;translate along Y axis (vertically)
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |right drag
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |Command + drag
|-
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |translate along Z axis (zoom in/out)
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |Shift + left drag
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |Shift + drag
|}

Operations such as changing display models and colors and saving the image, can be executed with a menu. The location of the menu is at the top of the application window in Windows and at the top of screen in Mac as the stand-alone application. As an applet usage, a popup menu appears by clicking the right mouse button on the display screen, or clicking with a "Command" button in case of Mac.

{| style="margin:auto;border:0"
|-
| [[File:Jv_menu_win.png|The location of menu in jV stand-alone version in Windows.|250px]]
| [[File:Jv_menu_mac.png|The location of menu in jV stand-alone version in Mac.|250px]]
| [[File:popupmenu_en.png|The location of menu in applet version.|250px]]
|-
| style="text-align:center" |Stand-alone (Windows)
| style="text-align:center" |Stand-alone (Mac)
| style="text-align:center" |Applet
|}

Basic menu operations are following (see also [[GUI]] for details):

{| style="margin:auto;border:1px solid gray;border-collapse:collapse"
! style="padding:0 0.5em;border:1px solid gray" | Operations
! style="padding:0 0.5em;border:1px solid gray" | Menu location
|-
| style="padding:0 0.5em;border:1px solid gray" | Save a static image
| style="padding:0 0.5em;border:1px solid gray" | [File]-[Save]-[PNG/JPEG]
|-
| style="padding:0 0.5em;border:1px solid gray" | Change the expression format
| style="padding:0 0.5em;border:1px solid gray" | [File]-[Display]-[Wireframe/Backbone/Sticks/Spacefill/Ball&amp;amp;Stick/Ribbons/Cartoon]
|-
| style="padding:0 0.5em;border:1px solid gray" | Change the color
| style="padding:0 0.5em;border:1px solid gray" | [File]-[Colors]-[Monochrome/CPK/Shapely/Group/Chain/Temperature/Structure/Charge/Amino]
|}

To execute more complicated operation such as diplaying some piece of the molecule or changing some part of molecule in another style, use command line operation.

See also [[#Other resources]] for details:


== Download ==
You can also download the program and start it up locally.
The following links take you to the download pages. (latest version is 4.5@2016/3/2)
* [http://service.ipr.pdbj.org/eF-site/servlet/DownloadViewerBinary binary (4.5)] 
* [http://service.ipr.pdbj.org/eF-site/servlet/Registration source code (4.5)] (registration will be required)

== Other resources ==
* [[How_to_use]] (in this site in English)
* [http://www.pdbj.org/jv/manual/index_ja.html Manual] (html in Japanese)</text>
    <sha1>6e2385adf0b9d414f8b89dc456a4b730462568a2</sha1>
  </revision>
  <revision>
    <id>618</id>
    <parentid>617</parentid>
    <timestamp>2016-05-10T05:13:29Z</timestamp>
    <contributor>
      <username>IMSsato</username>
      <id>4</id>
    </contributor>
    <comment>/* Download */</comment>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="6324" xml:space="preserve">&lt;big&gt;'''Welcome to jV wiki.'''&lt;/big&gt;

jV (formerly known as PDBjViewer) is a program to display molecular graphics of protein and nucleic acids. 
jV supports the following features:
* jV can read and display PDBML files, the canonical XML format for the Protein Data Bank.
* Of course, jV can read and display the traditional PDB format files, too.
* RasMol-like usability.
* jV can process more than one molecules.
* jV can display polygons specified by XML. ([http://www.pdbj.org/jv/polygonSchema XML Schema for polygons] is available.)
* Multiple polygons can be processed simultaneously, and be superimposed onto molecular images.
* Animation can be realized.
* jV runs on the Java Runtime Environment ([http://java.com/download/ JRE]) so that it can work as a stand-alone application as well as an applet.
* The graphics of jV is based on OpenGL ([http://jogamp.org/jogl/www/ JOGL]), thereby producing fairly beautiful pictures.


The program 'jV' has been developed by [http://www.hgc.jp/~kinosita/TOP.html Kengo Kinoshita] ([http://www.is.tohoku.ac.jp/index-e.html Graduate School of Information Sciences], [http://www.tohoku.ac.jp/english/ Tohoku University]) and [http://www.protein.osaka-u.ac.jp/rcsfp/pi/ Haruki Nakamura] ([http://www.protein.osaka-u.ac.jp/index_e.php Institute for Protein Research], [http://www.osaka-u.ac.jp/eng/index.html Osaka Univeristy]), with the support from [http://biosciencedbc.jp/ JST-NBDC] and [http://www.protein.osaka-u.ac.jp/index_e.php Institute for Protein Research IPR], [http://www.osaka-u.ac.jp/eng/index.html Osaka Univeristy].
      

&lt;gallery&gt;
File:Spacefill.jpg
File:Cartoon.jpg
File:Surface.jpg
File:edmap.jpg
&lt;/gallery&gt;


== Start up ==
You can start up jV (4.5.1) with Java Web Start technology immediately from here.
* [http://ef-site.hgc.jp/eF-site/servlet/stable/jV.jnlp stable JOGL version] (recommended)
* [http://ef-site.hgc.jp/eF-site/servlet/current/jV.jnlp recent JOGL version]
The current jV requires JRE 1.6 or later.
The previous version, jV version 4.0, can run with JRE 1.4 and 1.5.
* [http://ef-site.hgc.jp/jV/stable/jV_4_0.jnlp jV 4.0]

== Basic Usage ==
You can execute basic operations such as rotation and translation with mouse action. Major actions are described in the following table:
{| style="margin:auto;border:1px solid gray"
! rowspan="2" style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap;font-weight:bold" |Action
! colspan="2" style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap;font-weight:bold" |Mouse Operation
|-
! style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap;font-weight:bold" |Windows, Linux
! style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap;font-weight:bold" |Mac OS X
|-
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |rotate around X (horizontal) axis&lt;br /&gt;rotate around Y (vertical) axis
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |left drag
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |drag
|-
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |translate along X axis (holizontally)&lt;br /&gt;translate along Y axis (vertically)
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |right drag
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |Command + drag
|-
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |translate along Z axis (zoom in/out)
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |Shift + left drag
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |Shift + drag
|}

Operations such as changing display models and colors and saving the image, can be executed with a menu. The location of the menu is at the top of the application window in Windows and at the top of screen in Mac as the stand-alone application. As an applet usage, a popup menu appears by clicking the right mouse button on the display screen, or clicking with a "Command" button in case of Mac.

{| style="margin:auto;border:0"
|-
| [[File:Jv_menu_win.png|The location of menu in jV stand-alone version in Windows.|250px]]
| [[File:Jv_menu_mac.png|The location of menu in jV stand-alone version in Mac.|250px]]
| [[File:popupmenu_en.png|The location of menu in applet version.|250px]]
|-
| style="text-align:center" |Stand-alone (Windows)
| style="text-align:center" |Stand-alone (Mac)
| style="text-align:center" |Applet
|}

Basic menu operations are following (see also [[GUI]] for details):

{| style="margin:auto;border:1px solid gray;border-collapse:collapse"
! style="padding:0 0.5em;border:1px solid gray" | Operations
! style="padding:0 0.5em;border:1px solid gray" | Menu location
|-
| style="padding:0 0.5em;border:1px solid gray" | Save a static image
| style="padding:0 0.5em;border:1px solid gray" | [File]-[Save]-[PNG/JPEG]
|-
| style="padding:0 0.5em;border:1px solid gray" | Change the expression format
| style="padding:0 0.5em;border:1px solid gray" | [File]-[Display]-[Wireframe/Backbone/Sticks/Spacefill/Ball&amp;amp;Stick/Ribbons/Cartoon]
|-
| style="padding:0 0.5em;border:1px solid gray" | Change the color
| style="padding:0 0.5em;border:1px solid gray" | [File]-[Colors]-[Monochrome/CPK/Shapely/Group/Chain/Temperature/Structure/Charge/Amino]
|}

To execute more complicated operation such as diplaying some piece of the molecule or changing some part of molecule in another style, use command line operation.

See also [[#Other resources]] for details:


== Download ==
You can also download the program and start it up locally.
The following links take you to the download pages. (latest version is 4.5.1@2016/5/10)
* [http://service.ipr.pdbj.org/eF-site/servlet/DownloadViewerBinary binary (4.5.1)] 
* [http://service.ipr.pdbj.org/eF-site/servlet/Registration source code (4.5.1)] (registration will be required)

== Other resources ==
* [[How_to_use]] (in this site in English)
* [http://www.pdbj.org/jv/manual/index_ja.html Manual] (html in Japanese)</text>
    <sha1>ea4264b0b8a085df7e15fe371b78685c82ac3db6</sha1>
  </revision>
  <revision>
    <id>620</id>
    <parentid>618</parentid>
    <timestamp>2017-01-16T02:33:14Z</timestamp>
    <contributor>
      <username>IMSsato</username>
      <id>4</id>
    </contributor>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="6446" xml:space="preserve">&lt;big&gt;'''Welcome to jV wiki.'''&lt;/big&gt;

jV (formerly known as PDBjViewer) is a program to display molecular graphics of protein and nucleic acids. 
jV supports the following features:
* jV can read and display PDBML files, the canonical XML format for the Protein Data Bank.
* Of course, jV can read and display the traditional PDB format files, too.
* RasMol-like usability.
* jV can process more than one molecules.
* jV can display polygons specified by XML. ([http://www.pdbj.org/jv/polygonSchema XML Schema for polygons] is available.)
* Multiple polygons can be processed simultaneously, and be superimposed onto molecular images.
* Animation can be realized.
* jV runs on the Java Runtime Environment ([http://java.com/download/ JRE]) so that it can work as a stand-alone application as well as an applet.
* The graphics of jV is based on OpenGL ([http://jogamp.org/jogl/www/ JOGL]), thereby producing fairly beautiful pictures.


The program 'jV' has been developed by [http://www.hgc.jp/~kinosita/TOP.html Kengo Kinoshita] ([http://www.is.tohoku.ac.jp/index-e.html Graduate School of Information Sciences], [http://www.tohoku.ac.jp/english/ Tohoku University]) and [http://www.protein.osaka-u.ac.jp/rcsfp/pi/ Haruki Nakamura] ([http://www.protein.osaka-u.ac.jp/index_e.php Institute for Protein Research], [http://www.osaka-u.ac.jp/eng/index.html Osaka Univeristy]), with the support from [http://biosciencedbc.jp/ JST-NBDC] and [http://www.protein.osaka-u.ac.jp/index_e.php Institute for Protein Research IPR], [http://www.osaka-u.ac.jp/eng/index.html Osaka Univeristy].
      

&lt;gallery&gt;
File:Spacefill.jpg
File:Cartoon.jpg
File:Surface.jpg
File:edmap.jpg
&lt;/gallery&gt;


== Start up ==
You can start up jV (4.5.1) with Java Web Start technology immediately from here.
* [http://ef-site.hgc.jp/eF-site/servlet/stable/jV.jnlp stable JOGL version] (recommended)
* [http://ef-site.hgc.jp/eF-site/servlet/current/jV.jnlp recent JOGL version]
The current jV requires JRE 1.6 or later.
The previous version, jV version 4.0, can run with JRE 1.4 and 1.5.
* [http://ef-site.hgc.jp/jV/stable/jV_4_0.jnlp jV 4.0]

== Basic Usage ==
You can execute basic operations such as rotation and translation with mouse action. Major actions are described in the following table:
{| style="margin:auto;border:1px solid gray"
! rowspan="2" style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap;font-weight:bold" |Action
! colspan="2" style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap;font-weight:bold" |Mouse Operation
|-
! style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap;font-weight:bold" |Windows, Linux
! style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap;font-weight:bold" |Mac OS X
|-
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |rotate around X (horizontal) axis&lt;br /&gt;rotate around Y (vertical) axis
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |left drag
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |drag
|-
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |translate along X axis (holizontally)&lt;br /&gt;translate along Y axis (vertically)
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |right drag
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |Command + drag
|-
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |translate along Z axis (zoom in/out)
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |Shift + left drag
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |Shift + drag
|}

Operations such as changing display models and colors and saving the image, can be executed with a menu. The location of the menu is at the top of the application window in Windows and at the top of screen in Mac as the stand-alone application. As an applet usage, a popup menu appears by clicking the right mouse button on the display screen, or clicking with a "Command" button in case of Mac.

{| style="margin:auto;border:0"
|-
| [[File:Jv_menu_win.png|The location of menu in jV stand-alone version in Windows.|250px]]
| [[File:Jv_menu_mac.png|The location of menu in jV stand-alone version in Mac.|250px]]
| [[File:popupmenu_en.png|The location of menu in applet version.|250px]]
|-
| style="text-align:center" |Stand-alone (Windows)
| style="text-align:center" |Stand-alone (Mac)
| style="text-align:center" |Applet
|}

Basic menu operations are following (see also [[GUI]] for details):

{| style="margin:auto;border:1px solid gray;border-collapse:collapse"
! style="padding:0 0.5em;border:1px solid gray" | Operations
! style="padding:0 0.5em;border:1px solid gray" | Menu location
|-
| style="padding:0 0.5em;border:1px solid gray" | Save a static image
| style="padding:0 0.5em;border:1px solid gray" | [File]-[Save]-[PNG/JPEG]
|-
| style="padding:0 0.5em;border:1px solid gray" | Change the expression format
| style="padding:0 0.5em;border:1px solid gray" | [File]-[Display]-[Wireframe/Backbone/Sticks/Spacefill/Ball&amp;amp;Stick/Ribbons/Cartoon]
|-
| style="padding:0 0.5em;border:1px solid gray" | Change the color
| style="padding:0 0.5em;border:1px solid gray" | [File]-[Colors]-[Monochrome/CPK/Shapely/Group/Chain/Temperature/Structure/Charge/Amino]
|}

To execute more complicated operation such as diplaying some piece of the molecule or changing some part of molecule in another style, use command line operation.

See also [[#Other resources]] for details:


== Download ==
You can also download the program and start it up locally.
The following links take you to the download pages. (latest version is 4.5.1@2016/5/10)
* [http://service.ipr.pdbj.org/eF-site/servlet/DownloadViewerBinary binary (4.5.1)] 
* [http://service.ipr.pdbj.org/eF-site/servlet/Registration source code (4.5.1)] (registration will be required)

== Other resources ==
* [[How_to_use]] (in this site in English)
* [http://www.pdbj.org/jv/manual/index_ja.html Manual] (html in Japanese)

== Contact us ==
If you have any questions about jV, please feel free to contact us from [http://pdbj.org/contact here].</text>
    <sha1>31a0b34c38b3d3577e5009f43415afab141fa04b</sha1>
  </revision>
  <revision>
    <id>622</id>
    <parentid>620</parentid>
    <timestamp>2017-01-16T14:24:40Z</timestamp>
    <contributor>
      <username>IMSsato</username>
      <id>4</id>
    </contributor>
    <comment>/* Start up */</comment>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="6446" xml:space="preserve">&lt;big&gt;'''Welcome to jV wiki.'''&lt;/big&gt;

jV (formerly known as PDBjViewer) is a program to display molecular graphics of protein and nucleic acids. 
jV supports the following features:
* jV can read and display PDBML files, the canonical XML format for the Protein Data Bank.
* Of course, jV can read and display the traditional PDB format files, too.
* RasMol-like usability.
* jV can process more than one molecules.
* jV can display polygons specified by XML. ([http://www.pdbj.org/jv/polygonSchema XML Schema for polygons] is available.)
* Multiple polygons can be processed simultaneously, and be superimposed onto molecular images.
* Animation can be realized.
* jV runs on the Java Runtime Environment ([http://java.com/download/ JRE]) so that it can work as a stand-alone application as well as an applet.
* The graphics of jV is based on OpenGL ([http://jogamp.org/jogl/www/ JOGL]), thereby producing fairly beautiful pictures.


The program 'jV' has been developed by [http://www.hgc.jp/~kinosita/TOP.html Kengo Kinoshita] ([http://www.is.tohoku.ac.jp/index-e.html Graduate School of Information Sciences], [http://www.tohoku.ac.jp/english/ Tohoku University]) and [http://www.protein.osaka-u.ac.jp/rcsfp/pi/ Haruki Nakamura] ([http://www.protein.osaka-u.ac.jp/index_e.php Institute for Protein Research], [http://www.osaka-u.ac.jp/eng/index.html Osaka Univeristy]), with the support from [http://biosciencedbc.jp/ JST-NBDC] and [http://www.protein.osaka-u.ac.jp/index_e.php Institute for Protein Research IPR], [http://www.osaka-u.ac.jp/eng/index.html Osaka Univeristy].
      

&lt;gallery&gt;
File:Spacefill.jpg
File:Cartoon.jpg
File:Surface.jpg
File:edmap.jpg
&lt;/gallery&gt;


== Start up ==
You can start up jV (4.5.2) with Java Web Start technology immediately from here.
* [http://ef-site.hgc.jp/eF-site/servlet/stable/jV.jnlp stable JOGL version] (recommended)
* [http://ef-site.hgc.jp/eF-site/servlet/current/jV.jnlp recent JOGL version]
The current jV requires JRE 1.6 or later.
The previous version, jV version 4.0, can run with JRE 1.4 and 1.5.
* [http://ef-site.hgc.jp/jV/stable/jV_4_0.jnlp jV 4.0]

== Basic Usage ==
You can execute basic operations such as rotation and translation with mouse action. Major actions are described in the following table:
{| style="margin:auto;border:1px solid gray"
! rowspan="2" style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap;font-weight:bold" |Action
! colspan="2" style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap;font-weight:bold" |Mouse Operation
|-
! style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap;font-weight:bold" |Windows, Linux
! style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap;font-weight:bold" |Mac OS X
|-
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |rotate around X (horizontal) axis&lt;br /&gt;rotate around Y (vertical) axis
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |left drag
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |drag
|-
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |translate along X axis (holizontally)&lt;br /&gt;translate along Y axis (vertically)
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |right drag
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |Command + drag
|-
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |translate along Z axis (zoom in/out)
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |Shift + left drag
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |Shift + drag
|}

Operations such as changing display models and colors and saving the image, can be executed with a menu. The location of the menu is at the top of the application window in Windows and at the top of screen in Mac as the stand-alone application. As an applet usage, a popup menu appears by clicking the right mouse button on the display screen, or clicking with a "Command" button in case of Mac.

{| style="margin:auto;border:0"
|-
| [[File:Jv_menu_win.png|The location of menu in jV stand-alone version in Windows.|250px]]
| [[File:Jv_menu_mac.png|The location of menu in jV stand-alone version in Mac.|250px]]
| [[File:popupmenu_en.png|The location of menu in applet version.|250px]]
|-
| style="text-align:center" |Stand-alone (Windows)
| style="text-align:center" |Stand-alone (Mac)
| style="text-align:center" |Applet
|}

Basic menu operations are following (see also [[GUI]] for details):

{| style="margin:auto;border:1px solid gray;border-collapse:collapse"
! style="padding:0 0.5em;border:1px solid gray" | Operations
! style="padding:0 0.5em;border:1px solid gray" | Menu location
|-
| style="padding:0 0.5em;border:1px solid gray" | Save a static image
| style="padding:0 0.5em;border:1px solid gray" | [File]-[Save]-[PNG/JPEG]
|-
| style="padding:0 0.5em;border:1px solid gray" | Change the expression format
| style="padding:0 0.5em;border:1px solid gray" | [File]-[Display]-[Wireframe/Backbone/Sticks/Spacefill/Ball&amp;amp;Stick/Ribbons/Cartoon]
|-
| style="padding:0 0.5em;border:1px solid gray" | Change the color
| style="padding:0 0.5em;border:1px solid gray" | [File]-[Colors]-[Monochrome/CPK/Shapely/Group/Chain/Temperature/Structure/Charge/Amino]
|}

To execute more complicated operation such as diplaying some piece of the molecule or changing some part of molecule in another style, use command line operation.

See also [[#Other resources]] for details:


== Download ==
You can also download the program and start it up locally.
The following links take you to the download pages. (latest version is 4.5.1@2016/5/10)
* [http://service.ipr.pdbj.org/eF-site/servlet/DownloadViewerBinary binary (4.5.1)] 
* [http://service.ipr.pdbj.org/eF-site/servlet/Registration source code (4.5.1)] (registration will be required)

== Other resources ==
* [[How_to_use]] (in this site in English)
* [http://www.pdbj.org/jv/manual/index_ja.html Manual] (html in Japanese)

== Contact us ==
If you have any questions about jV, please feel free to contact us from [http://pdbj.org/contact here].</text>
    <sha1>a68507f8340c5e305ab94e47fe500c488aaa4665</sha1>
  </revision>
  <revision>
    <id>623</id>
    <parentid>622</parentid>
    <timestamp>2017-01-16T14:25:05Z</timestamp>
    <contributor>
      <username>IMSsato</username>
      <id>4</id>
    </contributor>
    <comment>/* Download */</comment>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="6446" xml:space="preserve">&lt;big&gt;'''Welcome to jV wiki.'''&lt;/big&gt;

jV (formerly known as PDBjViewer) is a program to display molecular graphics of protein and nucleic acids. 
jV supports the following features:
* jV can read and display PDBML files, the canonical XML format for the Protein Data Bank.
* Of course, jV can read and display the traditional PDB format files, too.
* RasMol-like usability.
* jV can process more than one molecules.
* jV can display polygons specified by XML. ([http://www.pdbj.org/jv/polygonSchema XML Schema for polygons] is available.)
* Multiple polygons can be processed simultaneously, and be superimposed onto molecular images.
* Animation can be realized.
* jV runs on the Java Runtime Environment ([http://java.com/download/ JRE]) so that it can work as a stand-alone application as well as an applet.
* The graphics of jV is based on OpenGL ([http://jogamp.org/jogl/www/ JOGL]), thereby producing fairly beautiful pictures.


The program 'jV' has been developed by [http://www.hgc.jp/~kinosita/TOP.html Kengo Kinoshita] ([http://www.is.tohoku.ac.jp/index-e.html Graduate School of Information Sciences], [http://www.tohoku.ac.jp/english/ Tohoku University]) and [http://www.protein.osaka-u.ac.jp/rcsfp/pi/ Haruki Nakamura] ([http://www.protein.osaka-u.ac.jp/index_e.php Institute for Protein Research], [http://www.osaka-u.ac.jp/eng/index.html Osaka Univeristy]), with the support from [http://biosciencedbc.jp/ JST-NBDC] and [http://www.protein.osaka-u.ac.jp/index_e.php Institute for Protein Research IPR], [http://www.osaka-u.ac.jp/eng/index.html Osaka Univeristy].
      

&lt;gallery&gt;
File:Spacefill.jpg
File:Cartoon.jpg
File:Surface.jpg
File:edmap.jpg
&lt;/gallery&gt;


== Start up ==
You can start up jV (4.5.2) with Java Web Start technology immediately from here.
* [http://ef-site.hgc.jp/eF-site/servlet/stable/jV.jnlp stable JOGL version] (recommended)
* [http://ef-site.hgc.jp/eF-site/servlet/current/jV.jnlp recent JOGL version]
The current jV requires JRE 1.6 or later.
The previous version, jV version 4.0, can run with JRE 1.4 and 1.5.
* [http://ef-site.hgc.jp/jV/stable/jV_4_0.jnlp jV 4.0]

== Basic Usage ==
You can execute basic operations such as rotation and translation with mouse action. Major actions are described in the following table:
{| style="margin:auto;border:1px solid gray"
! rowspan="2" style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap;font-weight:bold" |Action
! colspan="2" style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap;font-weight:bold" |Mouse Operation
|-
! style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap;font-weight:bold" |Windows, Linux
! style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap;font-weight:bold" |Mac OS X
|-
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |rotate around X (horizontal) axis&lt;br /&gt;rotate around Y (vertical) axis
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |left drag
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |drag
|-
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |translate along X axis (holizontally)&lt;br /&gt;translate along Y axis (vertically)
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |right drag
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |Command + drag
|-
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |translate along Z axis (zoom in/out)
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |Shift + left drag
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |Shift + drag
|}

Operations such as changing display models and colors and saving the image, can be executed with a menu. The location of the menu is at the top of the application window in Windows and at the top of screen in Mac as the stand-alone application. As an applet usage, a popup menu appears by clicking the right mouse button on the display screen, or clicking with a "Command" button in case of Mac.

{| style="margin:auto;border:0"
|-
| [[File:Jv_menu_win.png|The location of menu in jV stand-alone version in Windows.|250px]]
| [[File:Jv_menu_mac.png|The location of menu in jV stand-alone version in Mac.|250px]]
| [[File:popupmenu_en.png|The location of menu in applet version.|250px]]
|-
| style="text-align:center" |Stand-alone (Windows)
| style="text-align:center" |Stand-alone (Mac)
| style="text-align:center" |Applet
|}

Basic menu operations are following (see also [[GUI]] for details):

{| style="margin:auto;border:1px solid gray;border-collapse:collapse"
! style="padding:0 0.5em;border:1px solid gray" | Operations
! style="padding:0 0.5em;border:1px solid gray" | Menu location
|-
| style="padding:0 0.5em;border:1px solid gray" | Save a static image
| style="padding:0 0.5em;border:1px solid gray" | [File]-[Save]-[PNG/JPEG]
|-
| style="padding:0 0.5em;border:1px solid gray" | Change the expression format
| style="padding:0 0.5em;border:1px solid gray" | [File]-[Display]-[Wireframe/Backbone/Sticks/Spacefill/Ball&amp;amp;Stick/Ribbons/Cartoon]
|-
| style="padding:0 0.5em;border:1px solid gray" | Change the color
| style="padding:0 0.5em;border:1px solid gray" | [File]-[Colors]-[Monochrome/CPK/Shapely/Group/Chain/Temperature/Structure/Charge/Amino]
|}

To execute more complicated operation such as diplaying some piece of the molecule or changing some part of molecule in another style, use command line operation.

See also [[#Other resources]] for details:


== Download ==
You can also download the program and start it up locally.
The following links take you to the download pages. (latest version is 4.5.2@2017/1/16)
* [http://service.ipr.pdbj.org/eF-site/servlet/DownloadViewerBinary binary (4.5.2)] 
* [http://service.ipr.pdbj.org/eF-site/servlet/Registration source code (4.5.2)] (registration will be required)

== Other resources ==
* [[How_to_use]] (in this site in English)
* [http://www.pdbj.org/jv/manual/index_ja.html Manual] (html in Japanese)

== Contact us ==
If you have any questions about jV, please feel free to contact us from [http://pdbj.org/contact here].</text>
    <sha1>4744731414cb3d545f63cd434c274d54f8eb0f3b</sha1>
  </revision>
  <revision>
    <id>624</id>
    <parentid>623</parentid>
    <timestamp>2017-02-06T08:58:31Z</timestamp>
    <contributor>
      <username>IMSsato</username>
      <id>4</id>
    </contributor>
    <comment>/* Start up */</comment>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="6446" xml:space="preserve">&lt;big&gt;'''Welcome to jV wiki.'''&lt;/big&gt;

jV (formerly known as PDBjViewer) is a program to display molecular graphics of protein and nucleic acids. 
jV supports the following features:
* jV can read and display PDBML files, the canonical XML format for the Protein Data Bank.
* Of course, jV can read and display the traditional PDB format files, too.
* RasMol-like usability.
* jV can process more than one molecules.
* jV can display polygons specified by XML. ([http://www.pdbj.org/jv/polygonSchema XML Schema for polygons] is available.)
* Multiple polygons can be processed simultaneously, and be superimposed onto molecular images.
* Animation can be realized.
* jV runs on the Java Runtime Environment ([http://java.com/download/ JRE]) so that it can work as a stand-alone application as well as an applet.
* The graphics of jV is based on OpenGL ([http://jogamp.org/jogl/www/ JOGL]), thereby producing fairly beautiful pictures.


The program 'jV' has been developed by [http://www.hgc.jp/~kinosita/TOP.html Kengo Kinoshita] ([http://www.is.tohoku.ac.jp/index-e.html Graduate School of Information Sciences], [http://www.tohoku.ac.jp/english/ Tohoku University]) and [http://www.protein.osaka-u.ac.jp/rcsfp/pi/ Haruki Nakamura] ([http://www.protein.osaka-u.ac.jp/index_e.php Institute for Protein Research], [http://www.osaka-u.ac.jp/eng/index.html Osaka Univeristy]), with the support from [http://biosciencedbc.jp/ JST-NBDC] and [http://www.protein.osaka-u.ac.jp/index_e.php Institute for Protein Research IPR], [http://www.osaka-u.ac.jp/eng/index.html Osaka Univeristy].
      

&lt;gallery&gt;
File:Spacefill.jpg
File:Cartoon.jpg
File:Surface.jpg
File:edmap.jpg
&lt;/gallery&gt;


== Start up ==
You can start up jV (4.5.3) with Java Web Start technology immediately from here.
* [http://ef-site.hgc.jp/eF-site/servlet/stable/jV.jnlp stable JOGL version] (recommended)
* [http://ef-site.hgc.jp/eF-site/servlet/current/jV.jnlp recent JOGL version]
The current jV requires JRE 1.6 or later.
The previous version, jV version 4.0, can run with JRE 1.4 and 1.5.
* [http://ef-site.hgc.jp/jV/stable/jV_4_0.jnlp jV 4.0]

== Basic Usage ==
You can execute basic operations such as rotation and translation with mouse action. Major actions are described in the following table:
{| style="margin:auto;border:1px solid gray"
! rowspan="2" style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap;font-weight:bold" |Action
! colspan="2" style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap;font-weight:bold" |Mouse Operation
|-
! style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap;font-weight:bold" |Windows, Linux
! style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap;font-weight:bold" |Mac OS X
|-
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |rotate around X (horizontal) axis&lt;br /&gt;rotate around Y (vertical) axis
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |left drag
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |drag
|-
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |translate along X axis (holizontally)&lt;br /&gt;translate along Y axis (vertically)
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |right drag
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |Command + drag
|-
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |translate along Z axis (zoom in/out)
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |Shift + left drag
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |Shift + drag
|}

Operations such as changing display models and colors and saving the image, can be executed with a menu. The location of the menu is at the top of the application window in Windows and at the top of screen in Mac as the stand-alone application. As an applet usage, a popup menu appears by clicking the right mouse button on the display screen, or clicking with a "Command" button in case of Mac.

{| style="margin:auto;border:0"
|-
| [[File:Jv_menu_win.png|The location of menu in jV stand-alone version in Windows.|250px]]
| [[File:Jv_menu_mac.png|The location of menu in jV stand-alone version in Mac.|250px]]
| [[File:popupmenu_en.png|The location of menu in applet version.|250px]]
|-
| style="text-align:center" |Stand-alone (Windows)
| style="text-align:center" |Stand-alone (Mac)
| style="text-align:center" |Applet
|}

Basic menu operations are following (see also [[GUI]] for details):

{| style="margin:auto;border:1px solid gray;border-collapse:collapse"
! style="padding:0 0.5em;border:1px solid gray" | Operations
! style="padding:0 0.5em;border:1px solid gray" | Menu location
|-
| style="padding:0 0.5em;border:1px solid gray" | Save a static image
| style="padding:0 0.5em;border:1px solid gray" | [File]-[Save]-[PNG/JPEG]
|-
| style="padding:0 0.5em;border:1px solid gray" | Change the expression format
| style="padding:0 0.5em;border:1px solid gray" | [File]-[Display]-[Wireframe/Backbone/Sticks/Spacefill/Ball&amp;amp;Stick/Ribbons/Cartoon]
|-
| style="padding:0 0.5em;border:1px solid gray" | Change the color
| style="padding:0 0.5em;border:1px solid gray" | [File]-[Colors]-[Monochrome/CPK/Shapely/Group/Chain/Temperature/Structure/Charge/Amino]
|}

To execute more complicated operation such as diplaying some piece of the molecule or changing some part of molecule in another style, use command line operation.

See also [[#Other resources]] for details:


== Download ==
You can also download the program and start it up locally.
The following links take you to the download pages. (latest version is 4.5.2@2017/1/16)
* [http://service.ipr.pdbj.org/eF-site/servlet/DownloadViewerBinary binary (4.5.2)] 
* [http://service.ipr.pdbj.org/eF-site/servlet/Registration source code (4.5.2)] (registration will be required)

== Other resources ==
* [[How_to_use]] (in this site in English)
* [http://www.pdbj.org/jv/manual/index_ja.html Manual] (html in Japanese)

== Contact us ==
If you have any questions about jV, please feel free to contact us from [http://pdbj.org/contact here].</text>
    <sha1>3e7730edeff4b2e5acf254669838de0e88017c83</sha1>
  </revision>
  <revision>
    <id>625</id>
    <parentid>624</parentid>
    <timestamp>2017-02-06T08:58:49Z</timestamp>
    <contributor>
      <username>IMSsato</username>
      <id>4</id>
    </contributor>
    <comment>/* Download */</comment>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="6445" xml:space="preserve">&lt;big&gt;'''Welcome to jV wiki.'''&lt;/big&gt;

jV (formerly known as PDBjViewer) is a program to display molecular graphics of protein and nucleic acids. 
jV supports the following features:
* jV can read and display PDBML files, the canonical XML format for the Protein Data Bank.
* Of course, jV can read and display the traditional PDB format files, too.
* RasMol-like usability.
* jV can process more than one molecules.
* jV can display polygons specified by XML. ([http://www.pdbj.org/jv/polygonSchema XML Schema for polygons] is available.)
* Multiple polygons can be processed simultaneously, and be superimposed onto molecular images.
* Animation can be realized.
* jV runs on the Java Runtime Environment ([http://java.com/download/ JRE]) so that it can work as a stand-alone application as well as an applet.
* The graphics of jV is based on OpenGL ([http://jogamp.org/jogl/www/ JOGL]), thereby producing fairly beautiful pictures.


The program 'jV' has been developed by [http://www.hgc.jp/~kinosita/TOP.html Kengo Kinoshita] ([http://www.is.tohoku.ac.jp/index-e.html Graduate School of Information Sciences], [http://www.tohoku.ac.jp/english/ Tohoku University]) and [http://www.protein.osaka-u.ac.jp/rcsfp/pi/ Haruki Nakamura] ([http://www.protein.osaka-u.ac.jp/index_e.php Institute for Protein Research], [http://www.osaka-u.ac.jp/eng/index.html Osaka Univeristy]), with the support from [http://biosciencedbc.jp/ JST-NBDC] and [http://www.protein.osaka-u.ac.jp/index_e.php Institute for Protein Research IPR], [http://www.osaka-u.ac.jp/eng/index.html Osaka Univeristy].
      

&lt;gallery&gt;
File:Spacefill.jpg
File:Cartoon.jpg
File:Surface.jpg
File:edmap.jpg
&lt;/gallery&gt;


== Start up ==
You can start up jV (4.5.3) with Java Web Start technology immediately from here.
* [http://ef-site.hgc.jp/eF-site/servlet/stable/jV.jnlp stable JOGL version] (recommended)
* [http://ef-site.hgc.jp/eF-site/servlet/current/jV.jnlp recent JOGL version]
The current jV requires JRE 1.6 or later.
The previous version, jV version 4.0, can run with JRE 1.4 and 1.5.
* [http://ef-site.hgc.jp/jV/stable/jV_4_0.jnlp jV 4.0]

== Basic Usage ==
You can execute basic operations such as rotation and translation with mouse action. Major actions are described in the following table:
{| style="margin:auto;border:1px solid gray"
! rowspan="2" style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap;font-weight:bold" |Action
! colspan="2" style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap;font-weight:bold" |Mouse Operation
|-
! style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap;font-weight:bold" |Windows, Linux
! style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap;font-weight:bold" |Mac OS X
|-
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |rotate around X (horizontal) axis&lt;br /&gt;rotate around Y (vertical) axis
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |left drag
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |drag
|-
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |translate along X axis (holizontally)&lt;br /&gt;translate along Y axis (vertically)
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |right drag
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |Command + drag
|-
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |translate along Z axis (zoom in/out)
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |Shift + left drag
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |Shift + drag
|}

Operations such as changing display models and colors and saving the image, can be executed with a menu. The location of the menu is at the top of the application window in Windows and at the top of screen in Mac as the stand-alone application. As an applet usage, a popup menu appears by clicking the right mouse button on the display screen, or clicking with a "Command" button in case of Mac.

{| style="margin:auto;border:0"
|-
| [[File:Jv_menu_win.png|The location of menu in jV stand-alone version in Windows.|250px]]
| [[File:Jv_menu_mac.png|The location of menu in jV stand-alone version in Mac.|250px]]
| [[File:popupmenu_en.png|The location of menu in applet version.|250px]]
|-
| style="text-align:center" |Stand-alone (Windows)
| style="text-align:center" |Stand-alone (Mac)
| style="text-align:center" |Applet
|}

Basic menu operations are following (see also [[GUI]] for details):

{| style="margin:auto;border:1px solid gray;border-collapse:collapse"
! style="padding:0 0.5em;border:1px solid gray" | Operations
! style="padding:0 0.5em;border:1px solid gray" | Menu location
|-
| style="padding:0 0.5em;border:1px solid gray" | Save a static image
| style="padding:0 0.5em;border:1px solid gray" | [File]-[Save]-[PNG/JPEG]
|-
| style="padding:0 0.5em;border:1px solid gray" | Change the expression format
| style="padding:0 0.5em;border:1px solid gray" | [File]-[Display]-[Wireframe/Backbone/Sticks/Spacefill/Ball&amp;amp;Stick/Ribbons/Cartoon]
|-
| style="padding:0 0.5em;border:1px solid gray" | Change the color
| style="padding:0 0.5em;border:1px solid gray" | [File]-[Colors]-[Monochrome/CPK/Shapely/Group/Chain/Temperature/Structure/Charge/Amino]
|}

To execute more complicated operation such as diplaying some piece of the molecule or changing some part of molecule in another style, use command line operation.

See also [[#Other resources]] for details:


== Download ==
You can also download the program and start it up locally.
The following links take you to the download pages. (latest version is 4.5.3@2017/2/6)
* [http://service.ipr.pdbj.org/eF-site/servlet/DownloadViewerBinary binary (4.5.3)] 
* [http://service.ipr.pdbj.org/eF-site/servlet/Registration source code (4.5.3)] (registration will be required)

== Other resources ==
* [[How_to_use]] (in this site in English)
* [http://www.pdbj.org/jv/manual/index_ja.html Manual] (html in Japanese)

== Contact us ==
If you have any questions about jV, please feel free to contact us from [http://pdbj.org/contact here].</text>
    <sha1>3c26f380e5423d1ab75f9355b39a066d06b99574</sha1>
  </revision>
  <revision>
    <id>627</id>
    <parentid>625</parentid>
    <timestamp>2017-04-11T03:58:46Z</timestamp>
    <contributor>
      <username>IMSsato</username>
      <id>4</id>
    </contributor>
    <comment>/* Start up */</comment>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="6449" xml:space="preserve">&lt;big&gt;'''Welcome to jV wiki.'''&lt;/big&gt;

jV (formerly known as PDBjViewer) is a program to display molecular graphics of protein and nucleic acids. 
jV supports the following features:
* jV can read and display PDBML files, the canonical XML format for the Protein Data Bank.
* Of course, jV can read and display the traditional PDB format files, too.
* RasMol-like usability.
* jV can process more than one molecules.
* jV can display polygons specified by XML. ([http://www.pdbj.org/jv/polygonSchema XML Schema for polygons] is available.)
* Multiple polygons can be processed simultaneously, and be superimposed onto molecular images.
* Animation can be realized.
* jV runs on the Java Runtime Environment ([http://java.com/download/ JRE]) so that it can work as a stand-alone application as well as an applet.
* The graphics of jV is based on OpenGL ([http://jogamp.org/jogl/www/ JOGL]), thereby producing fairly beautiful pictures.


The program 'jV' has been developed by [http://www.hgc.jp/~kinosita/TOP.html Kengo Kinoshita] ([http://www.is.tohoku.ac.jp/index-e.html Graduate School of Information Sciences], [http://www.tohoku.ac.jp/english/ Tohoku University]) and [http://www.protein.osaka-u.ac.jp/rcsfp/pi/ Haruki Nakamura] ([http://www.protein.osaka-u.ac.jp/index_e.php Institute for Protein Research], [http://www.osaka-u.ac.jp/eng/index.html Osaka Univeristy]), with the support from [http://biosciencedbc.jp/ JST-NBDC] and [http://www.protein.osaka-u.ac.jp/index_e.php Institute for Protein Research IPR], [http://www.osaka-u.ac.jp/eng/index.html Osaka Univeristy].
      

&lt;gallery&gt;
File:Spacefill.jpg
File:Cartoon.jpg
File:Surface.jpg
File:edmap.jpg
&lt;/gallery&gt;


== Start up ==
You can start up jV (4.5.3) with Java Web Start technology immediately from here.
* [http://service.pdbj.org/eF-site/servlet/stable/jV.jnlp stable JOGL version] (recommended)
* [http://service.pdbj.org/eF-site/servlet/current/jV.jnlp recent JOGL version]
The current jV requires JRE 1.6 or later.
The previous version, jV version 4.0, can run with JRE 1.4 and 1.5.
* [http://ef-site.hgc.jp/jV/stable/jV_4_0.jnlp jV 4.0]

== Basic Usage ==
You can execute basic operations such as rotation and translation with mouse action. Major actions are described in the following table:
{| style="margin:auto;border:1px solid gray"
! rowspan="2" style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap;font-weight:bold" |Action
! colspan="2" style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap;font-weight:bold" |Mouse Operation
|-
! style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap;font-weight:bold" |Windows, Linux
! style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap;font-weight:bold" |Mac OS X
|-
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |rotate around X (horizontal) axis&lt;br /&gt;rotate around Y (vertical) axis
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |left drag
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |drag
|-
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |translate along X axis (holizontally)&lt;br /&gt;translate along Y axis (vertically)
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |right drag
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |Command + drag
|-
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |translate along Z axis (zoom in/out)
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |Shift + left drag
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |Shift + drag
|}

Operations such as changing display models and colors and saving the image, can be executed with a menu. The location of the menu is at the top of the application window in Windows and at the top of screen in Mac as the stand-alone application. As an applet usage, a popup menu appears by clicking the right mouse button on the display screen, or clicking with a "Command" button in case of Mac.

{| style="margin:auto;border:0"
|-
| [[File:Jv_menu_win.png|The location of menu in jV stand-alone version in Windows.|250px]]
| [[File:Jv_menu_mac.png|The location of menu in jV stand-alone version in Mac.|250px]]
| [[File:popupmenu_en.png|The location of menu in applet version.|250px]]
|-
| style="text-align:center" |Stand-alone (Windows)
| style="text-align:center" |Stand-alone (Mac)
| style="text-align:center" |Applet
|}

Basic menu operations are following (see also [[GUI]] for details):

{| style="margin:auto;border:1px solid gray;border-collapse:collapse"
! style="padding:0 0.5em;border:1px solid gray" | Operations
! style="padding:0 0.5em;border:1px solid gray" | Menu location
|-
| style="padding:0 0.5em;border:1px solid gray" | Save a static image
| style="padding:0 0.5em;border:1px solid gray" | [File]-[Save]-[PNG/JPEG]
|-
| style="padding:0 0.5em;border:1px solid gray" | Change the expression format
| style="padding:0 0.5em;border:1px solid gray" | [File]-[Display]-[Wireframe/Backbone/Sticks/Spacefill/Ball&amp;amp;Stick/Ribbons/Cartoon]
|-
| style="padding:0 0.5em;border:1px solid gray" | Change the color
| style="padding:0 0.5em;border:1px solid gray" | [File]-[Colors]-[Monochrome/CPK/Shapely/Group/Chain/Temperature/Structure/Charge/Amino]
|}

To execute more complicated operation such as diplaying some piece of the molecule or changing some part of molecule in another style, use command line operation.

See also [[#Other resources]] for details:


== Download ==
You can also download the program and start it up locally.
The following links take you to the download pages. (latest version is 4.5.3@2017/2/6)
* [http://service.ipr.pdbj.org/eF-site/servlet/DownloadViewerBinary binary (4.5.3)] 
* [http://service.ipr.pdbj.org/eF-site/servlet/Registration source code (4.5.3)] (registration will be required)

== Other resources ==
* [[How_to_use]] (in this site in English)
* [http://www.pdbj.org/jv/manual/index_ja.html Manual] (html in Japanese)

== Contact us ==
If you have any questions about jV, please feel free to contact us from [http://pdbj.org/contact here].</text>
    <sha1>1e3332605f748142f5baf23e7c94fcd03e5c5ba7</sha1>
  </revision>
  <revision>
    <id>628</id>
    <parentid>627</parentid>
    <timestamp>2018-02-06T06:32:31Z</timestamp>
    <contributor>
      <username>IMSsato</username>
      <id>4</id>
    </contributor>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="6449" xml:space="preserve">&lt;big&gt;'''Welcome to jV wiki.'''&lt;/big&gt;

jV (formerly known as PDBjViewer) is a program to display molecular graphics of protein and nucleic acids. 
jV supports the following features:
* jV can read and display PDBML files, the canonical XML format for the Protein Data Bank.
* Of course, jV can read and display the traditional PDB format files, too.
* RasMol-like usability.
* jV can process more than one molecules.
* jV can display polygons specified by XML. ([http://www.pdbj.org/jv/polygonSchema XML Schema for polygons] is available.)
* Multiple polygons can be processed simultaneously, and be superimposed onto molecular images.
* Animation can be realized.
* jV runs on the Java Runtime Environment ([http://java.com/download/ JRE]) so that it can work as a stand-alone application as well as an applet.
* The graphics of jV is based on OpenGL ([http://jogamp.org/jogl/www/ JOGL]), thereby producing fairly beautiful pictures.


The program 'jV' has been developed by [http://www.hgc.jp/~kinosita/TOP.html Kengo Kinoshita] ([http://www.is.tohoku.ac.jp/index-e.html Graduate School of Information Sciences], [http://www.tohoku.ac.jp/english/ Tohoku University]) and [http://www.protein.osaka-u.ac.jp/rcsfp/pi/ Haruki Nakamura] ([http://www.protein.osaka-u.ac.jp/index_e.php Institute for Protein Research], [http://www.osaka-u.ac.jp/eng/index.html Osaka Univeristy]), with the support from [http://biosciencedbc.jp/ JST-NBDC] and [http://www.protein.osaka-u.ac.jp/index_e.php Institute for Protein Research IPR], [http://www.osaka-u.ac.jp/eng/index.html Osaka Univeristy].
      

&lt;gallery&gt;
File:Spacefill.jpg
File:Cartoon.jpg
File:Surface.jpg
File:edmap.jpg
&lt;/gallery&gt;


== Start up ==
You can start up jV (4.5.4) with Java Web Start technology immediately from here.
* [http://service.pdbj.org/eF-site/servlet/stable/jV.jnlp stable JOGL version] (recommended)
* [http://service.pdbj.org/eF-site/servlet/current/jV.jnlp recent JOGL version]
The current jV requires JRE 1.6 or later.
The previous version, jV version 4.0, can run with JRE 1.4 and 1.5.
* [http://ef-site.hgc.jp/jV/stable/jV_4_0.jnlp jV 4.0]

== Basic Usage ==
You can execute basic operations such as rotation and translation with mouse action. Major actions are described in the following table:
{| style="margin:auto;border:1px solid gray"
! rowspan="2" style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap;font-weight:bold" |Action
! colspan="2" style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap;font-weight:bold" |Mouse Operation
|-
! style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap;font-weight:bold" |Windows, Linux
! style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap;font-weight:bold" |Mac OS X
|-
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |rotate around X (horizontal) axis&lt;br /&gt;rotate around Y (vertical) axis
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |left drag
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |drag
|-
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |translate along X axis (holizontally)&lt;br /&gt;translate along Y axis (vertically)
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |right drag
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |Command + drag
|-
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |translate along Z axis (zoom in/out)
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |Shift + left drag
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |Shift + drag
|}

Operations such as changing display models and colors and saving the image, can be executed with a menu. The location of the menu is at the top of the application window in Windows and at the top of screen in Mac as the stand-alone application. As an applet usage, a popup menu appears by clicking the right mouse button on the display screen, or clicking with a "Command" button in case of Mac.

{| style="margin:auto;border:0"
|-
| [[File:Jv_menu_win.png|The location of menu in jV stand-alone version in Windows.|250px]]
| [[File:Jv_menu_mac.png|The location of menu in jV stand-alone version in Mac.|250px]]
| [[File:popupmenu_en.png|The location of menu in applet version.|250px]]
|-
| style="text-align:center" |Stand-alone (Windows)
| style="text-align:center" |Stand-alone (Mac)
| style="text-align:center" |Applet
|}

Basic menu operations are following (see also [[GUI]] for details):

{| style="margin:auto;border:1px solid gray;border-collapse:collapse"
! style="padding:0 0.5em;border:1px solid gray" | Operations
! style="padding:0 0.5em;border:1px solid gray" | Menu location
|-
| style="padding:0 0.5em;border:1px solid gray" | Save a static image
| style="padding:0 0.5em;border:1px solid gray" | [File]-[Save]-[PNG/JPEG]
|-
| style="padding:0 0.5em;border:1px solid gray" | Change the expression format
| style="padding:0 0.5em;border:1px solid gray" | [File]-[Display]-[Wireframe/Backbone/Sticks/Spacefill/Ball&amp;amp;Stick/Ribbons/Cartoon]
|-
| style="padding:0 0.5em;border:1px solid gray" | Change the color
| style="padding:0 0.5em;border:1px solid gray" | [File]-[Colors]-[Monochrome/CPK/Shapely/Group/Chain/Temperature/Structure/Charge/Amino]
|}

To execute more complicated operation such as diplaying some piece of the molecule or changing some part of molecule in another style, use command line operation.

See also [[#Other resources]] for details:


== Download ==
You can also download the program and start it up locally.
The following links take you to the download pages. (latest version is 4.5.4@2018/2/3)
* [http://service.ipr.pdbj.org/eF-site/servlet/DownloadViewerBinary binary (4.5.4)] 
* [http://service.ipr.pdbj.org/eF-site/servlet/Registration source code (4.5.4)] (registration will be required)

== Other resources ==
* [[How_to_use]] (in this site in English)
* [http://www.pdbj.org/jv/manual/index_ja.html Manual] (html in Japanese)

== Contact us ==
If you have any questions about jV, please feel free to contact us from [http://pdbj.org/contact here].</text>
    <sha1>6f75283dfc4eaf1468e7d60e6d943cb57df5d43e</sha1>
  </revision>
  <revision>
    <id>630</id>
    <parentid>628</parentid>
    <timestamp>2018-02-06T06:35:54Z</timestamp>
    <contributor>
      <username>IMSsato</username>
      <id>4</id>
    </contributor>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="6413" xml:space="preserve">&lt;big&gt;'''Welcome to jV wiki.'''&lt;/big&gt;

jV (formerly known as PDBjViewer) is a program to display molecular graphics of protein and nucleic acids. 
jV supports the following features:
* jV can read and display PDBML files, the canonical XML format for the Protein Data Bank.
* Of course, jV can read and display the traditional PDB format files, too.
* RasMol-like usability.
* jV can process more than one molecules.
* jV can display polygons specified by XML. ([http://www.pdbj.org/jv/polygonSchema XML Schema for polygons] is available.)
* Multiple polygons can be processed simultaneously, and be superimposed onto molecular images.
* Animation can be realized.
* jV runs on the Java Runtime Environment ([http://java.com/download/ JRE]) so that it can work as a stand-alone application as well as an applet.
* The graphics of jV is based on OpenGL ([http://jogamp.org/jogl/www/ JOGL]), thereby producing fairly beautiful pictures.


The program 'jV' has been developed by [http://www.hgc.jp/~kinosita/TOP.html Kengo Kinoshita] ([http://www.is.tohoku.ac.jp/index-e.html Graduate School of Information Sciences], [http://www.tohoku.ac.jp/english/ Tohoku University]) and [http://www.protein.osaka-u.ac.jp/rcsfp/pi/ Haruki Nakamura] ([http://www.protein.osaka-u.ac.jp/index_e.php Institute for Protein Research], [http://www.osaka-u.ac.jp/eng/index.html Osaka Univeristy]), with the support from [http://biosciencedbc.jp/ JST-NBDC] and [http://www.protein.osaka-u.ac.jp/index_e.php Institute for Protein Research IPR], [http://www.osaka-u.ac.jp/eng/index.html Osaka Univeristy].
      

&lt;gallery&gt;
File:Spacefill.jpg
File:Cartoon.jpg
File:Surface.jpg
File:edmap.jpg
&lt;/gallery&gt;


== Start up ==
You can start up jV (4.5.4) with Java Web Start technology immediately from here.
* [https://pdbj.org/eF-site/servlet/stable/jV.jnlp stable JOGL version] (recommended)
* [https://pdbj.org/eF-site/servlet/current/jV.jnlp recent JOGL version]
The current jV requires JRE 1.6 or later.
The previous version, jV version 4.0, can run with JRE 1.4 and 1.5.
* [http://ef-site.hgc.jp/jV/stable/jV_4_0.jnlp jV 4.0]

== Basic Usage ==
You can execute basic operations such as rotation and translation with mouse action. Major actions are described in the following table:
{| style="margin:auto;border:1px solid gray"
! rowspan="2" style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap;font-weight:bold" |Action
! colspan="2" style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap;font-weight:bold" |Mouse Operation
|-
! style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap;font-weight:bold" |Windows, Linux
! style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap;font-weight:bold" |Mac OS X
|-
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |rotate around X (horizontal) axis&lt;br /&gt;rotate around Y (vertical) axis
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |left drag
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |drag
|-
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |translate along X axis (holizontally)&lt;br /&gt;translate along Y axis (vertically)
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |right drag
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |Command + drag
|-
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |translate along Z axis (zoom in/out)
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |Shift + left drag
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |Shift + drag
|}

Operations such as changing display models and colors and saving the image, can be executed with a menu. The location of the menu is at the top of the application window in Windows and at the top of screen in Mac as the stand-alone application. As an applet usage, a popup menu appears by clicking the right mouse button on the display screen, or clicking with a "Command" button in case of Mac.

{| style="margin:auto;border:0"
|-
| [[File:Jv_menu_win.png|The location of menu in jV stand-alone version in Windows.|250px]]
| [[File:Jv_menu_mac.png|The location of menu in jV stand-alone version in Mac.|250px]]
| [[File:popupmenu_en.png|The location of menu in applet version.|250px]]
|-
| style="text-align:center" |Stand-alone (Windows)
| style="text-align:center" |Stand-alone (Mac)
| style="text-align:center" |Applet
|}

Basic menu operations are following (see also [[GUI]] for details):

{| style="margin:auto;border:1px solid gray;border-collapse:collapse"
! style="padding:0 0.5em;border:1px solid gray" | Operations
! style="padding:0 0.5em;border:1px solid gray" | Menu location
|-
| style="padding:0 0.5em;border:1px solid gray" | Save a static image
| style="padding:0 0.5em;border:1px solid gray" | [File]-[Save]-[PNG/JPEG]
|-
| style="padding:0 0.5em;border:1px solid gray" | Change the expression format
| style="padding:0 0.5em;border:1px solid gray" | [File]-[Display]-[Wireframe/Backbone/Sticks/Spacefill/Ball&amp;amp;Stick/Ribbons/Cartoon]
|-
| style="padding:0 0.5em;border:1px solid gray" | Change the color
| style="padding:0 0.5em;border:1px solid gray" | [File]-[Colors]-[Monochrome/CPK/Shapely/Group/Chain/Temperature/Structure/Charge/Amino]
|}

To execute more complicated operation such as diplaying some piece of the molecule or changing some part of molecule in another style, use command line operation.

See also [[#Other resources]] for details:


== Download ==
You can also download the program and start it up locally.
The following links take you to the download pages. (latest version is 4.5.4@2018/2/3)
* [https://pdbj.org/eF-site/servlet/DownloadViewerBinary binary (4.5.4)] 
* [https://pdbj.org/eF-site/servlet/Registration source code (4.5.4)] (registration will be required)

== Other resources ==
* [[How_to_use]] (in this site in English)
* [http://www.pdbj.org/jv/manual/index_ja.html Manual] (html in Japanese)

== Contact us ==
If you have any questions about jV, please feel free to contact us from [http://pdbj.org/contact here].</text>
    <sha1>fe7bc878a734be4d0bc01c7c08b808f82ac32c27</sha1>
  </revision>
  <revision>
    <id>635</id>
    <parentid>630</parentid>
    <timestamp>2018-02-06T08:33:21Z</timestamp>
    <contributor>
      <username>Cudo29</username>
      <id>5</id>
    </contributor>
    <comment>Updated such as URLs.</comment>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="6387" xml:space="preserve">&lt;big&gt;'''Welcome to jV wiki.'''&lt;/big&gt;

jV (formerly known as PDBjViewer) is a program to display molecular graphics of protein and nucleic acids. 
jV supports the following features:
* jV can read and display PDBML files, the canonical XML format for the Protein Data Bank.
* Of course, jV can read and display the traditional PDB format files, too.
* RasMol-like usability.
* jV can process more than one molecules.
* jV can display polygons specified by XML. ([https://pdbj.org/eF-site/schema/polygon12.xsd XML Schema for polygons] is available.)
* Multiple polygons can be processed simultaneously, and be superimposed onto molecular images.
* Animation can be realized.
* jV runs on the Java Runtime Environment ([http://java.com/download/ JRE]) so that it can work as a stand-alone application as well as an applet.
* The graphics of jV is based on OpenGL ([http://jogamp.org/jogl/www/ JOGL]), thereby producing fairly beautiful pictures.


The program 'jV' has been developed by [http://www.sb.ecei.tohoku.ac.jp/index-en.html Kengo Kinoshita] ([https://www.is.tohoku.ac.jp/en/ Graduate School of Information Sciences], [http://www.tohoku.ac.jp/en/ Tohoku University]) and [http://www.protein.osaka-u.ac.jp/rcsfp/pi/index_en.html Haruki Nakamura] ([http://www.protein.osaka-u.ac.jp/en/ Institute for Protein Research], [http://www.osaka-u.ac.jp/en Osaka Univeristy]), with the support from [https://biosciencedbc.jp/en/ JST-NBDC] and [http://www.protein.osaka-u.ac.jp/en/ Institute for Protein Research IPR], [http://www.osaka-u.ac.jp/en Osaka Univeristy].
      

&lt;gallery&gt;
File:Spacefill.jpg
File:Cartoon.jpg
File:Surface.jpg
File:edmap.jpg
&lt;/gallery&gt;


== Start up ==
You can start up jV (4.5.4) with Java Web Start technology immediately from here.
* [https://pdbj.org/eF-site/servlet/stable/jV.jnlp stable JOGL version] (recommended)
* [https://pdbj.org/eF-site/servlet/current/jV.jnlp recent JOGL version]
The current jV requires JRE 1.6 or later.
The previous version, jV version 4.0, can run with JRE 1.4 and 1.5.
* [https://pdbj.org/jv/stable/jV_4_0.jnlp jV 4.0]

== Basic Usage ==
You can execute basic operations such as rotation and translation with mouse action. Major actions are described in the following table:
{| style="margin:auto;border:1px solid gray"
! rowspan="2" style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap;font-weight:bold" |Action
! colspan="2" style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap;font-weight:bold" |Mouse Operation
|-
! style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap;font-weight:bold" |Windows, Linux
! style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap;font-weight:bold" |Mac OS X
|-
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |rotate around X (horizontal) axis&lt;br /&gt;rotate around Y (vertical) axis
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |left drag
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |drag
|-
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |translate along X axis (holizontally)&lt;br /&gt;translate along Y axis (vertically)
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |right drag
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |Command + drag
|-
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |translate along Z axis (zoom in/out)
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |Shift + left drag
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |Shift + drag
|}

Operations such as changing display models and colors and saving the image, can be executed with a menu. The location of the menu is at the top of the application window in Windows and at the top of screen in Mac as the stand-alone application. As an applet usage, a popup menu appears by clicking the right mouse button on the display screen, or clicking with a "Command" button in case of Mac.

{| style="margin:auto;border:0"
|-
| [[File:Jv_menu_win.png|The location of menu in jV stand-alone version in Windows.|250px]]
| [[File:Jv_menu_mac.png|The location of menu in jV stand-alone version in Mac.|250px]]
| [[File:popupmenu_en.png|The location of menu in applet version.|250px]]
|-
| style="text-align:center" |Stand-alone (Windows)
| style="text-align:center" |Stand-alone (Mac)
| style="text-align:center" |Applet
|}

Basic menu operations are following (see also [[GUI]] for details):

{| style="margin:auto;border:1px solid gray;border-collapse:collapse"
! style="padding:0 0.5em;border:1px solid gray" | Operations
! style="padding:0 0.5em;border:1px solid gray" | Menu location
|-
| style="padding:0 0.5em;border:1px solid gray" | Save a static image
| style="padding:0 0.5em;border:1px solid gray" | [File]-[Save]-[PNG/JPEG]
|-
| style="padding:0 0.5em;border:1px solid gray" | Change the expression format
| style="padding:0 0.5em;border:1px solid gray" | [File]-[Display]-[Wireframe/Backbone/Sticks/Spacefill/Ball&amp;amp;Stick/Ribbons/Cartoon]
|-
| style="padding:0 0.5em;border:1px solid gray" | Change the color
| style="padding:0 0.5em;border:1px solid gray" | [File]-[Colors]-[Monochrome/CPK/Shapely/Group/Chain/Temperature/Structure/Charge/Amino]
|}

To execute more complicated operation such as diplaying some piece of the molecule or changing some part of molecule in another style, use command line operation.

See also [[#Other resources]] for details:


== Download ==
You can also download the program and start it up locally.
The following links take you to the download pages. (latest version is 4.5.4@2018/2/3)
* [https://pdbj.org/eF-site/servlet/DownloadViewerBinary binary (4.5.4)] 
* [https://pdbj.org/eF-site/servlet/Registration source code (4.5.4)] (registration will be required)

== Other resources ==
* [[How_to_use]] (in this site in English)
* [https://pdbj.org/jv/manual/index_ja.html Manual] (html in Japanese)

== Contact us ==
If you have any questions about jV, please feel free to contact us from [http://pdbj.org/contact here].</text>
    <sha1>f8d6fe60947b41f20c82ba71c9ebcfce7d39d632</sha1>
  </revision>
  <revision>
    <id>636</id>
    <parentid>635</parentid>
    <timestamp>2018-02-14T06:26:27Z</timestamp>
    <contributor>
      <username>IMSsato</username>
      <id>4</id>
    </contributor>
    <comment>/* Download */</comment>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="6359" xml:space="preserve">&lt;big&gt;'''Welcome to jV wiki.'''&lt;/big&gt;

jV (formerly known as PDBjViewer) is a program to display molecular graphics of protein and nucleic acids. 
jV supports the following features:
* jV can read and display PDBML files, the canonical XML format for the Protein Data Bank.
* Of course, jV can read and display the traditional PDB format files, too.
* RasMol-like usability.
* jV can process more than one molecules.
* jV can display polygons specified by XML. ([https://pdbj.org/eF-site/schema/polygon12.xsd XML Schema for polygons] is available.)
* Multiple polygons can be processed simultaneously, and be superimposed onto molecular images.
* Animation can be realized.
* jV runs on the Java Runtime Environment ([http://java.com/download/ JRE]) so that it can work as a stand-alone application as well as an applet.
* The graphics of jV is based on OpenGL ([http://jogamp.org/jogl/www/ JOGL]), thereby producing fairly beautiful pictures.


The program 'jV' has been developed by [http://www.sb.ecei.tohoku.ac.jp/index-en.html Kengo Kinoshita] ([https://www.is.tohoku.ac.jp/en/ Graduate School of Information Sciences], [http://www.tohoku.ac.jp/en/ Tohoku University]) and [http://www.protein.osaka-u.ac.jp/rcsfp/pi/index_en.html Haruki Nakamura] ([http://www.protein.osaka-u.ac.jp/en/ Institute for Protein Research], [http://www.osaka-u.ac.jp/en Osaka Univeristy]), with the support from [https://biosciencedbc.jp/en/ JST-NBDC] and [http://www.protein.osaka-u.ac.jp/en/ Institute for Protein Research IPR], [http://www.osaka-u.ac.jp/en Osaka Univeristy].
      

&lt;gallery&gt;
File:Spacefill.jpg
File:Cartoon.jpg
File:Surface.jpg
File:edmap.jpg
&lt;/gallery&gt;


== Start up ==
You can start up jV (4.5.4) with Java Web Start technology immediately from here.
* [https://pdbj.org/eF-site/servlet/stable/jV.jnlp stable JOGL version] (recommended)
* [https://pdbj.org/eF-site/servlet/current/jV.jnlp recent JOGL version]
The current jV requires JRE 1.6 or later.
The previous version, jV version 4.0, can run with JRE 1.4 and 1.5.
* [https://pdbj.org/jv/stable/jV_4_0.jnlp jV 4.0]

== Basic Usage ==
You can execute basic operations such as rotation and translation with mouse action. Major actions are described in the following table:
{| style="margin:auto;border:1px solid gray"
! rowspan="2" style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap;font-weight:bold" |Action
! colspan="2" style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap;font-weight:bold" |Mouse Operation
|-
! style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap;font-weight:bold" |Windows, Linux
! style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap;font-weight:bold" |Mac OS X
|-
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |rotate around X (horizontal) axis&lt;br /&gt;rotate around Y (vertical) axis
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |left drag
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |drag
|-
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |translate along X axis (holizontally)&lt;br /&gt;translate along Y axis (vertically)
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |right drag
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |Command + drag
|-
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |translate along Z axis (zoom in/out)
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |Shift + left drag
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |Shift + drag
|}

Operations such as changing display models and colors and saving the image, can be executed with a menu. The location of the menu is at the top of the application window in Windows and at the top of screen in Mac as the stand-alone application. As an applet usage, a popup menu appears by clicking the right mouse button on the display screen, or clicking with a "Command" button in case of Mac.

{| style="margin:auto;border:0"
|-
| [[File:Jv_menu_win.png|The location of menu in jV stand-alone version in Windows.|250px]]
| [[File:Jv_menu_mac.png|The location of menu in jV stand-alone version in Mac.|250px]]
| [[File:popupmenu_en.png|The location of menu in applet version.|250px]]
|-
| style="text-align:center" |Stand-alone (Windows)
| style="text-align:center" |Stand-alone (Mac)
| style="text-align:center" |Applet
|}

Basic menu operations are following (see also [[GUI]] for details):

{| style="margin:auto;border:1px solid gray;border-collapse:collapse"
! style="padding:0 0.5em;border:1px solid gray" | Operations
! style="padding:0 0.5em;border:1px solid gray" | Menu location
|-
| style="padding:0 0.5em;border:1px solid gray" | Save a static image
| style="padding:0 0.5em;border:1px solid gray" | [File]-[Save]-[PNG/JPEG]
|-
| style="padding:0 0.5em;border:1px solid gray" | Change the expression format
| style="padding:0 0.5em;border:1px solid gray" | [File]-[Display]-[Wireframe/Backbone/Sticks/Spacefill/Ball&amp;amp;Stick/Ribbons/Cartoon]
|-
| style="padding:0 0.5em;border:1px solid gray" | Change the color
| style="padding:0 0.5em;border:1px solid gray" | [File]-[Colors]-[Monochrome/CPK/Shapely/Group/Chain/Temperature/Structure/Charge/Amino]
|}

To execute more complicated operation such as diplaying some piece of the molecule or changing some part of molecule in another style, use command line operation.

See also [[#Other resources]] for details:


== Download ==
You can also download the program and start it up locally.
The following links take you to the download pages. (latest version is 4.5.4@2018/2/3)
* [https://pdbj.org/jv/download/binary binary (4.5.4)] 
* [https://pdbj.org/jv/download/source source code (4.5.4)] (registration will be required)

== Other resources ==
* [[How_to_use]] (in this site in English)
* [https://pdbj.org/jv/manual/index_ja.html Manual] (html in Japanese)

== Contact us ==
If you have any questions about jV, please feel free to contact us from [http://pdbj.org/contact here].</text>
    <sha1>d1ad7e7b06784d18601a38ed9f4171a32b223492</sha1>
  </revision>
  <revision>
    <id>638</id>
    <parentid>636</parentid>
    <timestamp>2020-02-26T06:33:58Z</timestamp>
    <contributor>
      <username>Cudo29</username>
      <id>5</id>
    </contributor>
    <comment>/* Start up */ The description of the current version was updated.</comment>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="6359" xml:space="preserve">&lt;big&gt;'''Welcome to jV wiki.'''&lt;/big&gt;

jV (formerly known as PDBjViewer) is a program to display molecular graphics of protein and nucleic acids. 
jV supports the following features:
* jV can read and display PDBML files, the canonical XML format for the Protein Data Bank.
* Of course, jV can read and display the traditional PDB format files, too.
* RasMol-like usability.
* jV can process more than one molecules.
* jV can display polygons specified by XML. ([https://pdbj.org/eF-site/schema/polygon12.xsd XML Schema for polygons] is available.)
* Multiple polygons can be processed simultaneously, and be superimposed onto molecular images.
* Animation can be realized.
* jV runs on the Java Runtime Environment ([http://java.com/download/ JRE]) so that it can work as a stand-alone application as well as an applet.
* The graphics of jV is based on OpenGL ([http://jogamp.org/jogl/www/ JOGL]), thereby producing fairly beautiful pictures.


The program 'jV' has been developed by [http://www.sb.ecei.tohoku.ac.jp/index-en.html Kengo Kinoshita] ([https://www.is.tohoku.ac.jp/en/ Graduate School of Information Sciences], [http://www.tohoku.ac.jp/en/ Tohoku University]) and [http://www.protein.osaka-u.ac.jp/rcsfp/pi/index_en.html Haruki Nakamura] ([http://www.protein.osaka-u.ac.jp/en/ Institute for Protein Research], [http://www.osaka-u.ac.jp/en Osaka Univeristy]), with the support from [https://biosciencedbc.jp/en/ JST-NBDC] and [http://www.protein.osaka-u.ac.jp/en/ Institute for Protein Research IPR], [http://www.osaka-u.ac.jp/en Osaka Univeristy].
      

&lt;gallery&gt;
File:Spacefill.jpg
File:Cartoon.jpg
File:Surface.jpg
File:edmap.jpg
&lt;/gallery&gt;


== Start up ==
You can start up jV (4.5.5) with Java Web Start technology immediately from here.
* [https://pdbj.org/eF-site/servlet/stable/jV.jnlp stable JOGL version] (recommended)
* [https://pdbj.org/eF-site/servlet/current/jV.jnlp recent JOGL version]
The current jV requires JRE 1.6 or later.
The previous version, jV version 4.0, can run with JRE 1.4 and 1.5.
* [https://pdbj.org/jv/stable/jV_4_0.jnlp jV 4.0]

== Basic Usage ==
You can execute basic operations such as rotation and translation with mouse action. Major actions are described in the following table:
{| style="margin:auto;border:1px solid gray"
! rowspan="2" style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap;font-weight:bold" |Action
! colspan="2" style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap;font-weight:bold" |Mouse Operation
|-
! style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap;font-weight:bold" |Windows, Linux
! style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap;font-weight:bold" |Mac OS X
|-
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |rotate around X (horizontal) axis&lt;br /&gt;rotate around Y (vertical) axis
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |left drag
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |drag
|-
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |translate along X axis (holizontally)&lt;br /&gt;translate along Y axis (vertically)
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |right drag
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |Command + drag
|-
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |translate along Z axis (zoom in/out)
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |Shift + left drag
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |Shift + drag
|}

Operations such as changing display models and colors and saving the image, can be executed with a menu. The location of the menu is at the top of the application window in Windows and at the top of screen in Mac as the stand-alone application. As an applet usage, a popup menu appears by clicking the right mouse button on the display screen, or clicking with a "Command" button in case of Mac.

{| style="margin:auto;border:0"
|-
| [[File:Jv_menu_win.png|The location of menu in jV stand-alone version in Windows.|250px]]
| [[File:Jv_menu_mac.png|The location of menu in jV stand-alone version in Mac.|250px]]
| [[File:popupmenu_en.png|The location of menu in applet version.|250px]]
|-
| style="text-align:center" |Stand-alone (Windows)
| style="text-align:center" |Stand-alone (Mac)
| style="text-align:center" |Applet
|}

Basic menu operations are following (see also [[GUI]] for details):

{| style="margin:auto;border:1px solid gray;border-collapse:collapse"
! style="padding:0 0.5em;border:1px solid gray" | Operations
! style="padding:0 0.5em;border:1px solid gray" | Menu location
|-
| style="padding:0 0.5em;border:1px solid gray" | Save a static image
| style="padding:0 0.5em;border:1px solid gray" | [File]-[Save]-[PNG/JPEG]
|-
| style="padding:0 0.5em;border:1px solid gray" | Change the expression format
| style="padding:0 0.5em;border:1px solid gray" | [File]-[Display]-[Wireframe/Backbone/Sticks/Spacefill/Ball&amp;amp;Stick/Ribbons/Cartoon]
|-
| style="padding:0 0.5em;border:1px solid gray" | Change the color
| style="padding:0 0.5em;border:1px solid gray" | [File]-[Colors]-[Monochrome/CPK/Shapely/Group/Chain/Temperature/Structure/Charge/Amino]
|}

To execute more complicated operation such as diplaying some piece of the molecule or changing some part of molecule in another style, use command line operation.

See also [[#Other resources]] for details:


== Download ==
You can also download the program and start it up locally.
The following links take you to the download pages. (latest version is 4.5.4@2018/2/3)
* [https://pdbj.org/jv/download/binary binary (4.5.4)] 
* [https://pdbj.org/jv/download/source source code (4.5.4)] (registration will be required)

== Other resources ==
* [[How_to_use]] (in this site in English)
* [https://pdbj.org/jv/manual/index_ja.html Manual] (html in Japanese)

== Contact us ==
If you have any questions about jV, please feel free to contact us from [http://pdbj.org/contact here].</text>
    <sha1>73f524540aff12dfdd4ca76ae195bbe0769e1db1</sha1>
  </revision>
  <revision>
    <id>639</id>
    <parentid>638</parentid>
    <timestamp>2020-02-26T06:35:04Z</timestamp>
    <contributor>
      <username>Cudo29</username>
      <id>5</id>
    </contributor>
    <comment>/* Download */ The description of the current version was updated.</comment>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="6360" xml:space="preserve">&lt;big&gt;'''Welcome to jV wiki.'''&lt;/big&gt;

jV (formerly known as PDBjViewer) is a program to display molecular graphics of protein and nucleic acids. 
jV supports the following features:
* jV can read and display PDBML files, the canonical XML format for the Protein Data Bank.
* Of course, jV can read and display the traditional PDB format files, too.
* RasMol-like usability.
* jV can process more than one molecules.
* jV can display polygons specified by XML. ([https://pdbj.org/eF-site/schema/polygon12.xsd XML Schema for polygons] is available.)
* Multiple polygons can be processed simultaneously, and be superimposed onto molecular images.
* Animation can be realized.
* jV runs on the Java Runtime Environment ([http://java.com/download/ JRE]) so that it can work as a stand-alone application as well as an applet.
* The graphics of jV is based on OpenGL ([http://jogamp.org/jogl/www/ JOGL]), thereby producing fairly beautiful pictures.


The program 'jV' has been developed by [http://www.sb.ecei.tohoku.ac.jp/index-en.html Kengo Kinoshita] ([https://www.is.tohoku.ac.jp/en/ Graduate School of Information Sciences], [http://www.tohoku.ac.jp/en/ Tohoku University]) and [http://www.protein.osaka-u.ac.jp/rcsfp/pi/index_en.html Haruki Nakamura] ([http://www.protein.osaka-u.ac.jp/en/ Institute for Protein Research], [http://www.osaka-u.ac.jp/en Osaka Univeristy]), with the support from [https://biosciencedbc.jp/en/ JST-NBDC] and [http://www.protein.osaka-u.ac.jp/en/ Institute for Protein Research IPR], [http://www.osaka-u.ac.jp/en Osaka Univeristy].
      

&lt;gallery&gt;
File:Spacefill.jpg
File:Cartoon.jpg
File:Surface.jpg
File:edmap.jpg
&lt;/gallery&gt;


== Start up ==
You can start up jV (4.5.5) with Java Web Start technology immediately from here.
* [https://pdbj.org/eF-site/servlet/stable/jV.jnlp stable JOGL version] (recommended)
* [https://pdbj.org/eF-site/servlet/current/jV.jnlp recent JOGL version]
The current jV requires JRE 1.6 or later.
The previous version, jV version 4.0, can run with JRE 1.4 and 1.5.
* [https://pdbj.org/jv/stable/jV_4_0.jnlp jV 4.0]

== Basic Usage ==
You can execute basic operations such as rotation and translation with mouse action. Major actions are described in the following table:
{| style="margin:auto;border:1px solid gray"
! rowspan="2" style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap;font-weight:bold" |Action
! colspan="2" style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap;font-weight:bold" |Mouse Operation
|-
! style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap;font-weight:bold" |Windows, Linux
! style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap;font-weight:bold" |Mac OS X
|-
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |rotate around X (horizontal) axis&lt;br /&gt;rotate around Y (vertical) axis
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |left drag
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |drag
|-
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |translate along X axis (holizontally)&lt;br /&gt;translate along Y axis (vertically)
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |right drag
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |Command + drag
|-
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |translate along Z axis (zoom in/out)
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |Shift + left drag
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |Shift + drag
|}

Operations such as changing display models and colors and saving the image, can be executed with a menu. The location of the menu is at the top of the application window in Windows and at the top of screen in Mac as the stand-alone application. As an applet usage, a popup menu appears by clicking the right mouse button on the display screen, or clicking with a "Command" button in case of Mac.

{| style="margin:auto;border:0"
|-
| [[File:Jv_menu_win.png|The location of menu in jV stand-alone version in Windows.|250px]]
| [[File:Jv_menu_mac.png|The location of menu in jV stand-alone version in Mac.|250px]]
| [[File:popupmenu_en.png|The location of menu in applet version.|250px]]
|-
| style="text-align:center" |Stand-alone (Windows)
| style="text-align:center" |Stand-alone (Mac)
| style="text-align:center" |Applet
|}

Basic menu operations are following (see also [[GUI]] for details):

{| style="margin:auto;border:1px solid gray;border-collapse:collapse"
! style="padding:0 0.5em;border:1px solid gray" | Operations
! style="padding:0 0.5em;border:1px solid gray" | Menu location
|-
| style="padding:0 0.5em;border:1px solid gray" | Save a static image
| style="padding:0 0.5em;border:1px solid gray" | [File]-[Save]-[PNG/JPEG]
|-
| style="padding:0 0.5em;border:1px solid gray" | Change the expression format
| style="padding:0 0.5em;border:1px solid gray" | [File]-[Display]-[Wireframe/Backbone/Sticks/Spacefill/Ball&amp;amp;Stick/Ribbons/Cartoon]
|-
| style="padding:0 0.5em;border:1px solid gray" | Change the color
| style="padding:0 0.5em;border:1px solid gray" | [File]-[Colors]-[Monochrome/CPK/Shapely/Group/Chain/Temperature/Structure/Charge/Amino]
|}

To execute more complicated operation such as diplaying some piece of the molecule or changing some part of molecule in another style, use command line operation.

See also [[#Other resources]] for details:


== Download ==
You can also download the program and start it up locally.
The following links take you to the download pages. (latest version is 4.5.5@2020/2/26)
* [https://pdbj.org/jv/download/binary binary (4.5.5)] 
* [https://pdbj.org/jv/download/source source code (4.5.5)] (registration will be required)

== Other resources ==
* [[How_to_use]] (in this site in English)
* [https://pdbj.org/jv/manual/index_ja.html Manual] (html in Japanese)

== Contact us ==
If you have any questions about jV, please feel free to contact us from [http://pdbj.org/contact here].</text>
    <sha1>4daa9d53e6691fa6f527ada6ab1000621e25faa4</sha1>
  </revision>
  <revision>
    <id>641</id>
    <parentid>639</parentid>
    <timestamp>2020-06-01T05:50:20Z</timestamp>
    <contributor>
      <username>IMSsato</username>
      <id>4</id>
    </contributor>
    <comment>/* Start up */</comment>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="6360" xml:space="preserve">&lt;big&gt;'''Welcome to jV wiki.'''&lt;/big&gt;

jV (formerly known as PDBjViewer) is a program to display molecular graphics of protein and nucleic acids. 
jV supports the following features:
* jV can read and display PDBML files, the canonical XML format for the Protein Data Bank.
* Of course, jV can read and display the traditional PDB format files, too.
* RasMol-like usability.
* jV can process more than one molecules.
* jV can display polygons specified by XML. ([https://pdbj.org/eF-site/schema/polygon12.xsd XML Schema for polygons] is available.)
* Multiple polygons can be processed simultaneously, and be superimposed onto molecular images.
* Animation can be realized.
* jV runs on the Java Runtime Environment ([http://java.com/download/ JRE]) so that it can work as a stand-alone application as well as an applet.
* The graphics of jV is based on OpenGL ([http://jogamp.org/jogl/www/ JOGL]), thereby producing fairly beautiful pictures.


The program 'jV' has been developed by [http://www.sb.ecei.tohoku.ac.jp/index-en.html Kengo Kinoshita] ([https://www.is.tohoku.ac.jp/en/ Graduate School of Information Sciences], [http://www.tohoku.ac.jp/en/ Tohoku University]) and [http://www.protein.osaka-u.ac.jp/rcsfp/pi/index_en.html Haruki Nakamura] ([http://www.protein.osaka-u.ac.jp/en/ Institute for Protein Research], [http://www.osaka-u.ac.jp/en Osaka Univeristy]), with the support from [https://biosciencedbc.jp/en/ JST-NBDC] and [http://www.protein.osaka-u.ac.jp/en/ Institute for Protein Research IPR], [http://www.osaka-u.ac.jp/en Osaka Univeristy].
      

&lt;gallery&gt;
File:Spacefill.jpg
File:Cartoon.jpg
File:Surface.jpg
File:edmap.jpg
&lt;/gallery&gt;


== Start up ==
You can start up jV (4.5.6) with Java Web Start technology immediately from here.
* [https://pdbj.org/eF-site/servlet/stable/jV.jnlp stable JOGL version] (recommended)
* [https://pdbj.org/eF-site/servlet/current/jV.jnlp recent JOGL version]
The current jV requires JRE 1.6 or later.
The previous version, jV version 4.0, can run with JRE 1.4 and 1.5.
* [https://pdbj.org/jv/stable/jV_4_0.jnlp jV 4.0]

== Basic Usage ==
You can execute basic operations such as rotation and translation with mouse action. Major actions are described in the following table:
{| style="margin:auto;border:1px solid gray"
! rowspan="2" style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap;font-weight:bold" |Action
! colspan="2" style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap;font-weight:bold" |Mouse Operation
|-
! style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap;font-weight:bold" |Windows, Linux
! style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap;font-weight:bold" |Mac OS X
|-
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |rotate around X (horizontal) axis&lt;br /&gt;rotate around Y (vertical) axis
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |left drag
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |drag
|-
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |translate along X axis (holizontally)&lt;br /&gt;translate along Y axis (vertically)
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |right drag
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |Command + drag
|-
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |translate along Z axis (zoom in/out)
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |Shift + left drag
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |Shift + drag
|}

Operations such as changing display models and colors and saving the image, can be executed with a menu. The location of the menu is at the top of the application window in Windows and at the top of screen in Mac as the stand-alone application. As an applet usage, a popup menu appears by clicking the right mouse button on the display screen, or clicking with a "Command" button in case of Mac.

{| style="margin:auto;border:0"
|-
| [[File:Jv_menu_win.png|The location of menu in jV stand-alone version in Windows.|250px]]
| [[File:Jv_menu_mac.png|The location of menu in jV stand-alone version in Mac.|250px]]
| [[File:popupmenu_en.png|The location of menu in applet version.|250px]]
|-
| style="text-align:center" |Stand-alone (Windows)
| style="text-align:center" |Stand-alone (Mac)
| style="text-align:center" |Applet
|}

Basic menu operations are following (see also [[GUI]] for details):

{| style="margin:auto;border:1px solid gray;border-collapse:collapse"
! style="padding:0 0.5em;border:1px solid gray" | Operations
! style="padding:0 0.5em;border:1px solid gray" | Menu location
|-
| style="padding:0 0.5em;border:1px solid gray" | Save a static image
| style="padding:0 0.5em;border:1px solid gray" | [File]-[Save]-[PNG/JPEG]
|-
| style="padding:0 0.5em;border:1px solid gray" | Change the expression format
| style="padding:0 0.5em;border:1px solid gray" | [File]-[Display]-[Wireframe/Backbone/Sticks/Spacefill/Ball&amp;amp;Stick/Ribbons/Cartoon]
|-
| style="padding:0 0.5em;border:1px solid gray" | Change the color
| style="padding:0 0.5em;border:1px solid gray" | [File]-[Colors]-[Monochrome/CPK/Shapely/Group/Chain/Temperature/Structure/Charge/Amino]
|}

To execute more complicated operation such as diplaying some piece of the molecule or changing some part of molecule in another style, use command line operation.

See also [[#Other resources]] for details:


== Download ==
You can also download the program and start it up locally.
The following links take you to the download pages. (latest version is 4.5.5@2020/2/26)
* [https://pdbj.org/jv/download/binary binary (4.5.5)] 
* [https://pdbj.org/jv/download/source source code (4.5.5)] (registration will be required)

== Other resources ==
* [[How_to_use]] (in this site in English)
* [https://pdbj.org/jv/manual/index_ja.html Manual] (html in Japanese)

== Contact us ==
If you have any questions about jV, please feel free to contact us from [http://pdbj.org/contact here].</text>
    <sha1>3eb652a65008d5f546cedd72ed0011a0e5e76925</sha1>
  </revision>
  <revision>
    <id>642</id>
    <parentid>641</parentid>
    <timestamp>2020-06-01T05:50:45Z</timestamp>
    <contributor>
      <username>IMSsato</username>
      <id>4</id>
    </contributor>
    <comment>/* Download */</comment>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="6359" xml:space="preserve">&lt;big&gt;'''Welcome to jV wiki.'''&lt;/big&gt;

jV (formerly known as PDBjViewer) is a program to display molecular graphics of protein and nucleic acids. 
jV supports the following features:
* jV can read and display PDBML files, the canonical XML format for the Protein Data Bank.
* Of course, jV can read and display the traditional PDB format files, too.
* RasMol-like usability.
* jV can process more than one molecules.
* jV can display polygons specified by XML. ([https://pdbj.org/eF-site/schema/polygon12.xsd XML Schema for polygons] is available.)
* Multiple polygons can be processed simultaneously, and be superimposed onto molecular images.
* Animation can be realized.
* jV runs on the Java Runtime Environment ([http://java.com/download/ JRE]) so that it can work as a stand-alone application as well as an applet.
* The graphics of jV is based on OpenGL ([http://jogamp.org/jogl/www/ JOGL]), thereby producing fairly beautiful pictures.


The program 'jV' has been developed by [http://www.sb.ecei.tohoku.ac.jp/index-en.html Kengo Kinoshita] ([https://www.is.tohoku.ac.jp/en/ Graduate School of Information Sciences], [http://www.tohoku.ac.jp/en/ Tohoku University]) and [http://www.protein.osaka-u.ac.jp/rcsfp/pi/index_en.html Haruki Nakamura] ([http://www.protein.osaka-u.ac.jp/en/ Institute for Protein Research], [http://www.osaka-u.ac.jp/en Osaka Univeristy]), with the support from [https://biosciencedbc.jp/en/ JST-NBDC] and [http://www.protein.osaka-u.ac.jp/en/ Institute for Protein Research IPR], [http://www.osaka-u.ac.jp/en Osaka Univeristy].
      

&lt;gallery&gt;
File:Spacefill.jpg
File:Cartoon.jpg
File:Surface.jpg
File:edmap.jpg
&lt;/gallery&gt;


== Start up ==
You can start up jV (4.5.6) with Java Web Start technology immediately from here.
* [https://pdbj.org/eF-site/servlet/stable/jV.jnlp stable JOGL version] (recommended)
* [https://pdbj.org/eF-site/servlet/current/jV.jnlp recent JOGL version]
The current jV requires JRE 1.6 or later.
The previous version, jV version 4.0, can run with JRE 1.4 and 1.5.
* [https://pdbj.org/jv/stable/jV_4_0.jnlp jV 4.0]

== Basic Usage ==
You can execute basic operations such as rotation and translation with mouse action. Major actions are described in the following table:
{| style="margin:auto;border:1px solid gray"
! rowspan="2" style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap;font-weight:bold" |Action
! colspan="2" style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap;font-weight:bold" |Mouse Operation
|-
! style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap;font-weight:bold" |Windows, Linux
! style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap;font-weight:bold" |Mac OS X
|-
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |rotate around X (horizontal) axis&lt;br /&gt;rotate around Y (vertical) axis
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |left drag
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |drag
|-
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |translate along X axis (holizontally)&lt;br /&gt;translate along Y axis (vertically)
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |right drag
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |Command + drag
|-
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |translate along Z axis (zoom in/out)
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |Shift + left drag
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |Shift + drag
|}

Operations such as changing display models and colors and saving the image, can be executed with a menu. The location of the menu is at the top of the application window in Windows and at the top of screen in Mac as the stand-alone application. As an applet usage, a popup menu appears by clicking the right mouse button on the display screen, or clicking with a "Command" button in case of Mac.

{| style="margin:auto;border:0"
|-
| [[File:Jv_menu_win.png|The location of menu in jV stand-alone version in Windows.|250px]]
| [[File:Jv_menu_mac.png|The location of menu in jV stand-alone version in Mac.|250px]]
| [[File:popupmenu_en.png|The location of menu in applet version.|250px]]
|-
| style="text-align:center" |Stand-alone (Windows)
| style="text-align:center" |Stand-alone (Mac)
| style="text-align:center" |Applet
|}

Basic menu operations are following (see also [[GUI]] for details):

{| style="margin:auto;border:1px solid gray;border-collapse:collapse"
! style="padding:0 0.5em;border:1px solid gray" | Operations
! style="padding:0 0.5em;border:1px solid gray" | Menu location
|-
| style="padding:0 0.5em;border:1px solid gray" | Save a static image
| style="padding:0 0.5em;border:1px solid gray" | [File]-[Save]-[PNG/JPEG]
|-
| style="padding:0 0.5em;border:1px solid gray" | Change the expression format
| style="padding:0 0.5em;border:1px solid gray" | [File]-[Display]-[Wireframe/Backbone/Sticks/Spacefill/Ball&amp;amp;Stick/Ribbons/Cartoon]
|-
| style="padding:0 0.5em;border:1px solid gray" | Change the color
| style="padding:0 0.5em;border:1px solid gray" | [File]-[Colors]-[Monochrome/CPK/Shapely/Group/Chain/Temperature/Structure/Charge/Amino]
|}

To execute more complicated operation such as diplaying some piece of the molecule or changing some part of molecule in another style, use command line operation.

See also [[#Other resources]] for details:


== Download ==
You can also download the program and start it up locally.
The following links take you to the download pages. (latest version is 4.5.6@2020/6/1)
* [https://pdbj.org/jv/download/binary binary (4.5.6)] 
* [https://pdbj.org/jv/download/source source code (4.5.6)] (registration will be required)

== Other resources ==
* [[How_to_use]] (in this site in English)
* [https://pdbj.org/jv/manual/index_ja.html Manual] (html in Japanese)

== Contact us ==
If you have any questions about jV, please feel free to contact us from [http://pdbj.org/contact here].</text>
    <sha1>db2c8f28fb9e0da70f669fe026d18baaf713f480</sha1>
  </revision>
  <revision>
    <id>644</id>
    <parentid>642</parentid>
    <timestamp>2020-09-16T08:14:49Z</timestamp>
    <contributor>
      <username>IMSsato</username>
      <id>4</id>
    </contributor>
    <comment>/* Start up */</comment>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="6359" xml:space="preserve">&lt;big&gt;'''Welcome to jV wiki.'''&lt;/big&gt;

jV (formerly known as PDBjViewer) is a program to display molecular graphics of protein and nucleic acids. 
jV supports the following features:
* jV can read and display PDBML files, the canonical XML format for the Protein Data Bank.
* Of course, jV can read and display the traditional PDB format files, too.
* RasMol-like usability.
* jV can process more than one molecules.
* jV can display polygons specified by XML. ([https://pdbj.org/eF-site/schema/polygon12.xsd XML Schema for polygons] is available.)
* Multiple polygons can be processed simultaneously, and be superimposed onto molecular images.
* Animation can be realized.
* jV runs on the Java Runtime Environment ([http://java.com/download/ JRE]) so that it can work as a stand-alone application as well as an applet.
* The graphics of jV is based on OpenGL ([http://jogamp.org/jogl/www/ JOGL]), thereby producing fairly beautiful pictures.


The program 'jV' has been developed by [http://www.sb.ecei.tohoku.ac.jp/index-en.html Kengo Kinoshita] ([https://www.is.tohoku.ac.jp/en/ Graduate School of Information Sciences], [http://www.tohoku.ac.jp/en/ Tohoku University]) and [http://www.protein.osaka-u.ac.jp/rcsfp/pi/index_en.html Haruki Nakamura] ([http://www.protein.osaka-u.ac.jp/en/ Institute for Protein Research], [http://www.osaka-u.ac.jp/en Osaka Univeristy]), with the support from [https://biosciencedbc.jp/en/ JST-NBDC] and [http://www.protein.osaka-u.ac.jp/en/ Institute for Protein Research IPR], [http://www.osaka-u.ac.jp/en Osaka Univeristy].
      

&lt;gallery&gt;
File:Spacefill.jpg
File:Cartoon.jpg
File:Surface.jpg
File:edmap.jpg
&lt;/gallery&gt;


== Start up ==
You can start up jV (4.5.7) with Java Web Start technology immediately from here.
* [https://pdbj.org/eF-site/servlet/stable/jV.jnlp stable JOGL version] (recommended)
* [https://pdbj.org/eF-site/servlet/current/jV.jnlp recent JOGL version]
The current jV requires JRE 1.6 or later.
The previous version, jV version 4.0, can run with JRE 1.4 and 1.5.
* [https://pdbj.org/jv/stable/jV_4_0.jnlp jV 4.0]

== Basic Usage ==
You can execute basic operations such as rotation and translation with mouse action. Major actions are described in the following table:
{| style="margin:auto;border:1px solid gray"
! rowspan="2" style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap;font-weight:bold" |Action
! colspan="2" style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap;font-weight:bold" |Mouse Operation
|-
! style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap;font-weight:bold" |Windows, Linux
! style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap;font-weight:bold" |Mac OS X
|-
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |rotate around X (horizontal) axis&lt;br /&gt;rotate around Y (vertical) axis
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |left drag
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |drag
|-
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |translate along X axis (holizontally)&lt;br /&gt;translate along Y axis (vertically)
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |right drag
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |Command + drag
|-
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |translate along Z axis (zoom in/out)
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |Shift + left drag
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |Shift + drag
|}

Operations such as changing display models and colors and saving the image, can be executed with a menu. The location of the menu is at the top of the application window in Windows and at the top of screen in Mac as the stand-alone application. As an applet usage, a popup menu appears by clicking the right mouse button on the display screen, or clicking with a "Command" button in case of Mac.

{| style="margin:auto;border:0"
|-
| [[File:Jv_menu_win.png|The location of menu in jV stand-alone version in Windows.|250px]]
| [[File:Jv_menu_mac.png|The location of menu in jV stand-alone version in Mac.|250px]]
| [[File:popupmenu_en.png|The location of menu in applet version.|250px]]
|-
| style="text-align:center" |Stand-alone (Windows)
| style="text-align:center" |Stand-alone (Mac)
| style="text-align:center" |Applet
|}

Basic menu operations are following (see also [[GUI]] for details):

{| style="margin:auto;border:1px solid gray;border-collapse:collapse"
! style="padding:0 0.5em;border:1px solid gray" | Operations
! style="padding:0 0.5em;border:1px solid gray" | Menu location
|-
| style="padding:0 0.5em;border:1px solid gray" | Save a static image
| style="padding:0 0.5em;border:1px solid gray" | [File]-[Save]-[PNG/JPEG]
|-
| style="padding:0 0.5em;border:1px solid gray" | Change the expression format
| style="padding:0 0.5em;border:1px solid gray" | [File]-[Display]-[Wireframe/Backbone/Sticks/Spacefill/Ball&amp;amp;Stick/Ribbons/Cartoon]
|-
| style="padding:0 0.5em;border:1px solid gray" | Change the color
| style="padding:0 0.5em;border:1px solid gray" | [File]-[Colors]-[Monochrome/CPK/Shapely/Group/Chain/Temperature/Structure/Charge/Amino]
|}

To execute more complicated operation such as diplaying some piece of the molecule or changing some part of molecule in another style, use command line operation.

See also [[#Other resources]] for details:


== Download ==
You can also download the program and start it up locally.
The following links take you to the download pages. (latest version is 4.5.6@2020/6/1)
* [https://pdbj.org/jv/download/binary binary (4.5.6)] 
* [https://pdbj.org/jv/download/source source code (4.5.6)] (registration will be required)

== Other resources ==
* [[How_to_use]] (in this site in English)
* [https://pdbj.org/jv/manual/index_ja.html Manual] (html in Japanese)

== Contact us ==
If you have any questions about jV, please feel free to contact us from [http://pdbj.org/contact here].</text>
    <sha1>a3aa91dcf968c82c33a5e650f19dce53be1b2ffb</sha1>
  </revision>
  <revision>
    <id>645</id>
    <parentid>644</parentid>
    <timestamp>2020-09-16T08:16:57Z</timestamp>
    <contributor>
      <username>IMSsato</username>
      <id>4</id>
    </contributor>
    <comment>/* Download */</comment>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="6360" xml:space="preserve">&lt;big&gt;'''Welcome to jV wiki.'''&lt;/big&gt;

jV (formerly known as PDBjViewer) is a program to display molecular graphics of protein and nucleic acids. 
jV supports the following features:
* jV can read and display PDBML files, the canonical XML format for the Protein Data Bank.
* Of course, jV can read and display the traditional PDB format files, too.
* RasMol-like usability.
* jV can process more than one molecules.
* jV can display polygons specified by XML. ([https://pdbj.org/eF-site/schema/polygon12.xsd XML Schema for polygons] is available.)
* Multiple polygons can be processed simultaneously, and be superimposed onto molecular images.
* Animation can be realized.
* jV runs on the Java Runtime Environment ([http://java.com/download/ JRE]) so that it can work as a stand-alone application as well as an applet.
* The graphics of jV is based on OpenGL ([http://jogamp.org/jogl/www/ JOGL]), thereby producing fairly beautiful pictures.


The program 'jV' has been developed by [http://www.sb.ecei.tohoku.ac.jp/index-en.html Kengo Kinoshita] ([https://www.is.tohoku.ac.jp/en/ Graduate School of Information Sciences], [http://www.tohoku.ac.jp/en/ Tohoku University]) and [http://www.protein.osaka-u.ac.jp/rcsfp/pi/index_en.html Haruki Nakamura] ([http://www.protein.osaka-u.ac.jp/en/ Institute for Protein Research], [http://www.osaka-u.ac.jp/en Osaka Univeristy]), with the support from [https://biosciencedbc.jp/en/ JST-NBDC] and [http://www.protein.osaka-u.ac.jp/en/ Institute for Protein Research IPR], [http://www.osaka-u.ac.jp/en Osaka Univeristy].
      

&lt;gallery&gt;
File:Spacefill.jpg
File:Cartoon.jpg
File:Surface.jpg
File:edmap.jpg
&lt;/gallery&gt;


== Start up ==
You can start up jV (4.5.7) with Java Web Start technology immediately from here.
* [https://pdbj.org/eF-site/servlet/stable/jV.jnlp stable JOGL version] (recommended)
* [https://pdbj.org/eF-site/servlet/current/jV.jnlp recent JOGL version]
The current jV requires JRE 1.6 or later.
The previous version, jV version 4.0, can run with JRE 1.4 and 1.5.
* [https://pdbj.org/jv/stable/jV_4_0.jnlp jV 4.0]

== Basic Usage ==
You can execute basic operations such as rotation and translation with mouse action. Major actions are described in the following table:
{| style="margin:auto;border:1px solid gray"
! rowspan="2" style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap;font-weight:bold" |Action
! colspan="2" style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap;font-weight:bold" |Mouse Operation
|-
! style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap;font-weight:bold" |Windows, Linux
! style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap;font-weight:bold" |Mac OS X
|-
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |rotate around X (horizontal) axis&lt;br /&gt;rotate around Y (vertical) axis
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |left drag
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |drag
|-
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |translate along X axis (holizontally)&lt;br /&gt;translate along Y axis (vertically)
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |right drag
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |Command + drag
|-
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |translate along Z axis (zoom in/out)
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |Shift + left drag
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |Shift + drag
|}

Operations such as changing display models and colors and saving the image, can be executed with a menu. The location of the menu is at the top of the application window in Windows and at the top of screen in Mac as the stand-alone application. As an applet usage, a popup menu appears by clicking the right mouse button on the display screen, or clicking with a "Command" button in case of Mac.

{| style="margin:auto;border:0"
|-
| [[File:Jv_menu_win.png|The location of menu in jV stand-alone version in Windows.|250px]]
| [[File:Jv_menu_mac.png|The location of menu in jV stand-alone version in Mac.|250px]]
| [[File:popupmenu_en.png|The location of menu in applet version.|250px]]
|-
| style="text-align:center" |Stand-alone (Windows)
| style="text-align:center" |Stand-alone (Mac)
| style="text-align:center" |Applet
|}

Basic menu operations are following (see also [[GUI]] for details):

{| style="margin:auto;border:1px solid gray;border-collapse:collapse"
! style="padding:0 0.5em;border:1px solid gray" | Operations
! style="padding:0 0.5em;border:1px solid gray" | Menu location
|-
| style="padding:0 0.5em;border:1px solid gray" | Save a static image
| style="padding:0 0.5em;border:1px solid gray" | [File]-[Save]-[PNG/JPEG]
|-
| style="padding:0 0.5em;border:1px solid gray" | Change the expression format
| style="padding:0 0.5em;border:1px solid gray" | [File]-[Display]-[Wireframe/Backbone/Sticks/Spacefill/Ball&amp;amp;Stick/Ribbons/Cartoon]
|-
| style="padding:0 0.5em;border:1px solid gray" | Change the color
| style="padding:0 0.5em;border:1px solid gray" | [File]-[Colors]-[Monochrome/CPK/Shapely/Group/Chain/Temperature/Structure/Charge/Amino]
|}

To execute more complicated operation such as diplaying some piece of the molecule or changing some part of molecule in another style, use command line operation.

See also [[#Other resources]] for details:


== Download ==
You can also download the program and start it up locally.
The following links take you to the download pages. (latest version is 4.5.7@2020/9/16)
* [https://pdbj.org/jv/download/binary binary (4.5.7)] 
* [https://pdbj.org/jv/download/source source code (4.5.7)] (registration will be required)

== Other resources ==
* [[How_to_use]] (in this site in English)
* [https://pdbj.org/jv/manual/index_ja.html Manual] (html in Japanese)

== Contact us ==
If you have any questions about jV, please feel free to contact us from [http://pdbj.org/contact here].</text>
    <sha1>c4c65b6d23f6856987b100b1dc57a0894bb562bc</sha1>
  </revision>
  <revision>
    <id>647</id>
    <parentid>645</parentid>
    <timestamp>2021-04-26T08:38:34Z</timestamp>
    <contributor>
      <username>IMSsato</username>
      <id>4</id>
    </contributor>
    <comment>/* Start up */</comment>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="6360" xml:space="preserve">&lt;big&gt;'''Welcome to jV wiki.'''&lt;/big&gt;

jV (formerly known as PDBjViewer) is a program to display molecular graphics of protein and nucleic acids. 
jV supports the following features:
* jV can read and display PDBML files, the canonical XML format for the Protein Data Bank.
* Of course, jV can read and display the traditional PDB format files, too.
* RasMol-like usability.
* jV can process more than one molecules.
* jV can display polygons specified by XML. ([https://pdbj.org/eF-site/schema/polygon12.xsd XML Schema for polygons] is available.)
* Multiple polygons can be processed simultaneously, and be superimposed onto molecular images.
* Animation can be realized.
* jV runs on the Java Runtime Environment ([http://java.com/download/ JRE]) so that it can work as a stand-alone application as well as an applet.
* The graphics of jV is based on OpenGL ([http://jogamp.org/jogl/www/ JOGL]), thereby producing fairly beautiful pictures.


The program 'jV' has been developed by [http://www.sb.ecei.tohoku.ac.jp/index-en.html Kengo Kinoshita] ([https://www.is.tohoku.ac.jp/en/ Graduate School of Information Sciences], [http://www.tohoku.ac.jp/en/ Tohoku University]) and [http://www.protein.osaka-u.ac.jp/rcsfp/pi/index_en.html Haruki Nakamura] ([http://www.protein.osaka-u.ac.jp/en/ Institute for Protein Research], [http://www.osaka-u.ac.jp/en Osaka Univeristy]), with the support from [https://biosciencedbc.jp/en/ JST-NBDC] and [http://www.protein.osaka-u.ac.jp/en/ Institute for Protein Research IPR], [http://www.osaka-u.ac.jp/en Osaka Univeristy].
      

&lt;gallery&gt;
File:Spacefill.jpg
File:Cartoon.jpg
File:Surface.jpg
File:edmap.jpg
&lt;/gallery&gt;


== Start up ==
You can start up jV (4.5.8) with Java Web Start technology immediately from here.
* [https://pdbj.org/eF-site/servlet/stable/jV.jnlp stable JOGL version] (recommended)
* [https://pdbj.org/eF-site/servlet/current/jV.jnlp recent JOGL version]
The current jV requires JRE 1.6 or later.
The previous version, jV version 4.0, can run with JRE 1.4 and 1.5.
* [https://pdbj.org/jv/stable/jV_4_0.jnlp jV 4.0]

== Basic Usage ==
You can execute basic operations such as rotation and translation with mouse action. Major actions are described in the following table:
{| style="margin:auto;border:1px solid gray"
! rowspan="2" style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap;font-weight:bold" |Action
! colspan="2" style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap;font-weight:bold" |Mouse Operation
|-
! style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap;font-weight:bold" |Windows, Linux
! style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap;font-weight:bold" |Mac OS X
|-
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |rotate around X (horizontal) axis&lt;br /&gt;rotate around Y (vertical) axis
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |left drag
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |drag
|-
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |translate along X axis (holizontally)&lt;br /&gt;translate along Y axis (vertically)
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |right drag
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |Command + drag
|-
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |translate along Z axis (zoom in/out)
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |Shift + left drag
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |Shift + drag
|}

Operations such as changing display models and colors and saving the image, can be executed with a menu. The location of the menu is at the top of the application window in Windows and at the top of screen in Mac as the stand-alone application. As an applet usage, a popup menu appears by clicking the right mouse button on the display screen, or clicking with a "Command" button in case of Mac.

{| style="margin:auto;border:0"
|-
| [[File:Jv_menu_win.png|The location of menu in jV stand-alone version in Windows.|250px]]
| [[File:Jv_menu_mac.png|The location of menu in jV stand-alone version in Mac.|250px]]
| [[File:popupmenu_en.png|The location of menu in applet version.|250px]]
|-
| style="text-align:center" |Stand-alone (Windows)
| style="text-align:center" |Stand-alone (Mac)
| style="text-align:center" |Applet
|}

Basic menu operations are following (see also [[GUI]] for details):

{| style="margin:auto;border:1px solid gray;border-collapse:collapse"
! style="padding:0 0.5em;border:1px solid gray" | Operations
! style="padding:0 0.5em;border:1px solid gray" | Menu location
|-
| style="padding:0 0.5em;border:1px solid gray" | Save a static image
| style="padding:0 0.5em;border:1px solid gray" | [File]-[Save]-[PNG/JPEG]
|-
| style="padding:0 0.5em;border:1px solid gray" | Change the expression format
| style="padding:0 0.5em;border:1px solid gray" | [File]-[Display]-[Wireframe/Backbone/Sticks/Spacefill/Ball&amp;amp;Stick/Ribbons/Cartoon]
|-
| style="padding:0 0.5em;border:1px solid gray" | Change the color
| style="padding:0 0.5em;border:1px solid gray" | [File]-[Colors]-[Monochrome/CPK/Shapely/Group/Chain/Temperature/Structure/Charge/Amino]
|}

To execute more complicated operation such as diplaying some piece of the molecule or changing some part of molecule in another style, use command line operation.

See also [[#Other resources]] for details:


== Download ==
You can also download the program and start it up locally.
The following links take you to the download pages. (latest version is 4.5.7@2020/9/16)
* [https://pdbj.org/jv/download/binary binary (4.5.7)] 
* [https://pdbj.org/jv/download/source source code (4.5.7)] (registration will be required)

== Other resources ==
* [[How_to_use]] (in this site in English)
* [https://pdbj.org/jv/manual/index_ja.html Manual] (html in Japanese)

== Contact us ==
If you have any questions about jV, please feel free to contact us from [http://pdbj.org/contact here].</text>
    <sha1>38869dc4c009f65467b1e05f977916b45a1b683d</sha1>
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  <revision>
    <id>648</id>
    <parentid>647</parentid>
    <timestamp>2021-04-26T08:39:02Z</timestamp>
    <contributor>
      <username>IMSsato</username>
      <id>4</id>
    </contributor>
    <comment>/* Download */</comment>
    <model>wikitext</model>
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    <text bytes="6360" xml:space="preserve">&lt;big&gt;'''Welcome to jV wiki.'''&lt;/big&gt;

jV (formerly known as PDBjViewer) is a program to display molecular graphics of protein and nucleic acids. 
jV supports the following features:
* jV can read and display PDBML files, the canonical XML format for the Protein Data Bank.
* Of course, jV can read and display the traditional PDB format files, too.
* RasMol-like usability.
* jV can process more than one molecules.
* jV can display polygons specified by XML. ([https://pdbj.org/eF-site/schema/polygon12.xsd XML Schema for polygons] is available.)
* Multiple polygons can be processed simultaneously, and be superimposed onto molecular images.
* Animation can be realized.
* jV runs on the Java Runtime Environment ([http://java.com/download/ JRE]) so that it can work as a stand-alone application as well as an applet.
* The graphics of jV is based on OpenGL ([http://jogamp.org/jogl/www/ JOGL]), thereby producing fairly beautiful pictures.


The program 'jV' has been developed by [http://www.sb.ecei.tohoku.ac.jp/index-en.html Kengo Kinoshita] ([https://www.is.tohoku.ac.jp/en/ Graduate School of Information Sciences], [http://www.tohoku.ac.jp/en/ Tohoku University]) and [http://www.protein.osaka-u.ac.jp/rcsfp/pi/index_en.html Haruki Nakamura] ([http://www.protein.osaka-u.ac.jp/en/ Institute for Protein Research], [http://www.osaka-u.ac.jp/en Osaka Univeristy]), with the support from [https://biosciencedbc.jp/en/ JST-NBDC] and [http://www.protein.osaka-u.ac.jp/en/ Institute for Protein Research IPR], [http://www.osaka-u.ac.jp/en Osaka Univeristy].
      

&lt;gallery&gt;
File:Spacefill.jpg
File:Cartoon.jpg
File:Surface.jpg
File:edmap.jpg
&lt;/gallery&gt;


== Start up ==
You can start up jV (4.5.8) with Java Web Start technology immediately from here.
* [https://pdbj.org/eF-site/servlet/stable/jV.jnlp stable JOGL version] (recommended)
* [https://pdbj.org/eF-site/servlet/current/jV.jnlp recent JOGL version]
The current jV requires JRE 1.6 or later.
The previous version, jV version 4.0, can run with JRE 1.4 and 1.5.
* [https://pdbj.org/jv/stable/jV_4_0.jnlp jV 4.0]

== Basic Usage ==
You can execute basic operations such as rotation and translation with mouse action. Major actions are described in the following table:
{| style="margin:auto;border:1px solid gray"
! rowspan="2" style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap;font-weight:bold" |Action
! colspan="2" style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap;font-weight:bold" |Mouse Operation
|-
! style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap;font-weight:bold" |Windows, Linux
! style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap;font-weight:bold" |Mac OS X
|-
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |rotate around X (horizontal) axis&lt;br /&gt;rotate around Y (vertical) axis
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |left drag
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |drag
|-
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |translate along X axis (holizontally)&lt;br /&gt;translate along Y axis (vertically)
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |right drag
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |Command + drag
|-
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |translate along Z axis (zoom in/out)
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |Shift + left drag
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |Shift + drag
|}

Operations such as changing display models and colors and saving the image, can be executed with a menu. The location of the menu is at the top of the application window in Windows and at the top of screen in Mac as the stand-alone application. As an applet usage, a popup menu appears by clicking the right mouse button on the display screen, or clicking with a "Command" button in case of Mac.

{| style="margin:auto;border:0"
|-
| [[File:Jv_menu_win.png|The location of menu in jV stand-alone version in Windows.|250px]]
| [[File:Jv_menu_mac.png|The location of menu in jV stand-alone version in Mac.|250px]]
| [[File:popupmenu_en.png|The location of menu in applet version.|250px]]
|-
| style="text-align:center" |Stand-alone (Windows)
| style="text-align:center" |Stand-alone (Mac)
| style="text-align:center" |Applet
|}

Basic menu operations are following (see also [[GUI]] for details):

{| style="margin:auto;border:1px solid gray;border-collapse:collapse"
! style="padding:0 0.5em;border:1px solid gray" | Operations
! style="padding:0 0.5em;border:1px solid gray" | Menu location
|-
| style="padding:0 0.5em;border:1px solid gray" | Save a static image
| style="padding:0 0.5em;border:1px solid gray" | [File]-[Save]-[PNG/JPEG]
|-
| style="padding:0 0.5em;border:1px solid gray" | Change the expression format
| style="padding:0 0.5em;border:1px solid gray" | [File]-[Display]-[Wireframe/Backbone/Sticks/Spacefill/Ball&amp;amp;Stick/Ribbons/Cartoon]
|-
| style="padding:0 0.5em;border:1px solid gray" | Change the color
| style="padding:0 0.5em;border:1px solid gray" | [File]-[Colors]-[Monochrome/CPK/Shapely/Group/Chain/Temperature/Structure/Charge/Amino]
|}

To execute more complicated operation such as diplaying some piece of the molecule or changing some part of molecule in another style, use command line operation.

See also [[#Other resources]] for details:


== Download ==
You can also download the program and start it up locally.
The following links take you to the download pages. (latest version is 4.5.8@2021/4/26)
* [https://pdbj.org/jv/download/binary binary (4.5.8)] 
* [https://pdbj.org/jv/download/source source code (4.5.8)] (registration will be required)

== Other resources ==
* [[How_to_use]] (in this site in English)
* [https://pdbj.org/jv/manual/index_ja.html Manual] (html in Japanese)

== Contact us ==
If you have any questions about jV, please feel free to contact us from [http://pdbj.org/contact here].</text>
    <sha1>966d51bcc9bf99acf0df2f28f60edf26b790c881</sha1>
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  <revision>
    <id>649</id>
    <parentid>648</parentid>
    <timestamp>2021-04-26T08:44:42Z</timestamp>
    <contributor>
      <username>IMSsato</username>
      <id>4</id>
    </contributor>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="6329" xml:space="preserve">&lt;big&gt;'''Welcome to jV wiki.'''&lt;/big&gt;

jV (formerly known as PDBjViewer) is a program to display molecular graphics of protein and nucleic acids. 
jV supports the following features:
* jV can read and display PDBML files, the canonical XML format for the Protein Data Bank.
* Of course, jV can read and display the traditional PDB format files, too.
* RasMol-like usability.
* jV can process more than one molecules.
* jV can display polygons specified by XML. ([https://pdbj.org/eF-site/schema/polygon12.xsd XML Schema for polygons] is available.)
* Multiple polygons can be processed simultaneously, and be superimposed onto molecular images.
* Animation can be realized.
* jV runs on the Java Runtime Environment ([http://java.com/download/ JRE]) and works as a stand-alone application.
* The graphics of jV is based on OpenGL ([http://jogamp.org/jogl/www/ JOGL]), thereby producing fairly beautiful pictures.


The program 'jV' has been developed by [http://www.sb.ecei.tohoku.ac.jp/index-en.html Kengo Kinoshita] ([https://www.is.tohoku.ac.jp/en/ Graduate School of Information Sciences], [http://www.tohoku.ac.jp/en/ Tohoku University]) and [http://www.protein.osaka-u.ac.jp/rcsfp/pi/index_en.html Haruki Nakamura] ([http://www.protein.osaka-u.ac.jp/en/ Institute for Protein Research], [http://www.osaka-u.ac.jp/en Osaka Univeristy]), with the support from [https://biosciencedbc.jp/en/ JST-NBDC] and [http://www.protein.osaka-u.ac.jp/en/ Institute for Protein Research IPR], [http://www.osaka-u.ac.jp/en Osaka Univeristy].
      

&lt;gallery&gt;
File:Spacefill.jpg
File:Cartoon.jpg
File:Surface.jpg
File:edmap.jpg
&lt;/gallery&gt;


== Start up ==
You can start up jV (4.5.8) with Java Web Start technology immediately from here.
* [https://pdbj.org/eF-site/servlet/stable/jV.jnlp stable JOGL version] (recommended)
* [https://pdbj.org/eF-site/servlet/current/jV.jnlp recent JOGL version]
The current jV requires JRE 1.6 or later.
The previous version, jV version 4.0, can run with JRE 1.4 and 1.5.
* [https://pdbj.org/jv/stable/jV_4_0.jnlp jV 4.0]

== Basic Usage ==
You can execute basic operations such as rotation and translation with mouse action. Major actions are described in the following table:
{| style="margin:auto;border:1px solid gray"
! rowspan="2" style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap;font-weight:bold" |Action
! colspan="2" style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap;font-weight:bold" |Mouse Operation
|-
! style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap;font-weight:bold" |Windows, Linux
! style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap;font-weight:bold" |Mac OS X
|-
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |rotate around X (horizontal) axis&lt;br /&gt;rotate around Y (vertical) axis
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |left drag
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |drag
|-
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |translate along X axis (holizontally)&lt;br /&gt;translate along Y axis (vertically)
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |right drag
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |Command + drag
|-
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |translate along Z axis (zoom in/out)
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |Shift + left drag
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |Shift + drag
|}

Operations such as changing display models and colors and saving the image, can be executed with a menu. The location of the menu is at the top of the application window in Windows and at the top of screen in Mac as the stand-alone application. As an applet usage, a popup menu appears by clicking the right mouse button on the display screen, or clicking with a "Command" button in case of Mac.

{| style="margin:auto;border:0"
|-
| [[File:Jv_menu_win.png|The location of menu in jV stand-alone version in Windows.|250px]]
| [[File:Jv_menu_mac.png|The location of menu in jV stand-alone version in Mac.|250px]]
| [[File:popupmenu_en.png|The location of menu in applet version.|250px]]
|-
| style="text-align:center" |Stand-alone (Windows)
| style="text-align:center" |Stand-alone (Mac)
| style="text-align:center" |Applet
|}

Basic menu operations are following (see also [[GUI]] for details):

{| style="margin:auto;border:1px solid gray;border-collapse:collapse"
! style="padding:0 0.5em;border:1px solid gray" | Operations
! style="padding:0 0.5em;border:1px solid gray" | Menu location
|-
| style="padding:0 0.5em;border:1px solid gray" | Save a static image
| style="padding:0 0.5em;border:1px solid gray" | [File]-[Save]-[PNG/JPEG]
|-
| style="padding:0 0.5em;border:1px solid gray" | Change the expression format
| style="padding:0 0.5em;border:1px solid gray" | [File]-[Display]-[Wireframe/Backbone/Sticks/Spacefill/Ball&amp;amp;Stick/Ribbons/Cartoon]
|-
| style="padding:0 0.5em;border:1px solid gray" | Change the color
| style="padding:0 0.5em;border:1px solid gray" | [File]-[Colors]-[Monochrome/CPK/Shapely/Group/Chain/Temperature/Structure/Charge/Amino]
|}

To execute more complicated operation such as diplaying some piece of the molecule or changing some part of molecule in another style, use command line operation.

See also [[#Other resources]] for details:


== Download ==
You can also download the program and start it up locally.
The following links take you to the download pages. (latest version is 4.5.8@2021/4/26)
* [https://pdbj.org/jv/download/binary binary (4.5.8)] 
* [https://pdbj.org/jv/download/source source code (4.5.8)] (registration will be required)

== Other resources ==
* [[How_to_use]] (in this site in English)
* [https://pdbj.org/jv/manual/index_ja.html Manual] (html in Japanese)

== Contact us ==
If you have any questions about jV, please feel free to contact us from [http://pdbj.org/contact here].</text>
    <sha1>8e405311354b75f199723866a4cccc90f729679e</sha1>
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<page arvcontinue="20151001071243|604">
  <title>Introduction</title>
  <ns>0</ns>
  <id>44</id>
  <revision>
    <id>606</id>
    <parentid>603</parentid>
    <timestamp>2015-10-01T07:18:42Z</timestamp>
    <contributor>
      <username>IMSsato</username>
      <id>4</id>
    </contributor>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="1905" xml:space="preserve">jV is an interactive 3D viewer program to visualize protein and nucleic acid molecules. The program reads in a PDBML file that is an XML format for PDB. Usual PDB format files are also accepted. More than one molecule files can be opened and displayed at the same time and their display models and transforms can be operated separately. In addition to molecule files, a polygon file written in XML can be read and displayed. More than one polygon files can be opened at the same time and superposed on molecule images. The [http://www.pdbj.org/jv/polygonSchema XML schema] of the polygon file is available. jV can perform an animation of molecules. The animation file is a PDB format file in which each frame is separated by a MODEL line.

jV runs on Java Runtime Environment ([http://java.com/download/ JRE]) and can be used both as a standalone program and an applet. The 3D rendering is performed with the use of [http://jogamp.org/jogl/www/ JOGL] API. The version requirements are as follows.

* JRE (includes Java Plug-in) 1.6 or later
* JOGL 2.2.4 or later

Here, [http://www.oracle.com/technetwork/java/index-jsp-141438.html Java Plug-in] is required in order to use the program as an applet.

The program allows an interactive mouse control and command execution. The commnad syntax follows that of [http://www.rasmol.org/ Rasmol] with some modifications. In order to handle the transform of each molecule and polygon separately, every files are set to be either selected or not selected. The transform operation commands, such as rotate or translate, act only on selected files. On the other hand, every atoms in a molecule are also set to be either selected or not selected independently of whether the molecule itself is selected or not selected. Only selected atoms are the target of display model operations, such as wireframe or spacefill commands, and coloring operations.

[[Release note]]</text>
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  </revision>
  <revision>
    <id>651</id>
    <parentid>606</parentid>
    <timestamp>2021-04-26T08:46:41Z</timestamp>
    <contributor>
      <username>IMSsato</username>
      <id>4</id>
    </contributor>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="1868" xml:space="preserve">jV is an interactive 3D viewer program to visualize protein and nucleic acid molecules. The program reads in a PDBML file that is an XML format for PDB. Usual PDB format files are also accepted. More than one molecule files can be opened and displayed at the same time and their display models and transforms can be operated separately. In addition to molecule files, a polygon file written in XML can be read and displayed. More than one polygon files can be opened at the same time and superposed on molecule images. The [http://www.pdbj.org/jv/polygonSchema XML schema] of the polygon file is available. jV can perform an animation of molecules. The animation file is a PDB format file in which each frame is separated by a MODEL line.

jV runs on Java Runtime Environment ([http://java.com/download/ JRE]) and can be used both as a standalone program . The 3D rendering is performed with the use of [http://jogamp.org/jogl/www/ JOGL] API. The version requirements are as follows.

* JRE 1.8 or later
* JOGL 2.2.4 or later

Here, [http://www.oracle.com/technetwork/java/index-jsp-141438.html Java Plug-in] is required in order to use the program as an applet.

The program allows an interactive mouse control and command execution. The commnad syntax follows that of [http://www.rasmol.org/ Rasmol] with some modifications. In order to handle the transform of each molecule and polygon separately, every files are set to be either selected or not selected. The transform operation commands, such as rotate or translate, act only on selected files. On the other hand, every atoms in a molecule are also set to be either selected or not selected independently of whether the molecule itself is selected or not selected. Only selected atoms are the target of display model operations, such as wireframe or spacefill commands, and coloring operations.

[[Release note]]</text>
    <sha1>f75c3a30b7d5077ca4c632a2f74a2500a19edb1a</sha1>
  </revision>
</page>
<page arvcontinue="20151001071243|604">
  <title>Release note</title>
  <ns>0</ns>
  <id>17</id>
  <revision>
    <id>607</id>
    <parentid>599</parentid>
    <timestamp>2015-10-01T07:19:22Z</timestamp>
    <contributor>
      <username>IMSsato</username>
      <id>4</id>
    </contributor>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="5826" xml:space="preserve">Changes and improvements have been made as follows.

* version 3.1
** The following commands have been added; 'animrange', 'set adjustview', 'show godata', and 'show xps3'.
** The xPSSS expression has been added in order to select a group of atoms.
** Several public methods have been added to the applet so as to append molecule or polygon files after the applet started.
** The applet can send information about mouse-picked atoms to JavaScript.
* version 3.1.1
** Some problems in GUI menu [Options]-[Hetero Atoms] and [Hydrogens] have been fixed.
** Some problems in 'trace' command have been fixed.
* version 3.1.2
** eF-site ID has been changed to a new format.
* version 3.1.3
** Some problems in xps3 atom selection have been fixed.
* version 3.1.4
** Some problems in finalization process of openGL rendering have been fixed.
* version 3.1.5
** The output of 'show xps3' command has been modified.
** Some problems in 'save png/jpeg' command have been fixed.
* version 3.1.6
** Some problems in loading an empty polygon file have been fixed.
* version 3.1.7
** Some problems in initialization process of the applet have been fixed.
* version 3.2
** 'show site' command has been added.
* version 3.3 beta 1
** Availabe JOGL version is restricted to JSR-231 beta 5 only.
* version 3.3
** Both the previous JOGL (version 1.1.1) and JSR-231 are available.
** The following commands have been added; 'set viewpoint', 'show viewpoint', 'set imagesize', and 'show imagesize'.
* version 3.3.1
** Some problems in reading a pdbMLplus file have been fixed.
* version 3.4
** PDB format version 3 can be processed.
* version 3.5
** Discrimination of DNA and RNA linking nucleotides is based on [http://remediation.wwpdb.org/ccd.html Chemical Component Dictionary] for PDB format version 3.
** The default representation of the cartoon model has been changed. Commands 'set cartoon_loop_tube', 'set cartoon_round' and 'set ribbonback' have been added.
** The default parameters of lighting have been changed. Commands 'set ambient', 'set diffuse1', 'set diffuse1_direction', 'set diffuse2' and 'set diffuse1_direction' have been added.
** Commands 'set pdbml_noatom_url', 'set pdbml_extatom_url', 'set pdbml_plus_url', 'set efsite_url', 'set ext_site_url', 'show pdbml_url', 'show efsite_url' and 'show ext_site_url' have been added.
** The command-line option '-stdin' has been added to receive commands from stdin stream.
* version 3.6
** Users can specify the JavaScript function name used in Applet-to-JavaScript Communication.
** Applet parameter 'file_load_message' has been added.
* version 3.6.1
** Predefined set of residues has been modified.
** Old JOGL API is not supported.
* version 3.6.2
** Latest version of PDBML can be processed.
** Some problems in mouse control on Mac have been fixed.
* version 3.6.3
** Molecule file parsing has been modified to detect chain breaks properly by reading the 'label_asym_id' column in PDBML and the TER line in PDB flat file, respectively.
* version 3.6.4
** Some problems in GUI menu on Mac have been fixed.
* version 3.6.5
** The jV applet can invoke a JavaScript function when it started.
* version 3.7
** Commands 'pdbj_describe' and 'pdbj_execute' have been added.
** Keyword 'xps3' have been replaced by 'pdbj'.
* version 3.7.1
** Default PDBML URLs have been changed.
* version 3.7.2
** Some problems in creating png/jpeg image files have been fixed.
* version 3.8
** Command 'displayatom' has been added.
** The signed jV applet can save PNG/JPEG image files.
* version 3.8.1
** In commands 'cartoon', 'ribbons' and 'trace', a backbone will be drawn instead when a chain does not have enough atoms to draw those models.
** Recognition of amino acids is based on [http://remediation.wwpdb.org/ccd.html Chemical Component Dictionary].
* version 3.8.2
** Command 'ball_and_stick' has been added.
* version 3.8.3
** Binary distribution contains the JOGL library and pre-installation of JOGL is not necessary to use jV.
* version 4.0
** The program supports PDB format version 4.0.
** Atom expression has been extended to handle case-sensitive chain ID and label_asym_id in PDBML.
* version 4.1
** The program runs with new JOGL library (2.0-rc4 or later) which enables jV applets to run on Mac.
** From this release, the program requires JRE 1.6 or later.
** Command 'add_backbone' has been added.
** The program uses MODRES data and chem_comp/type data (PDBML only) to determine residue types.
* version 4.2
** The program reads polygon CGO (PyMOL-specific Compiled Graphics Objects) files distributed at eF-site system. Command 'load polygon_cgo' has been added.
** A parameter 'pdbid' and a method 'loadFTP' have been added to applet.
** When the program loads a PDBML noatom file whose directory is 'all-noatom' or 'XML-noatom', the coordinate file is retrieved from the corresponding directory; '../all-extatom' or '../XML-extatom', respectively.
* version 4.2.1
** The program runs with new JOGL library (2.0-rc11).
* version 4.3
** Anaglyph 3D rendering is added to 'stereo' command.
* version 4.3.1
** A workaround for a cache problem in JRE 1.7 has been added.
* version 4.4
** The program can read and write mmCIF format files.
** The program handles biomolecule structures when reading and writing a molecule file.
** The default setting of PDBMLplus URL has been changed.
* version 4.4.1
** Some problems in reading mmCIF files have been fixed.
** The behavior of mouse picking when measuring the distance between two atoms has been changed. Rotation and translation of molecules between two mouse pickings do not affect the distance measurement.
* version 4.4.2
** The program files are signed with a new certificate.
* version 4.4.3
** Some problems in writing PDB files have been fixed.
* version 4.4.4
** Some problems in rendering polygons have been fixed.</text>
    <sha1>30ad998bc5c4201f9feebee558b70129d4ba6290</sha1>
  </revision>
  <revision>
    <id>613</id>
    <parentid>607</parentid>
    <timestamp>2016-01-08T07:24:12Z</timestamp>
    <contributor>
      <username>IMSsato</username>
      <id>4</id>
    </contributor>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="5978" xml:space="preserve">Changes and improvements have been made as follows.

* version 3.1
** The following commands have been added; 'animrange', 'set adjustview', 'show godata', and 'show xps3'.
** The xPSSS expression has been added in order to select a group of atoms.
** Several public methods have been added to the applet so as to append molecule or polygon files after the applet started.
** The applet can send information about mouse-picked atoms to JavaScript.
* version 3.1.1
** Some problems in GUI menu [Options]-[Hetero Atoms] and [Hydrogens] have been fixed.
** Some problems in 'trace' command have been fixed.
* version 3.1.2
** eF-site ID has been changed to a new format.
* version 3.1.3
** Some problems in xps3 atom selection have been fixed.
* version 3.1.4
** Some problems in finalization process of openGL rendering have been fixed.
* version 3.1.5
** The output of 'show xps3' command has been modified.
** Some problems in 'save png/jpeg' command have been fixed.
* version 3.1.6
** Some problems in loading an empty polygon file have been fixed.
* version 3.1.7
** Some problems in initialization process of the applet have been fixed.
* version 3.2
** 'show site' command has been added.
* version 3.3 beta 1
** Availabe JOGL version is restricted to JSR-231 beta 5 only.
* version 3.3
** Both the previous JOGL (version 1.1.1) and JSR-231 are available.
** The following commands have been added; 'set viewpoint', 'show viewpoint', 'set imagesize', and 'show imagesize'.
* version 3.3.1
** Some problems in reading a pdbMLplus file have been fixed.
* version 3.4
** PDB format version 3 can be processed.
* version 3.5
** Discrimination of DNA and RNA linking nucleotides is based on [http://remediation.wwpdb.org/ccd.html Chemical Component Dictionary] for PDB format version 3.
** The default representation of the cartoon model has been changed. Commands 'set cartoon_loop_tube', 'set cartoon_round' and 'set ribbonback' have been added.
** The default parameters of lighting have been changed. Commands 'set ambient', 'set diffuse1', 'set diffuse1_direction', 'set diffuse2' and 'set diffuse1_direction' have been added.
** Commands 'set pdbml_noatom_url', 'set pdbml_extatom_url', 'set pdbml_plus_url', 'set efsite_url', 'set ext_site_url', 'show pdbml_url', 'show efsite_url' and 'show ext_site_url' have been added.
** The command-line option '-stdin' has been added to receive commands from stdin stream.
* version 3.6
** Users can specify the JavaScript function name used in Applet-to-JavaScript Communication.
** Applet parameter 'file_load_message' has been added.
* version 3.6.1
** Predefined set of residues has been modified.
** Old JOGL API is not supported.
* version 3.6.2
** Latest version of PDBML can be processed.
** Some problems in mouse control on Mac have been fixed.
* version 3.6.3
** Molecule file parsing has been modified to detect chain breaks properly by reading the 'label_asym_id' column in PDBML and the TER line in PDB flat file, respectively.
* version 3.6.4
** Some problems in GUI menu on Mac have been fixed.
* version 3.6.5
** The jV applet can invoke a JavaScript function when it started.
* version 3.7
** Commands 'pdbj_describe' and 'pdbj_execute' have been added.
** Keyword 'xps3' have been replaced by 'pdbj'.
* version 3.7.1
** Default PDBML URLs have been changed.
* version 3.7.2
** Some problems in creating png/jpeg image files have been fixed.
* version 3.8
** Command 'displayatom' has been added.
** The signed jV applet can save PNG/JPEG image files.
* version 3.8.1
** In commands 'cartoon', 'ribbons' and 'trace', a backbone will be drawn instead when a chain does not have enough atoms to draw those models.
** Recognition of amino acids is based on [http://remediation.wwpdb.org/ccd.html Chemical Component Dictionary].
* version 3.8.2
** Command 'ball_and_stick' has been added.
* version 3.8.3
** Binary distribution contains the JOGL library and pre-installation of JOGL is not necessary to use jV.
* version 4.0
** The program supports PDB format version 4.0.
** Atom expression has been extended to handle case-sensitive chain ID and label_asym_id in PDBML.
* version 4.1
** The program runs with new JOGL library (2.0-rc4 or later) which enables jV applets to run on Mac.
** From this release, the program requires JRE 1.6 or later.
** Command 'add_backbone' has been added.
** The program uses MODRES data and chem_comp/type data (PDBML only) to determine residue types.
* version 4.2
** The program reads polygon CGO (PyMOL-specific Compiled Graphics Objects) files distributed at eF-site system. Command 'load polygon_cgo' has been added.
** A parameter 'pdbid' and a method 'loadFTP' have been added to applet.
** When the program loads a PDBML noatom file whose directory is 'all-noatom' or 'XML-noatom', the coordinate file is retrieved from the corresponding directory; '../all-extatom' or '../XML-extatom', respectively.
* version 4.2.1
** The program runs with new JOGL library (2.0-rc11).
* version 4.3
** Anaglyph 3D rendering is added to 'stereo' command.
* version 4.3.1
** A workaround for a cache problem in JRE 1.7 has been added.
* version 4.4
** The program can read and write mmCIF format files.
** The program handles biomolecule structures when reading and writing a molecule file.
** The default setting of PDBMLplus URL has been changed.
* version 4.4.1
** Some problems in reading mmCIF files have been fixed.
** The behavior of mouse picking when measuring the distance between two atoms has been changed. Rotation and translation of molecules between two mouse pickings do not affect the distance measurement.
* version 4.4.2
** The program files are signed with a new certificate.
* version 4.4.3
** Some problems in writing PDB files have been fixed.
* version 4.4.4
** Some problems in rendering polygons have been fixed.
* version 4.4.5
** The program shows an error dialog when an input file has no valid data.
** The program files are signed with an updated certificate.</text>
    <sha1>267da2f0aa380e3bd67fe6282edc00bce1a6c1d8</sha1>
  </revision>
  <revision>
    <id>616</id>
    <parentid>613</parentid>
    <timestamp>2016-03-02T04:52:18Z</timestamp>
    <contributor>
      <username>IMSsato</username>
      <id>4</id>
    </contributor>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="6061" xml:space="preserve">Changes and improvements have been made as follows.

* version 3.1
** The following commands have been added; 'animrange', 'set adjustview', 'show godata', and 'show xps3'.
** The xPSSS expression has been added in order to select a group of atoms.
** Several public methods have been added to the applet so as to append molecule or polygon files after the applet started.
** The applet can send information about mouse-picked atoms to JavaScript.
* version 3.1.1
** Some problems in GUI menu [Options]-[Hetero Atoms] and [Hydrogens] have been fixed.
** Some problems in 'trace' command have been fixed.
* version 3.1.2
** eF-site ID has been changed to a new format.
* version 3.1.3
** Some problems in xps3 atom selection have been fixed.
* version 3.1.4
** Some problems in finalization process of openGL rendering have been fixed.
* version 3.1.5
** The output of 'show xps3' command has been modified.
** Some problems in 'save png/jpeg' command have been fixed.
* version 3.1.6
** Some problems in loading an empty polygon file have been fixed.
* version 3.1.7
** Some problems in initialization process of the applet have been fixed.
* version 3.2
** 'show site' command has been added.
* version 3.3 beta 1
** Availabe JOGL version is restricted to JSR-231 beta 5 only.
* version 3.3
** Both the previous JOGL (version 1.1.1) and JSR-231 are available.
** The following commands have been added; 'set viewpoint', 'show viewpoint', 'set imagesize', and 'show imagesize'.
* version 3.3.1
** Some problems in reading a pdbMLplus file have been fixed.
* version 3.4
** PDB format version 3 can be processed.
* version 3.5
** Discrimination of DNA and RNA linking nucleotides is based on [http://remediation.wwpdb.org/ccd.html Chemical Component Dictionary] for PDB format version 3.
** The default representation of the cartoon model has been changed. Commands 'set cartoon_loop_tube', 'set cartoon_round' and 'set ribbonback' have been added.
** The default parameters of lighting have been changed. Commands 'set ambient', 'set diffuse1', 'set diffuse1_direction', 'set diffuse2' and 'set diffuse1_direction' have been added.
** Commands 'set pdbml_noatom_url', 'set pdbml_extatom_url', 'set pdbml_plus_url', 'set efsite_url', 'set ext_site_url', 'show pdbml_url', 'show efsite_url' and 'show ext_site_url' have been added.
** The command-line option '-stdin' has been added to receive commands from stdin stream.
* version 3.6
** Users can specify the JavaScript function name used in Applet-to-JavaScript Communication.
** Applet parameter 'file_load_message' has been added.
* version 3.6.1
** Predefined set of residues has been modified.
** Old JOGL API is not supported.
* version 3.6.2
** Latest version of PDBML can be processed.
** Some problems in mouse control on Mac have been fixed.
* version 3.6.3
** Molecule file parsing has been modified to detect chain breaks properly by reading the 'label_asym_id' column in PDBML and the TER line in PDB flat file, respectively.
* version 3.6.4
** Some problems in GUI menu on Mac have been fixed.
* version 3.6.5
** The jV applet can invoke a JavaScript function when it started.
* version 3.7
** Commands 'pdbj_describe' and 'pdbj_execute' have been added.
** Keyword 'xps3' have been replaced by 'pdbj'.
* version 3.7.1
** Default PDBML URLs have been changed.
* version 3.7.2
** Some problems in creating png/jpeg image files have been fixed.
* version 3.8
** Command 'displayatom' has been added.
** The signed jV applet can save PNG/JPEG image files.
* version 3.8.1
** In commands 'cartoon', 'ribbons' and 'trace', a backbone will be drawn instead when a chain does not have enough atoms to draw those models.
** Recognition of amino acids is based on [http://remediation.wwpdb.org/ccd.html Chemical Component Dictionary].
* version 3.8.2
** Command 'ball_and_stick' has been added.
* version 3.8.3
** Binary distribution contains the JOGL library and pre-installation of JOGL is not necessary to use jV.
* version 4.0
** The program supports PDB format version 4.0.
** Atom expression has been extended to handle case-sensitive chain ID and label_asym_id in PDBML.
* version 4.1
** The program runs with new JOGL library (2.0-rc4 or later) which enables jV applets to run on Mac.
** From this release, the program requires JRE 1.6 or later.
** Command 'add_backbone' has been added.
** The program uses MODRES data and chem_comp/type data (PDBML only) to determine residue types.
* version 4.2
** The program reads polygon CGO (PyMOL-specific Compiled Graphics Objects) files distributed at eF-site system. Command 'load polygon_cgo' has been added.
** A parameter 'pdbid' and a method 'loadFTP' have been added to applet.
** When the program loads a PDBML noatom file whose directory is 'all-noatom' or 'XML-noatom', the coordinate file is retrieved from the corresponding directory; '../all-extatom' or '../XML-extatom', respectively.
* version 4.2.1
** The program runs with new JOGL library (2.0-rc11).
* version 4.3
** Anaglyph 3D rendering is added to 'stereo' command.
* version 4.3.1
** A workaround for a cache problem in JRE 1.7 has been added.
* version 4.4
** The program can read and write mmCIF format files.
** The program handles biomolecule structures when reading and writing a molecule file.
** The default setting of PDBMLplus URL has been changed.
* version 4.4.1
** Some problems in reading mmCIF files have been fixed.
** The behavior of mouse picking when measuring the distance between two atoms has been changed. Rotation and translation of molecules between two mouse pickings do not affect the distance measurement.
* version 4.4.2
** The program files are signed with a new certificate.
* version 4.4.3
** Some problems in writing PDB files have been fixed.
* version 4.4.4
** Some problems in rendering polygons have been fixed.
* version 4.4.5
** The program shows an error dialog when an input file has no valid data.
** The program files are signed with an updated certificate.
* version 4.5
** The program can read and display mmCIF files for small molecules.</text>
    <sha1>49d4fc1fff2596f10dfa3bbd5df88a9c519a2efb</sha1>
  </revision>
  <revision>
    <id>619</id>
    <parentid>616</parentid>
    <timestamp>2016-05-10T05:15:14Z</timestamp>
    <contributor>
      <username>IMSsato</username>
      <id>4</id>
    </contributor>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="6145" xml:space="preserve">Changes and improvements have been made as follows.

* version 3.1
** The following commands have been added; 'animrange', 'set adjustview', 'show godata', and 'show xps3'.
** The xPSSS expression has been added in order to select a group of atoms.
** Several public methods have been added to the applet so as to append molecule or polygon files after the applet started.
** The applet can send information about mouse-picked atoms to JavaScript.
* version 3.1.1
** Some problems in GUI menu [Options]-[Hetero Atoms] and [Hydrogens] have been fixed.
** Some problems in 'trace' command have been fixed.
* version 3.1.2
** eF-site ID has been changed to a new format.
* version 3.1.3
** Some problems in xps3 atom selection have been fixed.
* version 3.1.4
** Some problems in finalization process of openGL rendering have been fixed.
* version 3.1.5
** The output of 'show xps3' command has been modified.
** Some problems in 'save png/jpeg' command have been fixed.
* version 3.1.6
** Some problems in loading an empty polygon file have been fixed.
* version 3.1.7
** Some problems in initialization process of the applet have been fixed.
* version 3.2
** 'show site' command has been added.
* version 3.3 beta 1
** Availabe JOGL version is restricted to JSR-231 beta 5 only.
* version 3.3
** Both the previous JOGL (version 1.1.1) and JSR-231 are available.
** The following commands have been added; 'set viewpoint', 'show viewpoint', 'set imagesize', and 'show imagesize'.
* version 3.3.1
** Some problems in reading a pdbMLplus file have been fixed.
* version 3.4
** PDB format version 3 can be processed.
* version 3.5
** Discrimination of DNA and RNA linking nucleotides is based on [http://remediation.wwpdb.org/ccd.html Chemical Component Dictionary] for PDB format version 3.
** The default representation of the cartoon model has been changed. Commands 'set cartoon_loop_tube', 'set cartoon_round' and 'set ribbonback' have been added.
** The default parameters of lighting have been changed. Commands 'set ambient', 'set diffuse1', 'set diffuse1_direction', 'set diffuse2' and 'set diffuse1_direction' have been added.
** Commands 'set pdbml_noatom_url', 'set pdbml_extatom_url', 'set pdbml_plus_url', 'set efsite_url', 'set ext_site_url', 'show pdbml_url', 'show efsite_url' and 'show ext_site_url' have been added.
** The command-line option '-stdin' has been added to receive commands from stdin stream.
* version 3.6
** Users can specify the JavaScript function name used in Applet-to-JavaScript Communication.
** Applet parameter 'file_load_message' has been added.
* version 3.6.1
** Predefined set of residues has been modified.
** Old JOGL API is not supported.
* version 3.6.2
** Latest version of PDBML can be processed.
** Some problems in mouse control on Mac have been fixed.
* version 3.6.3
** Molecule file parsing has been modified to detect chain breaks properly by reading the 'label_asym_id' column in PDBML and the TER line in PDB flat file, respectively.
* version 3.6.4
** Some problems in GUI menu on Mac have been fixed.
* version 3.6.5
** The jV applet can invoke a JavaScript function when it started.
* version 3.7
** Commands 'pdbj_describe' and 'pdbj_execute' have been added.
** Keyword 'xps3' have been replaced by 'pdbj'.
* version 3.7.1
** Default PDBML URLs have been changed.
* version 3.7.2
** Some problems in creating png/jpeg image files have been fixed.
* version 3.8
** Command 'displayatom' has been added.
** The signed jV applet can save PNG/JPEG image files.
* version 3.8.1
** In commands 'cartoon', 'ribbons' and 'trace', a backbone will be drawn instead when a chain does not have enough atoms to draw those models.
** Recognition of amino acids is based on [http://remediation.wwpdb.org/ccd.html Chemical Component Dictionary].
* version 3.8.2
** Command 'ball_and_stick' has been added.
* version 3.8.3
** Binary distribution contains the JOGL library and pre-installation of JOGL is not necessary to use jV.
* version 4.0
** The program supports PDB format version 4.0.
** Atom expression has been extended to handle case-sensitive chain ID and label_asym_id in PDBML.
* version 4.1
** The program runs with new JOGL library (2.0-rc4 or later) which enables jV applets to run on Mac.
** From this release, the program requires JRE 1.6 or later.
** Command 'add_backbone' has been added.
** The program uses MODRES data and chem_comp/type data (PDBML only) to determine residue types.
* version 4.2
** The program reads polygon CGO (PyMOL-specific Compiled Graphics Objects) files distributed at eF-site system. Command 'load polygon_cgo' has been added.
** A parameter 'pdbid' and a method 'loadFTP' have been added to applet.
** When the program loads a PDBML noatom file whose directory is 'all-noatom' or 'XML-noatom', the coordinate file is retrieved from the corresponding directory; '../all-extatom' or '../XML-extatom', respectively.
* version 4.2.1
** The program runs with new JOGL library (2.0-rc11).
* version 4.3
** Anaglyph 3D rendering is added to 'stereo' command.
* version 4.3.1
** A workaround for a cache problem in JRE 1.7 has been added.
* version 4.4
** The program can read and write mmCIF format files.
** The program handles biomolecule structures when reading and writing a molecule file.
** The default setting of PDBMLplus URL has been changed.
* version 4.4.1
** Some problems in reading mmCIF files have been fixed.
** The behavior of mouse picking when measuring the distance between two atoms has been changed. Rotation and translation of molecules between two mouse pickings do not affect the distance measurement.
* version 4.4.2
** The program files are signed with a new certificate.
* version 4.4.3
** Some problems in writing PDB files have been fixed.
* version 4.4.4
** Some problems in rendering polygons have been fixed.
* version 4.4.5
** The program shows an error dialog when an input file has no valid data.
** The program files are signed with an updated certificate.
* version 4.5
** The program can read and display mmCIF files for small molecules.
* version 4.5.1
** A file permission problem in writing image files has been fixed.</text>
    <sha1>374e31ad782944ba434a35c2eb4f5b4d5593da87</sha1>
  </revision>
  <revision>
    <id>626</id>
    <parentid>619</parentid>
    <timestamp>2017-02-06T09:00:09Z</timestamp>
    <contributor>
      <username>IMSsato</username>
      <id>4</id>
    </contributor>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="6375" xml:space="preserve">Changes and improvements have been made as follows.

* version 3.1
** The following commands have been added; 'animrange', 'set adjustview', 'show godata', and 'show xps3'.
** The xPSSS expression has been added in order to select a group of atoms.
** Several public methods have been added to the applet so as to append molecule or polygon files after the applet started.
** The applet can send information about mouse-picked atoms to JavaScript.
* version 3.1.1
** Some problems in GUI menu [Options]-[Hetero Atoms] and [Hydrogens] have been fixed.
** Some problems in 'trace' command have been fixed.
* version 3.1.2
** eF-site ID has been changed to a new format.
* version 3.1.3
** Some problems in xps3 atom selection have been fixed.
* version 3.1.4
** Some problems in finalization process of openGL rendering have been fixed.
* version 3.1.5
** The output of 'show xps3' command has been modified.
** Some problems in 'save png/jpeg' command have been fixed.
* version 3.1.6
** Some problems in loading an empty polygon file have been fixed.
* version 3.1.7
** Some problems in initialization process of the applet have been fixed.
* version 3.2
** 'show site' command has been added.
* version 3.3 beta 1
** Availabe JOGL version is restricted to JSR-231 beta 5 only.
* version 3.3
** Both the previous JOGL (version 1.1.1) and JSR-231 are available.
** The following commands have been added; 'set viewpoint', 'show viewpoint', 'set imagesize', and 'show imagesize'.
* version 3.3.1
** Some problems in reading a pdbMLplus file have been fixed.
* version 3.4
** PDB format version 3 can be processed.
* version 3.5
** Discrimination of DNA and RNA linking nucleotides is based on [http://remediation.wwpdb.org/ccd.html Chemical Component Dictionary] for PDB format version 3.
** The default representation of the cartoon model has been changed. Commands 'set cartoon_loop_tube', 'set cartoon_round' and 'set ribbonback' have been added.
** The default parameters of lighting have been changed. Commands 'set ambient', 'set diffuse1', 'set diffuse1_direction', 'set diffuse2' and 'set diffuse1_direction' have been added.
** Commands 'set pdbml_noatom_url', 'set pdbml_extatom_url', 'set pdbml_plus_url', 'set efsite_url', 'set ext_site_url', 'show pdbml_url', 'show efsite_url' and 'show ext_site_url' have been added.
** The command-line option '-stdin' has been added to receive commands from stdin stream.
* version 3.6
** Users can specify the JavaScript function name used in Applet-to-JavaScript Communication.
** Applet parameter 'file_load_message' has been added.
* version 3.6.1
** Predefined set of residues has been modified.
** Old JOGL API is not supported.
* version 3.6.2
** Latest version of PDBML can be processed.
** Some problems in mouse control on Mac have been fixed.
* version 3.6.3
** Molecule file parsing has been modified to detect chain breaks properly by reading the 'label_asym_id' column in PDBML and the TER line in PDB flat file, respectively.
* version 3.6.4
** Some problems in GUI menu on Mac have been fixed.
* version 3.6.5
** The jV applet can invoke a JavaScript function when it started.
* version 3.7
** Commands 'pdbj_describe' and 'pdbj_execute' have been added.
** Keyword 'xps3' have been replaced by 'pdbj'.
* version 3.7.1
** Default PDBML URLs have been changed.
* version 3.7.2
** Some problems in creating png/jpeg image files have been fixed.
* version 3.8
** Command 'displayatom' has been added.
** The signed jV applet can save PNG/JPEG image files.
* version 3.8.1
** In commands 'cartoon', 'ribbons' and 'trace', a backbone will be drawn instead when a chain does not have enough atoms to draw those models.
** Recognition of amino acids is based on [http://remediation.wwpdb.org/ccd.html Chemical Component Dictionary].
* version 3.8.2
** Command 'ball_and_stick' has been added.
* version 3.8.3
** Binary distribution contains the JOGL library and pre-installation of JOGL is not necessary to use jV.
* version 4.0
** The program supports PDB format version 4.0.
** Atom expression has been extended to handle case-sensitive chain ID and label_asym_id in PDBML.
* version 4.1
** The program runs with new JOGL library (2.0-rc4 or later) which enables jV applets to run on Mac.
** From this release, the program requires JRE 1.6 or later.
** Command 'add_backbone' has been added.
** The program uses MODRES data and chem_comp/type data (PDBML only) to determine residue types.
* version 4.2
** The program reads polygon CGO (PyMOL-specific Compiled Graphics Objects) files distributed at eF-site system. Command 'load polygon_cgo' has been added.
** A parameter 'pdbid' and a method 'loadFTP' have been added to applet.
** When the program loads a PDBML noatom file whose directory is 'all-noatom' or 'XML-noatom', the coordinate file is retrieved from the corresponding directory; '../all-extatom' or '../XML-extatom', respectively.
* version 4.2.1
** The program runs with new JOGL library (2.0-rc11).
* version 4.3
** Anaglyph 3D rendering is added to 'stereo' command.
* version 4.3.1
** A workaround for a cache problem in JRE 1.7 has been added.
* version 4.4
** The program can read and write mmCIF format files.
** The program handles biomolecule structures when reading and writing a molecule file.
** The default setting of PDBMLplus URL has been changed.
* version 4.4.1
** Some problems in reading mmCIF files have been fixed.
** The behavior of mouse picking when measuring the distance between two atoms has been changed. Rotation and translation of molecules between two mouse pickings do not affect the distance measurement.
* version 4.4.2
** The program files are signed with a new certificate.
* version 4.4.3
** Some problems in writing PDB files have been fixed.
* version 4.4.4
** Some problems in rendering polygons have been fixed.
* version 4.4.5
** The program shows an error dialog when an input file has no valid data.
** The program files are signed with an updated certificate.
* version 4.5
** The program can read and display mmCIF files for small molecules.
* version 4.5.1
** A file permission problem in writing image files has been fixed.
* version 4.5.2
** The contact address on the error dialog has been changed.
* version 4.5.3
** In applet parameters, data files on the same server as the web page can be specified by the path part of URL as well as the full URL.</text>
    <sha1>688ea628141267725eedaa7cb31f3e35c058e014</sha1>
  </revision>
  <revision>
    <id>633</id>
    <parentid>626</parentid>
    <timestamp>2018-02-06T06:40:15Z</timestamp>
    <contributor>
      <username>IMSsato</username>
      <id>4</id>
    </contributor>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="6447" xml:space="preserve">Changes and improvements have been made as follows.

* version 3.1
** The following commands have been added; 'animrange', 'set adjustview', 'show godata', and 'show xps3'.
** The xPSSS expression has been added in order to select a group of atoms.
** Several public methods have been added to the applet so as to append molecule or polygon files after the applet started.
** The applet can send information about mouse-picked atoms to JavaScript.
* version 3.1.1
** Some problems in GUI menu [Options]-[Hetero Atoms] and [Hydrogens] have been fixed.
** Some problems in 'trace' command have been fixed.
* version 3.1.2
** eF-site ID has been changed to a new format.
* version 3.1.3
** Some problems in xps3 atom selection have been fixed.
* version 3.1.4
** Some problems in finalization process of openGL rendering have been fixed.
* version 3.1.5
** The output of 'show xps3' command has been modified.
** Some problems in 'save png/jpeg' command have been fixed.
* version 3.1.6
** Some problems in loading an empty polygon file have been fixed.
* version 3.1.7
** Some problems in initialization process of the applet have been fixed.
* version 3.2
** 'show site' command has been added.
* version 3.3 beta 1
** Availabe JOGL version is restricted to JSR-231 beta 5 only.
* version 3.3
** Both the previous JOGL (version 1.1.1) and JSR-231 are available.
** The following commands have been added; 'set viewpoint', 'show viewpoint', 'set imagesize', and 'show imagesize'.
* version 3.3.1
** Some problems in reading a pdbMLplus file have been fixed.
* version 3.4
** PDB format version 3 can be processed.
* version 3.5
** Discrimination of DNA and RNA linking nucleotides is based on [http://remediation.wwpdb.org/ccd.html Chemical Component Dictionary] for PDB format version 3.
** The default representation of the cartoon model has been changed. Commands 'set cartoon_loop_tube', 'set cartoon_round' and 'set ribbonback' have been added.
** The default parameters of lighting have been changed. Commands 'set ambient', 'set diffuse1', 'set diffuse1_direction', 'set diffuse2' and 'set diffuse1_direction' have been added.
** Commands 'set pdbml_noatom_url', 'set pdbml_extatom_url', 'set pdbml_plus_url', 'set efsite_url', 'set ext_site_url', 'show pdbml_url', 'show efsite_url' and 'show ext_site_url' have been added.
** The command-line option '-stdin' has been added to receive commands from stdin stream.
* version 3.6
** Users can specify the JavaScript function name used in Applet-to-JavaScript Communication.
** Applet parameter 'file_load_message' has been added.
* version 3.6.1
** Predefined set of residues has been modified.
** Old JOGL API is not supported.
* version 3.6.2
** Latest version of PDBML can be processed.
** Some problems in mouse control on Mac have been fixed.
* version 3.6.3
** Molecule file parsing has been modified to detect chain breaks properly by reading the 'label_asym_id' column in PDBML and the TER line in PDB flat file, respectively.
* version 3.6.4
** Some problems in GUI menu on Mac have been fixed.
* version 3.6.5
** The jV applet can invoke a JavaScript function when it started.
* version 3.7
** Commands 'pdbj_describe' and 'pdbj_execute' have been added.
** Keyword 'xps3' have been replaced by 'pdbj'.
* version 3.7.1
** Default PDBML URLs have been changed.
* version 3.7.2
** Some problems in creating png/jpeg image files have been fixed.
* version 3.8
** Command 'displayatom' has been added.
** The signed jV applet can save PNG/JPEG image files.
* version 3.8.1
** In commands 'cartoon', 'ribbons' and 'trace', a backbone will be drawn instead when a chain does not have enough atoms to draw those models.
** Recognition of amino acids is based on [http://remediation.wwpdb.org/ccd.html Chemical Component Dictionary].
* version 3.8.2
** Command 'ball_and_stick' has been added.
* version 3.8.3
** Binary distribution contains the JOGL library and pre-installation of JOGL is not necessary to use jV.
* version 4.0
** The program supports PDB format version 4.0.
** Atom expression has been extended to handle case-sensitive chain ID and label_asym_id in PDBML.
* version 4.1
** The program runs with new JOGL library (2.0-rc4 or later) which enables jV applets to run on Mac.
** From this release, the program requires JRE 1.6 or later.
** Command 'add_backbone' has been added.
** The program uses MODRES data and chem_comp/type data (PDBML only) to determine residue types.
* version 4.2
** The program reads polygon CGO (PyMOL-specific Compiled Graphics Objects) files distributed at eF-site system. Command 'load polygon_cgo' has been added.
** A parameter 'pdbid' and a method 'loadFTP' have been added to applet.
** When the program loads a PDBML noatom file whose directory is 'all-noatom' or 'XML-noatom', the coordinate file is retrieved from the corresponding directory; '../all-extatom' or '../XML-extatom', respectively.
* version 4.2.1
** The program runs with new JOGL library (2.0-rc11).
* version 4.3
** Anaglyph 3D rendering is added to 'stereo' command.
* version 4.3.1
** A workaround for a cache problem in JRE 1.7 has been added.
* version 4.4
** The program can read and write mmCIF format files.
** The program handles biomolecule structures when reading and writing a molecule file.
** The default setting of PDBMLplus URL has been changed.
* version 4.4.1
** Some problems in reading mmCIF files have been fixed.
** The behavior of mouse picking when measuring the distance between two atoms has been changed. Rotation and translation of molecules between two mouse pickings do not affect the distance measurement.
* version 4.4.2
** The program files are signed with a new certificate.
* version 4.4.3
** Some problems in writing PDB files have been fixed.
* version 4.4.4
** Some problems in rendering polygons have been fixed.
* version 4.4.5
** The program shows an error dialog when an input file has no valid data.
** The program files are signed with an updated certificate.
* version 4.5
** The program can read and display mmCIF files for small molecules.
* version 4.5.1
** A file permission problem in writing image files has been fixed.
* version 4.5.2
** The contact address on the error dialog has been changed.
* version 4.5.3
** In applet parameters, data files on the same server as the web page can be specified by the path part of URL as well as the full URL.
* version 4.5.3
** The program files are signed with a new certificate.</text>
    <sha1>279993426a9d5671f1d06c9cf122e13ea04018fd</sha1>
  </revision>
  <revision>
    <id>634</id>
    <parentid>633</parentid>
    <timestamp>2018-02-06T06:40:40Z</timestamp>
    <contributor>
      <username>IMSsato</username>
      <id>4</id>
    </contributor>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="6447" xml:space="preserve">Changes and improvements have been made as follows.

* version 3.1
** The following commands have been added; 'animrange', 'set adjustview', 'show godata', and 'show xps3'.
** The xPSSS expression has been added in order to select a group of atoms.
** Several public methods have been added to the applet so as to append molecule or polygon files after the applet started.
** The applet can send information about mouse-picked atoms to JavaScript.
* version 3.1.1
** Some problems in GUI menu [Options]-[Hetero Atoms] and [Hydrogens] have been fixed.
** Some problems in 'trace' command have been fixed.
* version 3.1.2
** eF-site ID has been changed to a new format.
* version 3.1.3
** Some problems in xps3 atom selection have been fixed.
* version 3.1.4
** Some problems in finalization process of openGL rendering have been fixed.
* version 3.1.5
** The output of 'show xps3' command has been modified.
** Some problems in 'save png/jpeg' command have been fixed.
* version 3.1.6
** Some problems in loading an empty polygon file have been fixed.
* version 3.1.7
** Some problems in initialization process of the applet have been fixed.
* version 3.2
** 'show site' command has been added.
* version 3.3 beta 1
** Availabe JOGL version is restricted to JSR-231 beta 5 only.
* version 3.3
** Both the previous JOGL (version 1.1.1) and JSR-231 are available.
** The following commands have been added; 'set viewpoint', 'show viewpoint', 'set imagesize', and 'show imagesize'.
* version 3.3.1
** Some problems in reading a pdbMLplus file have been fixed.
* version 3.4
** PDB format version 3 can be processed.
* version 3.5
** Discrimination of DNA and RNA linking nucleotides is based on [http://remediation.wwpdb.org/ccd.html Chemical Component Dictionary] for PDB format version 3.
** The default representation of the cartoon model has been changed. Commands 'set cartoon_loop_tube', 'set cartoon_round' and 'set ribbonback' have been added.
** The default parameters of lighting have been changed. Commands 'set ambient', 'set diffuse1', 'set diffuse1_direction', 'set diffuse2' and 'set diffuse1_direction' have been added.
** Commands 'set pdbml_noatom_url', 'set pdbml_extatom_url', 'set pdbml_plus_url', 'set efsite_url', 'set ext_site_url', 'show pdbml_url', 'show efsite_url' and 'show ext_site_url' have been added.
** The command-line option '-stdin' has been added to receive commands from stdin stream.
* version 3.6
** Users can specify the JavaScript function name used in Applet-to-JavaScript Communication.
** Applet parameter 'file_load_message' has been added.
* version 3.6.1
** Predefined set of residues has been modified.
** Old JOGL API is not supported.
* version 3.6.2
** Latest version of PDBML can be processed.
** Some problems in mouse control on Mac have been fixed.
* version 3.6.3
** Molecule file parsing has been modified to detect chain breaks properly by reading the 'label_asym_id' column in PDBML and the TER line in PDB flat file, respectively.
* version 3.6.4
** Some problems in GUI menu on Mac have been fixed.
* version 3.6.5
** The jV applet can invoke a JavaScript function when it started.
* version 3.7
** Commands 'pdbj_describe' and 'pdbj_execute' have been added.
** Keyword 'xps3' have been replaced by 'pdbj'.
* version 3.7.1
** Default PDBML URLs have been changed.
* version 3.7.2
** Some problems in creating png/jpeg image files have been fixed.
* version 3.8
** Command 'displayatom' has been added.
** The signed jV applet can save PNG/JPEG image files.
* version 3.8.1
** In commands 'cartoon', 'ribbons' and 'trace', a backbone will be drawn instead when a chain does not have enough atoms to draw those models.
** Recognition of amino acids is based on [http://remediation.wwpdb.org/ccd.html Chemical Component Dictionary].
* version 3.8.2
** Command 'ball_and_stick' has been added.
* version 3.8.3
** Binary distribution contains the JOGL library and pre-installation of JOGL is not necessary to use jV.
* version 4.0
** The program supports PDB format version 4.0.
** Atom expression has been extended to handle case-sensitive chain ID and label_asym_id in PDBML.
* version 4.1
** The program runs with new JOGL library (2.0-rc4 or later) which enables jV applets to run on Mac.
** From this release, the program requires JRE 1.6 or later.
** Command 'add_backbone' has been added.
** The program uses MODRES data and chem_comp/type data (PDBML only) to determine residue types.
* version 4.2
** The program reads polygon CGO (PyMOL-specific Compiled Graphics Objects) files distributed at eF-site system. Command 'load polygon_cgo' has been added.
** A parameter 'pdbid' and a method 'loadFTP' have been added to applet.
** When the program loads a PDBML noatom file whose directory is 'all-noatom' or 'XML-noatom', the coordinate file is retrieved from the corresponding directory; '../all-extatom' or '../XML-extatom', respectively.
* version 4.2.1
** The program runs with new JOGL library (2.0-rc11).
* version 4.3
** Anaglyph 3D rendering is added to 'stereo' command.
* version 4.3.1
** A workaround for a cache problem in JRE 1.7 has been added.
* version 4.4
** The program can read and write mmCIF format files.
** The program handles biomolecule structures when reading and writing a molecule file.
** The default setting of PDBMLplus URL has been changed.
* version 4.4.1
** Some problems in reading mmCIF files have been fixed.
** The behavior of mouse picking when measuring the distance between two atoms has been changed. Rotation and translation of molecules between two mouse pickings do not affect the distance measurement.
* version 4.4.2
** The program files are signed with a new certificate.
* version 4.4.3
** Some problems in writing PDB files have been fixed.
* version 4.4.4
** Some problems in rendering polygons have been fixed.
* version 4.4.5
** The program shows an error dialog when an input file has no valid data.
** The program files are signed with an updated certificate.
* version 4.5
** The program can read and display mmCIF files for small molecules.
* version 4.5.1
** A file permission problem in writing image files has been fixed.
* version 4.5.2
** The contact address on the error dialog has been changed.
* version 4.5.3
** In applet parameters, data files on the same server as the web page can be specified by the path part of URL as well as the full URL.
* version 4.5.4
** The program files are signed with a new certificate.</text>
    <sha1>78687e48fdb736a5508a766e0e69f5a358f7dac3</sha1>
  </revision>
  <revision>
    <id>640</id>
    <parentid>634</parentid>
    <timestamp>2020-03-03T02:02:55Z</timestamp>
    <contributor>
      <username>IMSsato</username>
      <id>4</id>
    </contributor>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="6519" xml:space="preserve">Changes and improvements have been made as follows.

* version 3.1
** The following commands have been added; 'animrange', 'set adjustview', 'show godata', and 'show xps3'.
** The xPSSS expression has been added in order to select a group of atoms.
** Several public methods have been added to the applet so as to append molecule or polygon files after the applet started.
** The applet can send information about mouse-picked atoms to JavaScript.
* version 3.1.1
** Some problems in GUI menu [Options]-[Hetero Atoms] and [Hydrogens] have been fixed.
** Some problems in 'trace' command have been fixed.
* version 3.1.2
** eF-site ID has been changed to a new format.
* version 3.1.3
** Some problems in xps3 atom selection have been fixed.
* version 3.1.4
** Some problems in finalization process of openGL rendering have been fixed.
* version 3.1.5
** The output of 'show xps3' command has been modified.
** Some problems in 'save png/jpeg' command have been fixed.
* version 3.1.6
** Some problems in loading an empty polygon file have been fixed.
* version 3.1.7
** Some problems in initialization process of the applet have been fixed.
* version 3.2
** 'show site' command has been added.
* version 3.3 beta 1
** Availabe JOGL version is restricted to JSR-231 beta 5 only.
* version 3.3
** Both the previous JOGL (version 1.1.1) and JSR-231 are available.
** The following commands have been added; 'set viewpoint', 'show viewpoint', 'set imagesize', and 'show imagesize'.
* version 3.3.1
** Some problems in reading a pdbMLplus file have been fixed.
* version 3.4
** PDB format version 3 can be processed.
* version 3.5
** Discrimination of DNA and RNA linking nucleotides is based on [http://remediation.wwpdb.org/ccd.html Chemical Component Dictionary] for PDB format version 3.
** The default representation of the cartoon model has been changed. Commands 'set cartoon_loop_tube', 'set cartoon_round' and 'set ribbonback' have been added.
** The default parameters of lighting have been changed. Commands 'set ambient', 'set diffuse1', 'set diffuse1_direction', 'set diffuse2' and 'set diffuse1_direction' have been added.
** Commands 'set pdbml_noatom_url', 'set pdbml_extatom_url', 'set pdbml_plus_url', 'set efsite_url', 'set ext_site_url', 'show pdbml_url', 'show efsite_url' and 'show ext_site_url' have been added.
** The command-line option '-stdin' has been added to receive commands from stdin stream.
* version 3.6
** Users can specify the JavaScript function name used in Applet-to-JavaScript Communication.
** Applet parameter 'file_load_message' has been added.
* version 3.6.1
** Predefined set of residues has been modified.
** Old JOGL API is not supported.
* version 3.6.2
** Latest version of PDBML can be processed.
** Some problems in mouse control on Mac have been fixed.
* version 3.6.3
** Molecule file parsing has been modified to detect chain breaks properly by reading the 'label_asym_id' column in PDBML and the TER line in PDB flat file, respectively.
* version 3.6.4
** Some problems in GUI menu on Mac have been fixed.
* version 3.6.5
** The jV applet can invoke a JavaScript function when it started.
* version 3.7
** Commands 'pdbj_describe' and 'pdbj_execute' have been added.
** Keyword 'xps3' have been replaced by 'pdbj'.
* version 3.7.1
** Default PDBML URLs have been changed.
* version 3.7.2
** Some problems in creating png/jpeg image files have been fixed.
* version 3.8
** Command 'displayatom' has been added.
** The signed jV applet can save PNG/JPEG image files.
* version 3.8.1
** In commands 'cartoon', 'ribbons' and 'trace', a backbone will be drawn instead when a chain does not have enough atoms to draw those models.
** Recognition of amino acids is based on [http://remediation.wwpdb.org/ccd.html Chemical Component Dictionary].
* version 3.8.2
** Command 'ball_and_stick' has been added.
* version 3.8.3
** Binary distribution contains the JOGL library and pre-installation of JOGL is not necessary to use jV.
* version 4.0
** The program supports PDB format version 4.0.
** Atom expression has been extended to handle case-sensitive chain ID and label_asym_id in PDBML.
* version 4.1
** The program runs with new JOGL library (2.0-rc4 or later) which enables jV applets to run on Mac.
** From this release, the program requires JRE 1.6 or later.
** Command 'add_backbone' has been added.
** The program uses MODRES data and chem_comp/type data (PDBML only) to determine residue types.
* version 4.2
** The program reads polygon CGO (PyMOL-specific Compiled Graphics Objects) files distributed at eF-site system. Command 'load polygon_cgo' has been added.
** A parameter 'pdbid' and a method 'loadFTP' have been added to applet.
** When the program loads a PDBML noatom file whose directory is 'all-noatom' or 'XML-noatom', the coordinate file is retrieved from the corresponding directory; '../all-extatom' or '../XML-extatom', respectively.
* version 4.2.1
** The program runs with new JOGL library (2.0-rc11).
* version 4.3
** Anaglyph 3D rendering is added to 'stereo' command.
* version 4.3.1
** A workaround for a cache problem in JRE 1.7 has been added.
* version 4.4
** The program can read and write mmCIF format files.
** The program handles biomolecule structures when reading and writing a molecule file.
** The default setting of PDBMLplus URL has been changed.
* version 4.4.1
** Some problems in reading mmCIF files have been fixed.
** The behavior of mouse picking when measuring the distance between two atoms has been changed. Rotation and translation of molecules between two mouse pickings do not affect the distance measurement.
* version 4.4.2
** The program files are signed with a new certificate.
* version 4.4.3
** Some problems in writing PDB files have been fixed.
* version 4.4.4
** Some problems in rendering polygons have been fixed.
* version 4.4.5
** The program shows an error dialog when an input file has no valid data.
** The program files are signed with an updated certificate.
* version 4.5
** The program can read and display mmCIF files for small molecules.
* version 4.5.1
** A file permission problem in writing image files has been fixed.
* version 4.5.2
** The contact address on the error dialog has been changed.
* version 4.5.3
** In applet parameters, data files on the same server as the web page can be specified by the path part of URL as well as the full URL.
* version 4.5.4
** The program files are signed with a new certificate.
* version 4.5.5
** The program files are signed with a new certificate.</text>
    <sha1>231cb6ef391047e9b2f5e9eeae1e41d5ff025eae</sha1>
  </revision>
  <revision>
    <id>643</id>
    <parentid>640</parentid>
    <timestamp>2020-06-01T05:52:02Z</timestamp>
    <contributor>
      <username>IMSsato</username>
      <id>4</id>
    </contributor>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="6591" xml:space="preserve">Changes and improvements have been made as follows.

* version 3.1
** The following commands have been added; 'animrange', 'set adjustview', 'show godata', and 'show xps3'.
** The xPSSS expression has been added in order to select a group of atoms.
** Several public methods have been added to the applet so as to append molecule or polygon files after the applet started.
** The applet can send information about mouse-picked atoms to JavaScript.
* version 3.1.1
** Some problems in GUI menu [Options]-[Hetero Atoms] and [Hydrogens] have been fixed.
** Some problems in 'trace' command have been fixed.
* version 3.1.2
** eF-site ID has been changed to a new format.
* version 3.1.3
** Some problems in xps3 atom selection have been fixed.
* version 3.1.4
** Some problems in finalization process of openGL rendering have been fixed.
* version 3.1.5
** The output of 'show xps3' command has been modified.
** Some problems in 'save png/jpeg' command have been fixed.
* version 3.1.6
** Some problems in loading an empty polygon file have been fixed.
* version 3.1.7
** Some problems in initialization process of the applet have been fixed.
* version 3.2
** 'show site' command has been added.
* version 3.3 beta 1
** Availabe JOGL version is restricted to JSR-231 beta 5 only.
* version 3.3
** Both the previous JOGL (version 1.1.1) and JSR-231 are available.
** The following commands have been added; 'set viewpoint', 'show viewpoint', 'set imagesize', and 'show imagesize'.
* version 3.3.1
** Some problems in reading a pdbMLplus file have been fixed.
* version 3.4
** PDB format version 3 can be processed.
* version 3.5
** Discrimination of DNA and RNA linking nucleotides is based on [http://remediation.wwpdb.org/ccd.html Chemical Component Dictionary] for PDB format version 3.
** The default representation of the cartoon model has been changed. Commands 'set cartoon_loop_tube', 'set cartoon_round' and 'set ribbonback' have been added.
** The default parameters of lighting have been changed. Commands 'set ambient', 'set diffuse1', 'set diffuse1_direction', 'set diffuse2' and 'set diffuse1_direction' have been added.
** Commands 'set pdbml_noatom_url', 'set pdbml_extatom_url', 'set pdbml_plus_url', 'set efsite_url', 'set ext_site_url', 'show pdbml_url', 'show efsite_url' and 'show ext_site_url' have been added.
** The command-line option '-stdin' has been added to receive commands from stdin stream.
* version 3.6
** Users can specify the JavaScript function name used in Applet-to-JavaScript Communication.
** Applet parameter 'file_load_message' has been added.
* version 3.6.1
** Predefined set of residues has been modified.
** Old JOGL API is not supported.
* version 3.6.2
** Latest version of PDBML can be processed.
** Some problems in mouse control on Mac have been fixed.
* version 3.6.3
** Molecule file parsing has been modified to detect chain breaks properly by reading the 'label_asym_id' column in PDBML and the TER line in PDB flat file, respectively.
* version 3.6.4
** Some problems in GUI menu on Mac have been fixed.
* version 3.6.5
** The jV applet can invoke a JavaScript function when it started.
* version 3.7
** Commands 'pdbj_describe' and 'pdbj_execute' have been added.
** Keyword 'xps3' have been replaced by 'pdbj'.
* version 3.7.1
** Default PDBML URLs have been changed.
* version 3.7.2
** Some problems in creating png/jpeg image files have been fixed.
* version 3.8
** Command 'displayatom' has been added.
** The signed jV applet can save PNG/JPEG image files.
* version 3.8.1
** In commands 'cartoon', 'ribbons' and 'trace', a backbone will be drawn instead when a chain does not have enough atoms to draw those models.
** Recognition of amino acids is based on [http://remediation.wwpdb.org/ccd.html Chemical Component Dictionary].
* version 3.8.2
** Command 'ball_and_stick' has been added.
* version 3.8.3
** Binary distribution contains the JOGL library and pre-installation of JOGL is not necessary to use jV.
* version 4.0
** The program supports PDB format version 4.0.
** Atom expression has been extended to handle case-sensitive chain ID and label_asym_id in PDBML.
* version 4.1
** The program runs with new JOGL library (2.0-rc4 or later) which enables jV applets to run on Mac.
** From this release, the program requires JRE 1.6 or later.
** Command 'add_backbone' has been added.
** The program uses MODRES data and chem_comp/type data (PDBML only) to determine residue types.
* version 4.2
** The program reads polygon CGO (PyMOL-specific Compiled Graphics Objects) files distributed at eF-site system. Command 'load polygon_cgo' has been added.
** A parameter 'pdbid' and a method 'loadFTP' have been added to applet.
** When the program loads a PDBML noatom file whose directory is 'all-noatom' or 'XML-noatom', the coordinate file is retrieved from the corresponding directory; '../all-extatom' or '../XML-extatom', respectively.
* version 4.2.1
** The program runs with new JOGL library (2.0-rc11).
* version 4.3
** Anaglyph 3D rendering is added to 'stereo' command.
* version 4.3.1
** A workaround for a cache problem in JRE 1.7 has been added.
* version 4.4
** The program can read and write mmCIF format files.
** The program handles biomolecule structures when reading and writing a molecule file.
** The default setting of PDBMLplus URL has been changed.
* version 4.4.1
** Some problems in reading mmCIF files have been fixed.
** The behavior of mouse picking when measuring the distance between two atoms has been changed. Rotation and translation of molecules between two mouse pickings do not affect the distance measurement.
* version 4.4.2
** The program files are signed with a new certificate.
* version 4.4.3
** Some problems in writing PDB files have been fixed.
* version 4.4.4
** Some problems in rendering polygons have been fixed.
* version 4.4.5
** The program shows an error dialog when an input file has no valid data.
** The program files are signed with an updated certificate.
* version 4.5
** The program can read and display mmCIF files for small molecules.
* version 4.5.1
** A file permission problem in writing image files has been fixed.
* version 4.5.2
** The contact address on the error dialog has been changed.
* version 4.5.3
** In applet parameters, data files on the same server as the web page can be specified by the path part of URL as well as the full URL.
* version 4.5.4
** The program files are signed with a new certificate.
* version 4.5.5
** The program files are signed with a new certificate.
* version 4.5.6
** The program files are signed with a new certificate.</text>
    <sha1>ef8c924ae827f9f9cc26f93efc91b8f7d8b71c42</sha1>
  </revision>
  <revision>
    <id>646</id>
    <parentid>643</parentid>
    <timestamp>2020-09-16T08:20:38Z</timestamp>
    <contributor>
      <username>IMSsato</username>
      <id>4</id>
    </contributor>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="6704" xml:space="preserve">Changes and improvements have been made as follows.

* version 3.1
** The following commands have been added; 'animrange', 'set adjustview', 'show godata', and 'show xps3'.
** The xPSSS expression has been added in order to select a group of atoms.
** Several public methods have been added to the applet so as to append molecule or polygon files after the applet started.
** The applet can send information about mouse-picked atoms to JavaScript.
* version 3.1.1
** Some problems in GUI menu [Options]-[Hetero Atoms] and [Hydrogens] have been fixed.
** Some problems in 'trace' command have been fixed.
* version 3.1.2
** eF-site ID has been changed to a new format.
* version 3.1.3
** Some problems in xps3 atom selection have been fixed.
* version 3.1.4
** Some problems in finalization process of openGL rendering have been fixed.
* version 3.1.5
** The output of 'show xps3' command has been modified.
** Some problems in 'save png/jpeg' command have been fixed.
* version 3.1.6
** Some problems in loading an empty polygon file have been fixed.
* version 3.1.7
** Some problems in initialization process of the applet have been fixed.
* version 3.2
** 'show site' command has been added.
* version 3.3 beta 1
** Availabe JOGL version is restricted to JSR-231 beta 5 only.
* version 3.3
** Both the previous JOGL (version 1.1.1) and JSR-231 are available.
** The following commands have been added; 'set viewpoint', 'show viewpoint', 'set imagesize', and 'show imagesize'.
* version 3.3.1
** Some problems in reading a pdbMLplus file have been fixed.
* version 3.4
** PDB format version 3 can be processed.
* version 3.5
** Discrimination of DNA and RNA linking nucleotides is based on [http://remediation.wwpdb.org/ccd.html Chemical Component Dictionary] for PDB format version 3.
** The default representation of the cartoon model has been changed. Commands 'set cartoon_loop_tube', 'set cartoon_round' and 'set ribbonback' have been added.
** The default parameters of lighting have been changed. Commands 'set ambient', 'set diffuse1', 'set diffuse1_direction', 'set diffuse2' and 'set diffuse1_direction' have been added.
** Commands 'set pdbml_noatom_url', 'set pdbml_extatom_url', 'set pdbml_plus_url', 'set efsite_url', 'set ext_site_url', 'show pdbml_url', 'show efsite_url' and 'show ext_site_url' have been added.
** The command-line option '-stdin' has been added to receive commands from stdin stream.
* version 3.6
** Users can specify the JavaScript function name used in Applet-to-JavaScript Communication.
** Applet parameter 'file_load_message' has been added.
* version 3.6.1
** Predefined set of residues has been modified.
** Old JOGL API is not supported.
* version 3.6.2
** Latest version of PDBML can be processed.
** Some problems in mouse control on Mac have been fixed.
* version 3.6.3
** Molecule file parsing has been modified to detect chain breaks properly by reading the 'label_asym_id' column in PDBML and the TER line in PDB flat file, respectively.
* version 3.6.4
** Some problems in GUI menu on Mac have been fixed.
* version 3.6.5
** The jV applet can invoke a JavaScript function when it started.
* version 3.7
** Commands 'pdbj_describe' and 'pdbj_execute' have been added.
** Keyword 'xps3' have been replaced by 'pdbj'.
* version 3.7.1
** Default PDBML URLs have been changed.
* version 3.7.2
** Some problems in creating png/jpeg image files have been fixed.
* version 3.8
** Command 'displayatom' has been added.
** The signed jV applet can save PNG/JPEG image files.
* version 3.8.1
** In commands 'cartoon', 'ribbons' and 'trace', a backbone will be drawn instead when a chain does not have enough atoms to draw those models.
** Recognition of amino acids is based on [http://remediation.wwpdb.org/ccd.html Chemical Component Dictionary].
* version 3.8.2
** Command 'ball_and_stick' has been added.
* version 3.8.3
** Binary distribution contains the JOGL library and pre-installation of JOGL is not necessary to use jV.
* version 4.0
** The program supports PDB format version 4.0.
** Atom expression has been extended to handle case-sensitive chain ID and label_asym_id in PDBML.
* version 4.1
** The program runs with new JOGL library (2.0-rc4 or later) which enables jV applets to run on Mac.
** From this release, the program requires JRE 1.6 or later.
** Command 'add_backbone' has been added.
** The program uses MODRES data and chem_comp/type data (PDBML only) to determine residue types.
* version 4.2
** The program reads polygon CGO (PyMOL-specific Compiled Graphics Objects) files distributed at eF-site system. Command 'load polygon_cgo' has been added.
** A parameter 'pdbid' and a method 'loadFTP' have been added to applet.
** When the program loads a PDBML noatom file whose directory is 'all-noatom' or 'XML-noatom', the coordinate file is retrieved from the corresponding directory; '../all-extatom' or '../XML-extatom', respectively.
* version 4.2.1
** The program runs with new JOGL library (2.0-rc11).
* version 4.3
** Anaglyph 3D rendering is added to 'stereo' command.
* version 4.3.1
** A workaround for a cache problem in JRE 1.7 has been added.
* version 4.4
** The program can read and write mmCIF format files.
** The program handles biomolecule structures when reading and writing a molecule file.
** The default setting of PDBMLplus URL has been changed.
* version 4.4.1
** Some problems in reading mmCIF files have been fixed.
** The behavior of mouse picking when measuring the distance between two atoms has been changed. Rotation and translation of molecules between two mouse pickings do not affect the distance measurement.
* version 4.4.2
** The program files are signed with a new certificate.
* version 4.4.3
** Some problems in writing PDB files have been fixed.
* version 4.4.4
** Some problems in rendering polygons have been fixed.
* version 4.4.5
** The program shows an error dialog when an input file has no valid data.
** The program files are signed with an updated certificate.
* version 4.5
** The program can read and display mmCIF files for small molecules.
* version 4.5.1
** A file permission problem in writing image files has been fixed.
* version 4.5.2
** The contact address on the error dialog has been changed.
* version 4.5.3
** In applet parameters, data files on the same server as the web page can be specified by the path part of URL as well as the full URL.
* version 4.5.4
** The program files are signed with a new certificate.
* version 4.5.5
** The program files are signed with a new certificate.
* version 4.5.6
** The program files are signed with a new certificate.
* version 4.5.7
** The program files were signed with a new certificate because of the CA certification renewal.</text>
    <sha1>8af57c21f37a422bcbc92cd9b958931a6ba34491</sha1>
  </revision>
  <revision>
    <id>652</id>
    <parentid>646</parentid>
    <timestamp>2021-04-26T08:47:31Z</timestamp>
    <contributor>
      <username>IMSsato</username>
      <id>4</id>
    </contributor>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="6829" xml:space="preserve">Changes and improvements have been made as follows.

* version 3.1
** The following commands have been added; 'animrange', 'set adjustview', 'show godata', and 'show xps3'.
** The xPSSS expression has been added in order to select a group of atoms.
** Several public methods have been added to the applet so as to append molecule or polygon files after the applet started.
** The applet can send information about mouse-picked atoms to JavaScript.
* version 3.1.1
** Some problems in GUI menu [Options]-[Hetero Atoms] and [Hydrogens] have been fixed.
** Some problems in 'trace' command have been fixed.
* version 3.1.2
** eF-site ID has been changed to a new format.
* version 3.1.3
** Some problems in xps3 atom selection have been fixed.
* version 3.1.4
** Some problems in finalization process of openGL rendering have been fixed.
* version 3.1.5
** The output of 'show xps3' command has been modified.
** Some problems in 'save png/jpeg' command have been fixed.
* version 3.1.6
** Some problems in loading an empty polygon file have been fixed.
* version 3.1.7
** Some problems in initialization process of the applet have been fixed.
* version 3.2
** 'show site' command has been added.
* version 3.3 beta 1
** Availabe JOGL version is restricted to JSR-231 beta 5 only.
* version 3.3
** Both the previous JOGL (version 1.1.1) and JSR-231 are available.
** The following commands have been added; 'set viewpoint', 'show viewpoint', 'set imagesize', and 'show imagesize'.
* version 3.3.1
** Some problems in reading a pdbMLplus file have been fixed.
* version 3.4
** PDB format version 3 can be processed.
* version 3.5
** Discrimination of DNA and RNA linking nucleotides is based on [http://remediation.wwpdb.org/ccd.html Chemical Component Dictionary] for PDB format version 3.
** The default representation of the cartoon model has been changed. Commands 'set cartoon_loop_tube', 'set cartoon_round' and 'set ribbonback' have been added.
** The default parameters of lighting have been changed. Commands 'set ambient', 'set diffuse1', 'set diffuse1_direction', 'set diffuse2' and 'set diffuse1_direction' have been added.
** Commands 'set pdbml_noatom_url', 'set pdbml_extatom_url', 'set pdbml_plus_url', 'set efsite_url', 'set ext_site_url', 'show pdbml_url', 'show efsite_url' and 'show ext_site_url' have been added.
** The command-line option '-stdin' has been added to receive commands from stdin stream.
* version 3.6
** Users can specify the JavaScript function name used in Applet-to-JavaScript Communication.
** Applet parameter 'file_load_message' has been added.
* version 3.6.1
** Predefined set of residues has been modified.
** Old JOGL API is not supported.
* version 3.6.2
** Latest version of PDBML can be processed.
** Some problems in mouse control on Mac have been fixed.
* version 3.6.3
** Molecule file parsing has been modified to detect chain breaks properly by reading the 'label_asym_id' column in PDBML and the TER line in PDB flat file, respectively.
* version 3.6.4
** Some problems in GUI menu on Mac have been fixed.
* version 3.6.5
** The jV applet can invoke a JavaScript function when it started.
* version 3.7
** Commands 'pdbj_describe' and 'pdbj_execute' have been added.
** Keyword 'xps3' have been replaced by 'pdbj'.
* version 3.7.1
** Default PDBML URLs have been changed.
* version 3.7.2
** Some problems in creating png/jpeg image files have been fixed.
* version 3.8
** Command 'displayatom' has been added.
** The signed jV applet can save PNG/JPEG image files.
* version 3.8.1
** In commands 'cartoon', 'ribbons' and 'trace', a backbone will be drawn instead when a chain does not have enough atoms to draw those models.
** Recognition of amino acids is based on [http://remediation.wwpdb.org/ccd.html Chemical Component Dictionary].
* version 3.8.2
** Command 'ball_and_stick' has been added.
* version 3.8.3
** Binary distribution contains the JOGL library and pre-installation of JOGL is not necessary to use jV.
* version 4.0
** The program supports PDB format version 4.0.
** Atom expression has been extended to handle case-sensitive chain ID and label_asym_id in PDBML.
* version 4.1
** The program runs with new JOGL library (2.0-rc4 or later) which enables jV applets to run on Mac.
** From this release, the program requires JRE 1.6 or later.
** Command 'add_backbone' has been added.
** The program uses MODRES data and chem_comp/type data (PDBML only) to determine residue types.
* version 4.2
** The program reads polygon CGO (PyMOL-specific Compiled Graphics Objects) files distributed at eF-site system. Command 'load polygon_cgo' has been added.
** A parameter 'pdbid' and a method 'loadFTP' have been added to applet.
** When the program loads a PDBML noatom file whose directory is 'all-noatom' or 'XML-noatom', the coordinate file is retrieved from the corresponding directory; '../all-extatom' or '../XML-extatom', respectively.
* version 4.2.1
** The program runs with new JOGL library (2.0-rc11).
* version 4.3
** Anaglyph 3D rendering is added to 'stereo' command.
* version 4.3.1
** A workaround for a cache problem in JRE 1.7 has been added.
* version 4.4
** The program can read and write mmCIF format files.
** The program handles biomolecule structures when reading and writing a molecule file.
** The default setting of PDBMLplus URL has been changed.
* version 4.4.1
** Some problems in reading mmCIF files have been fixed.
** The behavior of mouse picking when measuring the distance between two atoms has been changed. Rotation and translation of molecules between two mouse pickings do not affect the distance measurement.
* version 4.4.2
** The program files are signed with a new certificate.
* version 4.4.3
** Some problems in writing PDB files have been fixed.
* version 4.4.4
** Some problems in rendering polygons have been fixed.
* version 4.4.5
** The program shows an error dialog when an input file has no valid data.
** The program files are signed with an updated certificate.
* version 4.5
** The program can read and display mmCIF files for small molecules.
* version 4.5.1
** A file permission problem in writing image files has been fixed.
* version 4.5.2
** The contact address on the error dialog has been changed.
* version 4.5.3
** In applet parameters, data files on the same server as the web page can be specified by the path part of URL as well as the full URL.
* version 4.5.4
** The program files are signed with a new certificate.
* version 4.5.5
** The program files are signed with a new certificate.
* version 4.5.6
** The program files are signed with a new certificate.
* version 4.5.7
** The program files were signed with a new certificate because of the CA certification renewal.
* version 4.5.8
** PDBML URL to fetch molecule information files has been updated.
** Applet functionality has been removed.</text>
    <sha1>b04f61b5aeec80ebd8fb7a96f32e81a662174890</sha1>
  </revision>
</page>
<page arvcontinue="20151001071243|604">
  <title>Use as Applet</title>
  <ns>0</ns>
  <id>24</id>
  <revision>
    <id>608</id>
    <parentid>559</parentid>
    <timestamp>2015-10-01T07:21:19Z</timestamp>
    <contributor>
      <username>IMSsato</username>
      <id>4</id>
    </contributor>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="5540" xml:space="preserve">{| style="float:right"
 |__TOC__
 |}

== Introduction ==
In order to use jV as an applet, your browser must support the
[http://www.oracle.com/technetwork/java/index-jsp-141438.html Java Plug-in] technology.
The applet is called from OBJECT tags in HTML, where class name that should be called is "org.pdbj.viewer.gui.ViewerApplet". The program has following features.
* whether to use the command line interface or not can be specified
* whether to use the file control panel or not can be specified
* whether to use the popup menu or not can be specified
* witihin applets in the same web page, mouse events can be shared
* applet can receive a command string from JaveScript
* applet can send information about mouse-picked atoms to JavaScript.

== Parameters ==
To initialize the applet, the following parameters can be specified in HTML.
{| class="wikitable" border="1"
 ! parameter !! value 
 |-
 | pdbid || PDB ID to be loaded from the PDBj FTP site (delimited by comma for more than one files). This parameter works only in a signed applet.
 |-
 | mmcifURL || URL of the mmCIF files to be loaded (delimited by comma for more than one files).
 |-
 | pdbmlURL || URL of the PDBML files to be loaded (delimited by comma for more than one files).
 |-
 | pdbURL || URL of the PDB files to be loaded (delimited by comma for more than one files).
 |-
 | polygonURL || URL of the polygon files to be loaded (delimited by comma for more than one files).
 |-
 | animURL || URL of the animation files to be loaded (delimited by comma for more than one files).
 |-
 | command_area || whether to use the command line interface or not (true or false).
 |-
 | file_control || whether to use the file control panel or not (true or false).
 |-
 | popup_menu || whether to use the popup menu or not (true or false).
 |-
 | mouse_send_to || name property of applets with which mouse events are shared (delimited by comma for more than one applets).
 |-
 | commands || initial commands that are executed when the applet starts (delimited by semicolon for more than one commands).
 |-
 | report_picking || whether to send information about mouse-picked atoms to JavaScript or not (true or false).
 |-
 | picking_receiver || JavaScript function name that receives mouse-picking data.
 |-
 | file_load_message || whether to show a message dialog while loading a file (true or false).
 |-
 | call_on_start || whether to call a JavaScript function when the applet started (true or false).
 |-
 | newt || whether to use JOGL's native windowing toolkit (true or false). At the current version, applets on Mac need this parameter set to true. On other platforms, however, this parameter must be set to fasle. Therefore the parameter should be dynamically determined in applet tags in HTML based on the platform. When set to true, two other parameters, command_area and file_control, are automatically set to false and the stereo command becomes unavailable.
|}

== JavaScript-to-Applet Communication ==
The ViewerApplet class has some public methods, which can be called from JavaScript.

 void executeCommand(String commands)

Through this method, the applet can receive some arbitrary commands (delimited by semicolon).

 void loadMmcif(String fileLocation)
 void loadPDB(String fileLocation)
 void loadPDBML(String fileLocation)
 void loadFTP(String pdbId)
 void loadPolygon(String fileLocation)
 void loadPolygonCGO(String fileLocation)
 void loadAnim(String fileLocation)

Using these methods, mmCIF file, PDB file, PDBML file, polygon file, and animation file specified by URL can be loaded respectively.
The loadFTP method receives a PDB ID and retrieves a PDBML file from the PDBj FTP site, which works only in a signed applet.

 void loadMmcif(String fileLocation, int fitTo)
 void loadPDB(String fileLocation, int fitTo)
 void loadPDBML(String fileLocation, int fitTo)
 void loadFTP(String pdbId, int fitTo)
 void loadPolygon(String fileLocation, int fitTo)
 void loadPolygonCGO(String fileLocation, int fitTo)
 void loadAnim(String fileLocation, int fitTo)

When these methods are used, the transform matrix of the loaded file is set identical to that of the specified file.

 void loadMmcif(String fileLocation, int fitTo, String biomolecule, String filter)
 void loadPDB(String fileLocation, int fitTo, String filter)
 void loadPDBML(String fileLocation, int fitTo, String biomolecule, String filter)
 void loadFTP(String pdbId, int fitTo, String biomolecule, String filter)
 void loadAnim(String fileLocation, int fitTo, String filter)

When these methods are used, biomolecule structure and filter can also be specified. The arguments fitTo, biomolecule and filter can be set as -1, null and null, respectively, if you do not need to use some of them.

== Applet-to-JavaScript Communication ==
In order to send the result of mouse-picking to JavaScript, the following function must be defined in JavaScript.

 function receiveMousePick(file, model, chain, res, atom, altloc, resName, atomName, x, y, z)

The function name 'receiveMousePick' is a default name. It can be changed by specifying the 'picking_receiver' parameter in the OBJECT tag.

When the applet started, it invokes the following JavScript function 

 function jvOnStart(name)

if it is configured to do so by the applet parameter 'call_on_start'. Here the function receives the name of the applet as its argument. 

== Available applet code for each environment ==
Which type of applet code works or not in each environment is described [http://pdbj.org/jv/test/applet.php here].</text>
    <sha1>51798ebde5d844c345eaeeec8dcc566e023d8517</sha1>
  </revision>
</page>
<page arvcontinue="20151001071243|604">
  <title>Old version</title>
  <ns>0</ns>
  <id>6</id>
  <revision>
    <id>612</id>
    <parentid>314</parentid>
    <timestamp>2016-01-08T07:22:48Z</timestamp>
    <contributor>
      <username>IMSsato</username>
      <id>4</id>
    </contributor>
    <comment>/* Download */</comment>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="1452" xml:space="preserve">== jV version 1 (PDBjViewer) ==
Visualization of structure and surface of molecules is performed by a Java applet program called 'PDBjViewer'.

In order to use PDBjViewer, [http://java.sun.com/products/plugin/ Java Plug-in] and
[http://java.sun.com/products/java-media/3D/ Java 3D API] must be installed on your computer.
The version requirements are as follows.&lt;br /&gt;
* JRE (includes Java Plug-in) 1.4.1 or later (recommend 1.4.2)
* Java 3D API (OpenGL) 1.2.1 or later (recommend 1.2.1_04)
Important notes
# You can select two kinds of implementation of Java 3D, OpenGL version and DirectX version. But, PDBjViewer only work with OpenGL version at present.
# PDBjViewer does not work with JRE from 1.4.1_03 to 1.4.1_06.&lt;br /&gt;

== jV version 2 ==
jV version 2 is an advanced version of PDBjViewer, which can be used only as a stand-alone program. It enables to display more than one molecule images at the same time and their display models and transforms can be operated separately. An animation of molecules can be also performed. jV version 2 runs with .NET framework 1.1 on the Windows platform. Therefore the .NET framework must be installed on your computer.

== Download ==
You can download the older versions from the same download pages with the current version.
* [http://service.ipr.pdbj.org/eF-site/servlet/DownloadViewerBinary binary]
* [http://service.ipr.pdbj.org/eF-site/servlet/Registration source code] (registration will be required)</text>
    <sha1>5fe27df27638ef880c2cc9bf9eab44381e1d3a3c</sha1>
  </revision>
  <revision>
    <id>631</id>
    <parentid>612</parentid>
    <timestamp>2018-02-06T06:36:31Z</timestamp>
    <contributor>
      <username>IMSsato</username>
      <id>4</id>
    </contributor>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="1430" xml:space="preserve">== jV version 1 (PDBjViewer) ==
Visualization of structure and surface of molecules is performed by a Java applet program called 'PDBjViewer'.

In order to use PDBjViewer, [http://java.sun.com/products/plugin/ Java Plug-in] and
[http://java.sun.com/products/java-media/3D/ Java 3D API] must be installed on your computer.
The version requirements are as follows.&lt;br /&gt;
* JRE (includes Java Plug-in) 1.4.1 or later (recommend 1.4.2)
* Java 3D API (OpenGL) 1.2.1 or later (recommend 1.2.1_04)
Important notes
# You can select two kinds of implementation of Java 3D, OpenGL version and DirectX version. But, PDBjViewer only work with OpenGL version at present.
# PDBjViewer does not work with JRE from 1.4.1_03 to 1.4.1_06.&lt;br /&gt;

== jV version 2 ==
jV version 2 is an advanced version of PDBjViewer, which can be used only as a stand-alone program. It enables to display more than one molecule images at the same time and their display models and transforms can be operated separately. An animation of molecules can be also performed. jV version 2 runs with .NET framework 1.1 on the Windows platform. Therefore the .NET framework must be installed on your computer.

== Download ==
You can download the older versions from the same download pages with the current version.
* [https://pdbj.org/eF-site/servlet/DownloadViewerBinary binary]
* [https://pdbj.org/eF-site/servlet/Registration source code] (registration will be required)</text>
    <sha1>cd077c989ea583768fd32aa179c4cd874d2dd869</sha1>
  </revision>
  <revision>
    <id>637</id>
    <parentid>631</parentid>
    <timestamp>2018-02-14T06:27:18Z</timestamp>
    <contributor>
      <username>IMSsato</username>
      <id>4</id>
    </contributor>
    <comment>/* Download */</comment>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="1402" xml:space="preserve">== jV version 1 (PDBjViewer) ==
Visualization of structure and surface of molecules is performed by a Java applet program called 'PDBjViewer'.

In order to use PDBjViewer, [http://java.sun.com/products/plugin/ Java Plug-in] and
[http://java.sun.com/products/java-media/3D/ Java 3D API] must be installed on your computer.
The version requirements are as follows.&lt;br /&gt;
* JRE (includes Java Plug-in) 1.4.1 or later (recommend 1.4.2)
* Java 3D API (OpenGL) 1.2.1 or later (recommend 1.2.1_04)
Important notes
# You can select two kinds of implementation of Java 3D, OpenGL version and DirectX version. But, PDBjViewer only work with OpenGL version at present.
# PDBjViewer does not work with JRE from 1.4.1_03 to 1.4.1_06.&lt;br /&gt;

== jV version 2 ==
jV version 2 is an advanced version of PDBjViewer, which can be used only as a stand-alone program. It enables to display more than one molecule images at the same time and their display models and transforms can be operated separately. An animation of molecules can be also performed. jV version 2 runs with .NET framework 1.1 on the Windows platform. Therefore the .NET framework must be installed on your computer.

== Download ==
You can download the older versions from the same download pages with the current version.
* [https://pdbj.org/jv/download/binary binary]
* [https://pdbj.org/jv/download/source source code] (registration will be required)</text>
    <sha1>ec4539978374c0f0c68de4203bdb07360c215a15</sha1>
  </revision>
</page>
<page arvcontinue="20151001071243|604">
  <title>JV:About</title>
  <ns>4</ns>
  <id>39</id>
  <revision>
    <id>621</id>
    <parentid>274</parentid>
    <timestamp>2017-01-16T02:36:24Z</timestamp>
    <contributor>
      <username>IMSsato</username>
      <id>4</id>
    </contributor>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="642" xml:space="preserve">The program 'jV' has been developed by [http://www.hgc.jp/~kinosita/TOP.html Kengo Kinoshita] ([http://www.is.tohoku.ac.jp/index-e.html Graduate School of Information Sciences], [http://www.tohoku.ac.jp/english/ Tohoku University]) and [http://www.protein.osaka-u.ac.jp/rcsfp/pi/ Haruki Nakamura] ([http://www.protein.osaka-u.ac.jp/index_e.php Institute for Protein Research], [http://www.osaka-u.ac.jp/eng/index.html Osaka Univeristy]), with the support from [http://biosciencedbc.jp/ JST-NBDC] and [http://www.protein.osaka-u.ac.jp/index_e.php Institute for Protein Research IPR], [http://www.osaka-u.ac.jp/eng/index.html Osaka Univeristy].</text>
    <sha1>e4956e85e1318e8cb6c3f74429e8dcacdeefd5b7</sha1>
  </revision>
</page>
<page arvcontinue="20151001071243|604">
  <title>Color Expression</title>
  <ns>0</ns>
  <id>23</id>
  <revision>
    <id>629</id>
    <parentid>177</parentid>
    <timestamp>2018-02-06T06:33:50Z</timestamp>
    <contributor>
      <username>IMSsato</username>
      <id>4</id>
    </contributor>
    <comment>/* amino */</comment>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="11549" xml:space="preserve">{| style="float:right"
 |__TOC__
 |}
== RGB values ==
A color can be specified by a comma separated triple of Red, Green and Blue (RGB) components enclosed in square brackets, where RGB values are from 0 to 255, respectively. 

== Predefined Color ==
The following 24 colors can be specified by their name.

&lt;table border="1"&gt;
 &lt;tr&gt;
  &lt;td&gt;color name&lt;/td&gt;
  &lt;td&gt;RGB values&lt;/td&gt;
  &lt;td&gt;color&lt;/td&gt;
 &lt;/tr&gt;
 &lt;tr&gt;
  &lt;td&gt;BLACK&lt;/td&gt;
  &lt;td&gt;[0, 0, 0]&lt;/td&gt;
  &lt;td width=100 style="background: #000000"&gt;&lt;/td&gt;
 &lt;/tr&gt;
 &lt;tr&gt;
  &lt;td&gt;BLUE&lt;/td&gt;
  &lt;td&gt;[0, 0, 255]&lt;/td&gt;
  &lt;td width=100 style="background: #0000FF"&gt;&lt;/td&gt;
 &lt;/tr&gt;
 &lt;tr&gt;
  &lt;td&gt;BLUETINT&lt;/td&gt;
  &lt;td&gt;[175, 214, 255]&lt;/td&gt;
  &lt;td width=100 style="background: #AFD6FF"&gt;&lt;/td&gt;
 &lt;/tr&gt;
 &lt;tr&gt;
  &lt;td&gt;BROWN&lt;/td&gt;
  &lt;td&gt;[175, 117, 89]&lt;/td&gt;
  &lt;td width=100 style="background: #AF7559"&gt;&lt;/td&gt;
 &lt;/tr&gt;
 &lt;tr&gt;
  &lt;td&gt;CYAN&lt;/td&gt;
  &lt;td&gt;[0, 255, 255]&lt;/td&gt;
  &lt;td width=100 style="background: #00FFFF"&gt;&lt;/td&gt;
 &lt;/tr&gt;
 &lt;tr&gt;
  &lt;td&gt;GOLD&lt;/td&gt;
  &lt;td&gt;[255, 156, 0]&lt;/td&gt;
  &lt;td width=100 style="background: #FF9C00"&gt;&lt;/td&gt;
 &lt;/tr&gt;
 &lt;tr&gt;
  &lt;td&gt;GREY&lt;/td&gt;
  &lt;td&gt;[125, 125, 125]&lt;/td&gt;
  &lt;td width=100 style="background: #7D7D7D"&gt;&lt;/td&gt;
 &lt;/tr&gt;
 &lt;tr&gt;
  &lt;td&gt;GREEN&lt;/td&gt;
  &lt;td&gt;[0, 255, 0]&lt;/td&gt;
  &lt;td width=100 style="background: #00FF00"&gt;&lt;/td&gt;
 &lt;/tr&gt;
 &lt;tr&gt;
  &lt;td&gt;GREENBLUE&lt;/td&gt;
  &lt;td&gt;[46, 139, 87]&lt;/td&gt;
  &lt;td width=100 style="background: #2E8B57"&gt;&lt;/td&gt;
 &lt;/tr&gt;
 &lt;tr&gt;
  &lt;td&gt;GreenTint&lt;/td&gt;
  &lt;td&gt;[152, 255, 179]&lt;/td&gt;
  &lt;td width=100 style="background: #98FFB3"&gt;&lt;/td&gt;
 &lt;/tr&gt;
 &lt;tr&gt;
  &lt;td&gt;HOTPINK&lt;/td&gt;
  &lt;td&gt;[255, 0, 101]&lt;/td&gt;
  &lt;td width=100 style="background: #FF0065"&gt;&lt;/td&gt;
 &lt;/tr&gt;
 &lt;tr&gt;
  &lt;td&gt;MAGENTA&lt;/td&gt;
  &lt;td&gt;[255, 0, 255]&lt;/td&gt;
  &lt;td width=100 style="background: #FF00FF"&gt;&lt;/td&gt;
 &lt;/tr&gt;
 &lt;tr&gt;
  &lt;td&gt;ORANGE&lt;/td&gt;
  &lt;td&gt;[255, 165, 0]&lt;/td&gt;
  &lt;td width=100 style="background: #FFA500"&gt;&lt;/td&gt;
 &lt;/tr&gt;
 &lt;tr&gt;
  &lt;td&gt;PINK&lt;/td&gt;
  &lt;td&gt;[255, 101, 117]&lt;/td&gt;
  &lt;td width=100 style="background: #FF6575"&gt;&lt;/td&gt;
 &lt;/tr&gt;
 &lt;tr&gt;
  &lt;td&gt;PINKTINT&lt;/td&gt;
  &lt;td&gt;[255, 171, 187]&lt;/td&gt;
  &lt;td width=100 style="background: #FFABBB"&gt;&lt;/td&gt;
 &lt;/tr&gt;
 &lt;tr&gt;
  &lt;td&gt;PURPLE&lt;/td&gt;
  &lt;td&gt;[160, 32, 240]&lt;/td&gt;
  &lt;td width=100 style="background: #A020F0"&gt;&lt;/td&gt;
 &lt;/tr&gt;
 &lt;tr&gt;
  &lt;td&gt;RED&lt;/td&gt;
  &lt;td&gt;[255, 0, 0]&lt;/td&gt;
  &lt;td width=100 style="background: #FF0000"&gt;&lt;/td&gt;
 &lt;/tr&gt;
 &lt;tr&gt;
  &lt;td&gt;REDORANGE&lt;/td&gt;
  &lt;td&gt;[255, 69, 0]&lt;/td&gt;
  &lt;td width=100 style="background: #FF4500"&gt;&lt;/td&gt;
 &lt;/tr&gt;
 &lt;tr&gt;
  &lt;td&gt;SEAGREEN&lt;/td&gt;
  &lt;td&gt;[0, 250, 109]&lt;/td&gt;
  &lt;td width=100 style="background: #00FA6D"&gt;&lt;/td&gt;
 &lt;/tr&gt;
 &lt;tr&gt;
  &lt;td&gt;SKYBLUE&lt;/td&gt;
  &lt;td&gt;[58, 144, 255]&lt;/td&gt;
  &lt;td width=100 style="background: #3A90FF"&gt;&lt;/td&gt;
 &lt;/tr&gt;
 &lt;tr&gt;
  &lt;td&gt;VIOLET&lt;/td&gt;
  &lt;td&gt;[238, 130, 238]&lt;/td&gt;
  &lt;td width=100 style="background: #EE82EE"&gt;&lt;/td&gt;
 &lt;/tr&gt;
 &lt;tr&gt;
  &lt;td&gt;WHITE&lt;/td&gt;
  &lt;td&gt;[255, 255, 255]&lt;/td&gt;
  &lt;td width=100 style="background: #FFFFFF"&gt;&lt;/td&gt;
 &lt;/tr&gt;
 &lt;tr&gt;
  &lt;td&gt;YELLOW&lt;/td&gt;
  &lt;td&gt;[255, 255, 0]&lt;/td&gt;
  &lt;td width=100 style="background: #FFFF00"&gt;&lt;/td&gt;
 &lt;/tr&gt;
 &lt;tr&gt;
  &lt;td&gt;YELLOWTINT&lt;/td&gt;
  &lt;td&gt;[246, 246, 117]&lt;/td&gt;
  &lt;td width=100 style="background: #F6F675"&gt;&lt;/td&gt;
 &lt;/tr&gt;
&lt;/table&gt;

== Color Scheme ==

=== amino ===
The color scheme 'amino' colors amino acids as follows.

&lt;table border="1"&gt;
 &lt;tr&gt;
  &lt;td&gt;amino acids&lt;/td&gt;
  &lt;td&gt;RGB values&lt;/td&gt;
  &lt;td&gt;color&lt;/td&gt;
 &lt;/tr&gt;
 &lt;tr&gt;
  &lt;td&gt;ASP, GLU&lt;/td&gt;
  &lt;td&gt;[230, 10, 10]&lt;/td&gt;
  &lt;td width=100 style="background: #E60A0A"&gt;&lt;/td&gt;
 &lt;/tr&gt;
 &lt;tr&gt;
  &lt;td&gt;CYS, MET&lt;/td&gt;
  &lt;td&gt;[230,230, 0]&lt;/td&gt;
  &lt;td width=100 style="background: #E6E600"&gt;&lt;/td&gt;
 &lt;/tr&gt;
 &lt;tr&gt;
  &lt;td&gt;LYS, ARG&lt;/td&gt;
  &lt;td&gt;[20, 90,255]&lt;/td&gt;
  &lt;td width=100 style="background: #145AFF"&gt;&lt;/td&gt;
 &lt;/tr&gt;
 &lt;tr&gt;
  &lt;td&gt;SER, THR&lt;/td&gt;
  &lt;td&gt;[250,150, 0]&lt;/td&gt;
  &lt;td width=100 style="background: #FA9600"&gt;&lt;/td&gt;
 &lt;/tr&gt;
 &lt;tr&gt;
  &lt;td&gt;PHE, TYR&lt;/td&gt;
  &lt;td&gt;[50, 50,170]&lt;/td&gt;
  &lt;td width=100 style="background: #3232AA"&gt;&lt;/td&gt;
 &lt;/tr&gt;
 &lt;tr&gt;
  &lt;td&gt;ASN, GLN&lt;/td&gt;
  &lt;td&gt;[0,220,220]&lt;/td&gt;
  &lt;td width=100 style="background: #00DCDC"&gt;&lt;/td&gt;
 &lt;/tr&gt;
 &lt;tr&gt;
  &lt;td&gt;GLY&lt;/td&gt;
  &lt;td&gt;[235,235,235]&lt;/td&gt;
  &lt;td width=100 style="background: #EBEBEB"&gt;&lt;/td&gt;
 &lt;/tr&gt;
 &lt;tr&gt;
  &lt;td&gt;LEU, VAL, ILE&lt;/td&gt;
  &lt;td&gt;[15,130, 15]&lt;/td&gt;
  &lt;td width=100 style="background: #0F820F"&gt;&lt;/td&gt;
 &lt;/tr&gt;
 &lt;tr&gt;
  &lt;td&gt;ALA&lt;/td&gt;
  &lt;td&gt;[200,200,200]&lt;/td&gt;
  &lt;td width=100 style="background: #C8C8C8"&gt;&lt;/td&gt;
 &lt;/tr&gt;
 &lt;tr&gt;
  &lt;td&gt;TRP&lt;/td&gt;
  &lt;td&gt;[180, 90,180]&lt;/td&gt;
  &lt;td width=100 style="background: #B45AB4"&gt;&lt;/td&gt;
 &lt;/tr&gt;
 &lt;tr&gt;
  &lt;td&gt;HIS&lt;/td&gt;
  &lt;td&gt;[130,130,210]&lt;/td&gt;
  &lt;td width=100 style="background: #8282D2"&gt;&lt;/td&gt;
 &lt;/tr&gt;
 &lt;tr&gt;
  &lt;td&gt;PRO&lt;/td&gt;
  &lt;td&gt;[220,150,130]&lt;/td&gt;
  &lt;td width=100 style="background: #DC9682"&gt;&lt;/td&gt;
 &lt;/tr&gt;
 &lt;tr&gt;
  &lt;td&gt;Others&lt;/td&gt;
  &lt;td&gt;[190,160,110]&lt;/td&gt;
  &lt;td width=100 style="background: #BEA06E"&gt;&lt;/td&gt;
 &lt;/tr&gt;
&lt;/table&gt;

=== chain ===
The color scheme 'chain' assigns each macromolecular chain a unique colour.

=== charge ===
The color scheme 'charge' colors atoms according to their temperature factor. High values are coloured in blue and lower values coloured in red. 

=== cpk ===
The color scheme 'cpk' colors atoms according to the element type as follows. 

&lt;table border="1"&gt;
 &lt;tr&gt;
  &lt;td&gt;element&lt;/td&gt;
  &lt;td&gt;RGB values&lt;/td&gt;
  &lt;td&gt;color&lt;/td&gt;
 &lt;/tr&gt;
 &lt;tr&gt;
  &lt;td&gt;C&lt;/td&gt;
  &lt;td&gt;[200, 200, 200]&lt;/td&gt;
  &lt;td width=100 style="background: #C8C8C8"&gt;&lt;/td&gt;
 &lt;/tr&gt;
 &lt;tr&gt;
  &lt;td&gt;N&lt;/td&gt;
  &lt;td&gt;[143, 143, 255]&lt;/td&gt;
  &lt;td width=100 style="background: #8F8FFF"&gt;&lt;/td&gt;
 &lt;/tr&gt;
 &lt;tr&gt;
  &lt;td&gt;O&lt;/td&gt;
  &lt;td&gt;[240, 0, 0]&lt;/td&gt;
  &lt;td width=100 style="background: #F00000"&gt;&lt;/td&gt;
 &lt;/tr&gt;
 &lt;tr&gt;
  &lt;td&gt;S&lt;/td&gt;
  &lt;td&gt;[255, 200, 50]&lt;/td&gt;
  &lt;td width=100 style="background: #FFC832"&gt;&lt;/td&gt;
 &lt;/tr&gt;
 &lt;tr&gt;
  &lt;td&gt;H&lt;/td&gt;
  &lt;td&gt;[255, 255, 255]&lt;/td&gt;
  &lt;td width=100 style="background: #FFFFFF"&gt;&lt;/td&gt;
 &lt;/tr&gt;
 &lt;tr&gt;
  &lt;td&gt;He&lt;/td&gt;
  &lt;td&gt;[255, 192, 203]&lt;/td&gt;
  &lt;td width=100 style="background: #FFC0CB"&gt;&lt;/td&gt;
 &lt;/tr&gt;
 &lt;tr&gt;
  &lt;td&gt;F, Si, Au&lt;/td&gt;
  &lt;td&gt;[218, 165, 32]&lt;/td&gt;
  &lt;td width=100 style="background: #DAA520"&gt;&lt;/td&gt;
 &lt;/tr&gt;
 &lt;tr&gt;
  &lt;td&gt;Na&lt;/td&gt;
  &lt;td&gt;[0, 0, 255]&lt;/td&gt;
  &lt;td width=100 style="background: #0000FF"&gt;&lt;/td&gt;
 &lt;/tr&gt;
 &lt;tr&gt;
  &lt;td&gt;P, Fe, Ba&lt;/td&gt;
  &lt;td&gt;[255, 165, 0]&lt;/td&gt;
  &lt;td width=100 style="background: #FFA500"&gt;&lt;/td&gt;
 &lt;/tr&gt;
 &lt;tr&gt;
  &lt;td&gt;Al, Ca, Ti, Cr, Mn, Ag&lt;/td&gt;
  &lt;td&gt;[128, 128, 144]&lt;/td&gt;
  &lt;td width=100 style="background: #808090"&gt;&lt;/td&gt;
 &lt;/tr&gt;
 &lt;tr&gt;
  &lt;td&gt;Ni, Cu, Zn, Br&lt;/td&gt;
  &lt;td&gt;[165, 42, 42]&lt;/td&gt;
  &lt;td width=100 style="background: #A52A2A"&gt;&lt;/td&gt;
 &lt;/tr&gt;
 &lt;tr&gt;
  &lt;td&gt;I&lt;/td&gt;
  &lt;td&gt;[160, 32, 240]&lt;/td&gt;
  &lt;td width=100 style="background: #A020F0"&gt;&lt;/td&gt;
 &lt;/tr&gt;
 &lt;tr&gt;
  &lt;td&gt;B, Cl&lt;/td&gt;
  &lt;td&gt;[0, 255, 0]&lt;/td&gt;
  &lt;td width=100 style="background: #00FF00"&gt;&lt;/td&gt;
 &lt;/tr&gt;
 &lt;tr&gt;
  &lt;td&gt;Li&lt;/td&gt;
  &lt;td&gt;[178, 34, 34]&lt;/td&gt;
  &lt;td width=100 style="background: #B22222"&gt;&lt;/td&gt;
 &lt;/tr&gt;
 &lt;tr&gt;
  &lt;td&gt;Mg&lt;/td&gt;
  &lt;td&gt;[34, 139, 34]&lt;/td&gt;
  &lt;td width=100 style="background: #228B22"&gt;&lt;/td&gt;
 &lt;/tr&gt;
 &lt;tr&gt;
  &lt;td&gt;Others&lt;/td&gt;
  &lt;td&gt;[255, 20, 147]&lt;/td&gt;
  &lt;td width=100 style="background: #FF1493"&gt;&lt;/td&gt;
 &lt;/tr&gt;
&lt;/table&gt;

=== group ===
The color scheme 'group' colors residues by their position in a macromolecular chain. Each chain is drawn as a smooth spectrum from blue to red. The N terminus of proteins and 5' terminus of nucleic acids are colored red and the C terminus of proteins and 3' terminus of nucleic acids are drawn in blue. 

=== shapely ===
The color scheme 'shapely' colors residues as follows.

&lt;table border="1"&gt;
 &lt;tr&gt;
  &lt;td&gt;residue&lt;/td&gt;
  &lt;td&gt;RGB values&lt;/td&gt;
  &lt;td&gt;color&lt;/td&gt;
 &lt;/tr&gt;
 &lt;tr&gt;
  &lt;td&gt;ALA&lt;/td&gt;
  &lt;td&gt;[140, 255, 140]&lt;/td&gt;
  &lt;td width=100 style="background: #8CFF8C"&gt;&lt;/td&gt;
 &lt;/tr&gt;
 &lt;tr&gt;
  &lt;td&gt;GLY&lt;/td&gt;
  &lt;td&gt;[255, 255, 255]&lt;/td&gt;
  &lt;td width=100 style="background: #FFFFFF"&gt;&lt;/td&gt;
 &lt;/tr&gt;
 &lt;tr&gt;
  &lt;td&gt;LEU&lt;/td&gt;
  &lt;td&gt;[69, 94, 69]&lt;/td&gt;
  &lt;td width=100 style="background: #455E45"&gt;&lt;/td&gt;
 &lt;/tr&gt;
 &lt;tr&gt;
  &lt;td&gt;SER&lt;/td&gt;
  &lt;td&gt;[255, 112, 66]&lt;/td&gt;
  &lt;td width=100 style="background: #FF7042"&gt;&lt;/td&gt;
 &lt;/tr&gt;
 &lt;tr&gt;
  &lt;td&gt;VAL&lt;/td&gt;
  &lt;td&gt;[255, 140, 255]&lt;/td&gt;
  &lt;td width=100 style="background: #FF8CFF"&gt;&lt;/td&gt;
 &lt;/tr&gt;
 &lt;tr&gt;
  &lt;td&gt;THR&lt;/td&gt;
  &lt;td&gt;[184, 76, 0]&lt;/td&gt;
  &lt;td width=100 style="background: #B84C00"&gt;&lt;/td&gt;
 &lt;/tr&gt;
 &lt;tr&gt;
  &lt;td&gt;LYS&lt;/td&gt;
  &lt;td&gt;[71, 71, 184]&lt;/td&gt;
  &lt;td width=100 style="background: #4747B8"&gt;&lt;/td&gt;
 &lt;/tr&gt;
 &lt;tr&gt;
  &lt;td&gt;ASP&lt;/td&gt;
  &lt;td&gt;[160, 0, 66]&lt;/td&gt;
  &lt;td width=100 style="background: #A00042"&gt;&lt;/td&gt;
 &lt;/tr&gt;
 &lt;tr&gt;
  &lt;td&gt;ILE&lt;/td&gt;
  &lt;td&gt;[0, 76, 0]&lt;/td&gt;
  &lt;td width=100 style="background: #004C00"&gt;&lt;/td&gt;
 &lt;/tr&gt;
 &lt;tr&gt;
  &lt;td&gt;ASN&lt;/td&gt;
  &lt;td&gt;[255, 124, 112]&lt;/td&gt;
  &lt;td width=100 style="background: #FF7C70"&gt;&lt;/td&gt;
 &lt;/tr&gt;
 &lt;tr&gt;
  &lt;td&gt;GLU&lt;/td&gt;
  &lt;td&gt;[102, 0, 0]&lt;/td&gt;
  &lt;td width=100 style="background: #660000"&gt;&lt;/td&gt;
 &lt;/tr&gt;
 &lt;tr&gt;
  &lt;td&gt;PRO&lt;/td&gt;
  &lt;td&gt;[82, 82, 82]&lt;/td&gt;
  &lt;td width=100 style="background: #525252"&gt;&lt;/td&gt;
 &lt;/tr&gt;
 &lt;tr&gt;
  &lt;td&gt;ARG&lt;/td&gt;
  &lt;td&gt;[0, 0, 124]&lt;/td&gt;
  &lt;td width=100 style="background: #00007C"&gt;&lt;/td&gt;
 &lt;/tr&gt;
 &lt;tr&gt;
  &lt;td&gt;PHE&lt;/td&gt;
  &lt;td&gt;[83, 76, 66]&lt;/td&gt;
  &lt;td width=100 style="background: #534C42"&gt;&lt;/td&gt;
 &lt;/tr&gt;
 &lt;tr&gt;
  &lt;td&gt;GLN&lt;/td&gt;
  &lt;td&gt;[255, 76, 76]&lt;/td&gt;
  &lt;td width=100 style="background: #FF4C4C"&gt;&lt;/td&gt;
 &lt;/tr&gt;
 &lt;tr&gt;
  &lt;td&gt;TYR&lt;/td&gt;
  &lt;td&gt;[140, 112, 76]&lt;/td&gt;
  &lt;td width=100 style="background: #8C704C"&gt;&lt;/td&gt;
 &lt;/tr&gt;
 &lt;tr&gt;
  &lt;td&gt;HIS&lt;/td&gt;
  &lt;td&gt;[112, 112, 255]&lt;/td&gt;
  &lt;td width=100 style="background: #7070FF"&gt;&lt;/td&gt;
 &lt;/tr&gt;
 &lt;tr&gt;
  &lt;td&gt;CYS&lt;/td&gt;
  &lt;td&gt;[255, 255, 112]&lt;/td&gt;
  &lt;td width=100 style="background: #FFFF70"&gt;&lt;/td&gt;
 &lt;/tr&gt;
 &lt;tr&gt;
  &lt;td&gt;MET&lt;/td&gt;
  &lt;td&gt;[184, 160, 66]&lt;/td&gt;
  &lt;td width=100 style="background: #B8A042"&gt;&lt;/td&gt;
 &lt;/tr&gt;
 &lt;tr&gt;
  &lt;td&gt;TRP&lt;/td&gt;
  &lt;td&gt;[79, 70, 0]&lt;/td&gt;
  &lt;td width=100 style="background: #4F4600"&gt;&lt;/td&gt;
 &lt;/tr&gt;
 &lt;tr&gt;
  &lt;td&gt;A&lt;/td&gt;
  &lt;td&gt;[160, 160, 255]&lt;/td&gt;
  &lt;td width=100 style="background: #A0A0FF"&gt;&lt;/td&gt;
 &lt;/tr&gt;
 &lt;tr&gt;
  &lt;td&gt;C&lt;/td&gt;
  &lt;td&gt;[255, 140, 75]&lt;/td&gt;
  &lt;td width=100 style="background: #FF8C4B"&gt;&lt;/td&gt;
 &lt;/tr&gt;
 &lt;tr&gt;
  &lt;td&gt;G&lt;/td&gt;
  &lt;td&gt;[255, 112, 112]&lt;/td&gt;
  &lt;td width=100 style="background: #FF7070"&gt;&lt;/td&gt;
 &lt;/tr&gt;
 &lt;tr&gt;
  &lt;td&gt;T&lt;/td&gt;
  &lt;td&gt;[160, 255, 160]&lt;/td&gt;
  &lt;td width=100 style="background: #A0FFA0"&gt;&lt;/td&gt;
 &lt;/tr&gt;
 &lt;tr&gt;
  &lt;td&gt;Others&lt;/td&gt;
  &lt;td&gt;[255, 0, 255]&lt;/td&gt;
  &lt;td width=100 style="background: #FF00FF"&gt;&lt;/td&gt;
 &lt;/tr&gt;
&lt;/table&gt;

=== structure ===
The color scheme 'structure' colors residues according to the secondary structure as follows.

&lt;table border="1"&gt;
 &lt;tr&gt;
  &lt;td&gt;secondary structure&lt;/td&gt;
  &lt;td&gt;RGB values&lt;/td&gt;
  &lt;td&gt;color&lt;/td&gt;
 &lt;/tr&gt;
 &lt;tr&gt;
  &lt;td&gt;alpha helix&lt;/td&gt;
  &lt;td&gt;[255, 0, 128]&lt;/td&gt;
  &lt;td width=100 style="background: #FF0080"&gt;&lt;/td&gt;
 &lt;/tr&gt;
 &lt;tr&gt;
  &lt;td&gt;beta sheet&lt;/td&gt;
  &lt;td&gt;[255, 200, 0]&lt;/td&gt;
  &lt;td width=100 style="background: #FFC800"&gt;&lt;/td&gt;
 &lt;/tr&gt;
 &lt;tr&gt;
  &lt;td&gt;turn&lt;/td&gt;
  &lt;td&gt;[96, 128, 255]&lt;/td&gt;
  &lt;td width=100 style="background: #6080FF"&gt;&lt;/td&gt;
 &lt;/tr&gt;
 &lt;tr&gt;
  &lt;td&gt;none&lt;/td&gt;
  &lt;td&gt;[255, 255, 255]&lt;/td&gt;
  &lt;td width=100 style="background: #FFFFFF"&gt;&lt;/td&gt;
 &lt;/tr&gt;
&lt;/table&gt;

=== temperature ===
The color scheme 'temperature' colors atoms according to their temperature factor. High values are coloured in red and lower values coloured in blue. 

=== type ===
This color scheme 'type' colors each hydrogen bond according to the distance along a protein chain between hydrogen bond donor and acceptor as follows. 

&lt;table border="1"&gt;
 &lt;tr&gt;
  &lt;td&gt;offset&lt;/td&gt;
  &lt;td&gt;RGB values&lt;/td&gt;
  &lt;td&gt;color&lt;/td&gt;
 &lt;/tr&gt;
 &lt;tr&gt;
  &lt;td&gt;+2&lt;/td&gt;
  &lt;td&gt;[255, 255, 255]&lt;/td&gt;
  &lt;td width=100 style="background: #FFFFFF"&gt;&lt;/td&gt;
 &lt;/tr&gt;
 &lt;tr&gt;
  &lt;td&gt;+3&lt;/td&gt;
  &lt;td&gt;[255, 0, 255]&lt;/td&gt;
  &lt;td width=100 style="background: #FF00FF"&gt;&lt;/td&gt;
 &lt;/tr&gt;
 &lt;tr&gt;
  &lt;td&gt;+4&lt;/td&gt;
  &lt;td&gt;[255, 0, 0]&lt;/td&gt;
  &lt;td width=100 style="background: #FF0000"&gt;&lt;/td&gt;
 &lt;/tr&gt;
 &lt;tr&gt;
  &lt;td&gt;+5&lt;/td&gt;
  &lt;td&gt;[255, 165, 0]&lt;/td&gt;
  &lt;td width=100 style="background: #FFA500"&gt;&lt;/td&gt;
 &lt;/tr&gt;
 &lt;tr&gt;
  &lt;td&gt;-3&lt;/td&gt;
  &lt;td&gt;[0, 255, 255]&lt;/td&gt;
  &lt;td width=100 style="background: #00FFFF"&gt;&lt;/td&gt;
 &lt;/tr&gt;
 &lt;tr&gt;
  &lt;td&gt;-4&lt;/td&gt;
  &lt;td&gt;[0, 255, 0]&lt;/td&gt;
  &lt;td width=100 style="background: #00FF00"&gt;&lt;/td&gt;
 &lt;/tr&gt;
 &lt;tr&gt;
  &lt;td&gt;Others&lt;/td&gt;
  &lt;td&gt;[255, 255, 0]&lt;/td&gt;
  &lt;td width=100 style="background: #FFFF00"&gt;&lt;/td&gt;
 &lt;/tr&gt;
&lt;/table&gt;</text>
    <sha1>6652c8b3cbeb3d928adf30fbe206fbd6fa57518c</sha1>
  </revision>
</page>
<page arvcontinue="20151001071243|604">
  <title>Links</title>
  <ns>0</ns>
  <id>4</id>
  <revision>
    <id>632</id>
    <parentid>368</parentid>
    <timestamp>2018-02-06T06:38:36Z</timestamp>
    <contributor>
      <username>IMSsato</username>
      <id>4</id>
    </contributor>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="1226" xml:space="preserve">== Organization ==
* [http://www-bird.jst.go.jp/index_e.html JST-BIRD]
* [http://www.hgc.jp/english/ Human Genome Center]
* [http://www.protein.osaka-u.ac.jp/home_e/index_e.html Institute for Protein Research]
&lt;br /&gt;

== DBs ==
* [https://pdbj.org/eF-site/ eF-site] (DB of electrostatic surface of functional site of proteins)
* [https://pdbj.org/eF-seek/ eF-seek] (Prediction of ligand binding site of proteins)
* [https://pdbj.org/eF-surf/ eF-surf] (Calculate the molecular surface and electrostatic potential of proteins)
&lt;br /&gt;
* [http://pre-s.protein.osaka-u.ac.jp/~preds/ P&lt;i&gt;re&lt;/i&gt;D&lt;i&gt;s&lt;/i&gt;] (Prediction of DNA-binding site)
* [http://pre-s.protein.osaka-u.ac.jp/~prebi/ PreBI] (Prediction of biological interface of proteins homo-interface)
* [http://pre-s.protein.osaka-u.ac.jp/~preds classPPI] (Classification of homo protein-protein interfaces)
&lt;br /&gt;
* [http://p-cats.hgc.jp/p-cats/ P-cats] (Prediction of Catalytic residues in proteins)
&lt;br /&gt;
* [http://service.pdbj.org/mine/ PDBj Mine] (protein structure search service)
* [http://www.pdbj.org/eprots/index_en.cgi eProtS] (Encyclopedia of protein structures)
* [http://cube.socs.waseda.ac.jp/pages/jsp/index.jsp ProMode] (DB of normal mode analysis of proteins)</text>
    <sha1>e0dfacc6978fadf93194e0401b54a1cdeb007bc6</sha1>
  </revision>
</page>
<page arvcontinue="20151001071243|604">
  <title>Installation of jV</title>
  <ns>0</ns>
  <id>38</id>
  <revision>
    <id>650</id>
    <parentid>602</parentid>
    <timestamp>2021-04-26T08:45:26Z</timestamp>
    <contributor>
      <username>IMSsato</username>
      <id>4</id>
    </contributor>
    <comment>/* System requirements */</comment>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="745" xml:space="preserve">__NOTOC__
== System requirements ==
jV runs on the Java Runtime Environment (JRE) with JOGL API. The version requirements are as follows.
* [http://java.com/download/ JRE] 1.8 or later
* [http://jogamp.org/jogl/www/ JOGL] API 2.2.4 or later 
These softwares are available on typical operation systems such as Windows (XP/Vista/7/8/8.1), Mac OS X 10.6 or later, and Red Hat Linux 7.3 or later.

== Installation ==
From the version 3.8.3, binary distribution of jV contains the JOGL library
and pre-installation of JOGL is not necessary.
Just JRE is required on your computer in advance.
With JRE properly installed, you can download the binary distribution of jV 
and immediately use jV by running a start-up script contained in the distribution.</text>
    <sha1>ac19df6d8825b474482586ce7d096bdf70569ffc</sha1>
  </revision>
</page>
<page arvcontinue="20151001071243|604">
  <title>How to use</title>
  <ns>0</ns>
  <id>11</id>
  <revision>
    <id>653</id>
    <parentid>548</parentid>
    <timestamp>2021-04-26T08:48:39Z</timestamp>
    <contributor>
      <username>IMSsato</username>
      <id>4</id>
    </contributor>
    <comment>/* Reference manual */</comment>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="1219" xml:space="preserve">The following table shows how to do the minimum things with jV; the mouse controls.
For the detail, see the reference manual and User's guide.&lt;br /&gt;
{| class="wikitable" border="1" style="margin:0 auto" 
 ! Action !! Window, Linux !! Mac OS X 
 |-
 ! style="text-align:left" | rotate around X,Y axes
 | left drag || drag
 |-
 ! style="text-align:left" | rotate around Z axis
 | Shift + right drag || Shift + command + drag
 |-
 ! style="text-align:left" | translate along X,Y axes
 | right drag || command + drag
 |-
 ! style="text-align:left" | translate along Z axis (zoom in/out)
 | Shift + left drag || Shift + drag
 |-
 ! style="text-align:left" | translate slab plane along Z axis
 | (Alt or Ctrl) + left drag || Alt + drag
 |}


== Reference manual ==
# [[Introduction]]
# [[Command List]]
# [[Atom Expression]]
# [[Vertex Expression]]
# [[Color Expression]]
# [[Use as Applet]] (removed from version 4.5.8)

== User's Guide ==
# [[Tutorials]]
# [[GUI]]
# [[Document type of the polygon file]]
# [[Functional site information for molecules]]


== Some examples ==
# [[Basic examples]]
# [[Animation]]
# [[Use jV applet with object tag]]
# [[Use jV applet with JNLP file]]
# [[Use jV applet with applet launcher]]</text>
    <sha1>e076f68906323ad2440743134b0484fe9b55d153</sha1>
  </revision>
</page>
<page arvcontinue="20210426085749|654">
  <title>Release note</title>
  <ns>0</ns>
  <id>17</id>
  <revision>
    <id>654</id>
    <parentid>652</parentid>
    <timestamp>2021-04-26T08:57:49Z</timestamp>
    <contributor>
      <username>IMSsato</username>
      <id>4</id>
    </contributor>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="6833" xml:space="preserve">Changes and improvements have been made as follows.

* version 3.1
** The following commands have been added; 'animrange', 'set adjustview', 'show godata', and 'show xps3'.
** The xPSSS expression has been added in order to select a group of atoms.
** Several public methods have been added to the applet so as to append molecule or polygon files after the applet started.
** The applet can send information about mouse-picked atoms to JavaScript.
* version 3.1.1
** Some problems in GUI menu [Options]-[Hetero Atoms] and [Hydrogens] have been fixed.
** Some problems in 'trace' command have been fixed.
* version 3.1.2
** eF-site ID has been changed to a new format.
* version 3.1.3
** Some problems in xps3 atom selection have been fixed.
* version 3.1.4
** Some problems in finalization process of openGL rendering have been fixed.
* version 3.1.5
** The output of 'show xps3' command has been modified.
** Some problems in 'save png/jpeg' command have been fixed.
* version 3.1.6
** Some problems in loading an empty polygon file have been fixed.
* version 3.1.7
** Some problems in initialization process of the applet have been fixed.
* version 3.2
** 'show site' command has been added.
* version 3.3 beta 1
** Availabe JOGL version is restricted to JSR-231 beta 5 only.
* version 3.3
** Both the previous JOGL (version 1.1.1) and JSR-231 are available.
** The following commands have been added; 'set viewpoint', 'show viewpoint', 'set imagesize', and 'show imagesize'.
* version 3.3.1
** Some problems in reading a pdbMLplus file have been fixed.
* version 3.4
** PDB format version 3 can be processed.
* version 3.5
** Discrimination of DNA and RNA linking nucleotides is based on [http://remediation.wwpdb.org/ccd.html Chemical Component Dictionary] for PDB format version 3.
** The default representation of the cartoon model has been changed. Commands 'set cartoon_loop_tube', 'set cartoon_round' and 'set ribbonback' have been added.
** The default parameters of lighting have been changed. Commands 'set ambient', 'set diffuse1', 'set diffuse1_direction', 'set diffuse2' and 'set diffuse1_direction' have been added.
** Commands 'set pdbml_noatom_url', 'set pdbml_extatom_url', 'set pdbml_plus_url', 'set efsite_url', 'set ext_site_url', 'show pdbml_url', 'show efsite_url' and 'show ext_site_url' have been added.
** The command-line option '-stdin' has been added to receive commands from stdin stream.
* version 3.6
** Users can specify the JavaScript function name used in Applet-to-JavaScript Communication.
** Applet parameter 'file_load_message' has been added.
* version 3.6.1
** Predefined set of residues has been modified.
** Old JOGL API is not supported.
* version 3.6.2
** Latest version of PDBML can be processed.
** Some problems in mouse control on Mac have been fixed.
* version 3.6.3
** Molecule file parsing has been modified to detect chain breaks properly by reading the 'label_asym_id' column in PDBML and the TER line in PDB flat file, respectively.
* version 3.6.4
** Some problems in GUI menu on Mac have been fixed.
* version 3.6.5
** The jV applet can invoke a JavaScript function when it started.
* version 3.7
** Commands 'pdbj_describe' and 'pdbj_execute' have been added.
** Keyword 'xps3' have been replaced by 'pdbj'.
* version 3.7.1
** Default PDBML URLs have been changed.
* version 3.7.2
** Some problems in creating png/jpeg image files have been fixed.
* version 3.8
** Command 'displayatom' has been added.
** The signed jV applet can save PNG/JPEG image files.
* version 3.8.1
** In commands 'cartoon', 'ribbons' and 'trace', a backbone will be drawn instead when a chain does not have enough atoms to draw those models.
** Recognition of amino acids is based on [http://remediation.wwpdb.org/ccd.html Chemical Component Dictionary].
* version 3.8.2
** Command 'ball_and_stick' has been added.
* version 3.8.3
** Binary distribution contains the JOGL library and pre-installation of JOGL is not necessary to use jV.
* version 4.0
** The program supports PDB format version 4.0.
** Atom expression has been extended to handle case-sensitive chain ID and label_asym_id in PDBML.
* version 4.1
** The program runs with new JOGL library (2.0-rc4 or later) which enables jV applets to run on Mac.
** From this release, the program requires JRE 1.6 or later.
** Command 'add_backbone' has been added.
** The program uses MODRES data and chem_comp/type data (PDBML only) to determine residue types.
* version 4.2
** The program reads polygon CGO (PyMOL-specific Compiled Graphics Objects) files distributed at eF-site system. Command 'load polygon_cgo' has been added.
** A parameter 'pdbid' and a method 'loadFTP' have been added to applet.
** When the program loads a PDBML noatom file whose directory is 'all-noatom' or 'XML-noatom', the coordinate file is retrieved from the corresponding directory; '../all-extatom' or '../XML-extatom', respectively.
* version 4.2.1
** The program runs with new JOGL library (2.0-rc11).
* version 4.3
** Anaglyph 3D rendering is added to 'stereo' command.
* version 4.3.1
** A workaround for a cache problem in JRE 1.7 has been added.
* version 4.4
** The program can read and write mmCIF format files.
** The program handles biomolecule structures when reading and writing a molecule file.
** The default setting of PDBMLplus URL has been changed.
* version 4.4.1
** Some problems in reading mmCIF files have been fixed.
** The behavior of mouse picking when measuring the distance between two atoms has been changed. Rotation and translation of molecules between two mouse pickings do not affect the distance measurement.
* version 4.4.2
** The program files are signed with a new certificate.
* version 4.4.3
** Some problems in writing PDB files have been fixed.
* version 4.4.4
** Some problems in rendering polygons have been fixed.
* version 4.4.5
** The program shows an error dialog when an input file has no valid data.
** The program files are signed with an updated certificate.
* version 4.5
** The program can read and display mmCIF files for small molecules.
* version 4.5.1
** A file permission problem in writing image files has been fixed.
* version 4.5.2
** The contact address on the error dialog has been changed.
* version 4.5.3
** In applet parameters, data files on the same server as the web page can be specified by the path part of URL as well as the full URL.
* version 4.5.4
** The program files are signed with a new certificate.
* version 4.5.5
** The program files are signed with a new certificate.
* version 4.5.6
** The program files are signed with a new certificate.
* version 4.5.7
** The program files were signed with a new certificate because of the CA certification renewal.
* version 4.5.8
** PDBML URL to fetch molecule information files has been updated.
** The applet functionality has been removed.</text>
    <sha1>f7ffe91be1c57b12f6eb49c28f710ee61f95a1ac</sha1>
  </revision>
  <revision>
    <id>657</id>
    <parentid>654</parentid>
    <timestamp>2021-06-28T06:30:02Z</timestamp>
    <contributor>
      <username>IMSsato</username>
      <id>4</id>
    </contributor>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="6908" xml:space="preserve">Changes and improvements have been made as follows.

* version 3.1
** The following commands have been added; 'animrange', 'set adjustview', 'show godata', and 'show xps3'.
** The xPSSS expression has been added in order to select a group of atoms.
** Several public methods have been added to the applet so as to append molecule or polygon files after the applet started.
** The applet can send information about mouse-picked atoms to JavaScript.
* version 3.1.1
** Some problems in GUI menu [Options]-[Hetero Atoms] and [Hydrogens] have been fixed.
** Some problems in 'trace' command have been fixed.
* version 3.1.2
** eF-site ID has been changed to a new format.
* version 3.1.3
** Some problems in xps3 atom selection have been fixed.
* version 3.1.4
** Some problems in finalization process of openGL rendering have been fixed.
* version 3.1.5
** The output of 'show xps3' command has been modified.
** Some problems in 'save png/jpeg' command have been fixed.
* version 3.1.6
** Some problems in loading an empty polygon file have been fixed.
* version 3.1.7
** Some problems in initialization process of the applet have been fixed.
* version 3.2
** 'show site' command has been added.
* version 3.3 beta 1
** Availabe JOGL version is restricted to JSR-231 beta 5 only.
* version 3.3
** Both the previous JOGL (version 1.1.1) and JSR-231 are available.
** The following commands have been added; 'set viewpoint', 'show viewpoint', 'set imagesize', and 'show imagesize'.
* version 3.3.1
** Some problems in reading a pdbMLplus file have been fixed.
* version 3.4
** PDB format version 3 can be processed.
* version 3.5
** Discrimination of DNA and RNA linking nucleotides is based on [http://remediation.wwpdb.org/ccd.html Chemical Component Dictionary] for PDB format version 3.
** The default representation of the cartoon model has been changed. Commands 'set cartoon_loop_tube', 'set cartoon_round' and 'set ribbonback' have been added.
** The default parameters of lighting have been changed. Commands 'set ambient', 'set diffuse1', 'set diffuse1_direction', 'set diffuse2' and 'set diffuse1_direction' have been added.
** Commands 'set pdbml_noatom_url', 'set pdbml_extatom_url', 'set pdbml_plus_url', 'set efsite_url', 'set ext_site_url', 'show pdbml_url', 'show efsite_url' and 'show ext_site_url' have been added.
** The command-line option '-stdin' has been added to receive commands from stdin stream.
* version 3.6
** Users can specify the JavaScript function name used in Applet-to-JavaScript Communication.
** Applet parameter 'file_load_message' has been added.
* version 3.6.1
** Predefined set of residues has been modified.
** Old JOGL API is not supported.
* version 3.6.2
** Latest version of PDBML can be processed.
** Some problems in mouse control on Mac have been fixed.
* version 3.6.3
** Molecule file parsing has been modified to detect chain breaks properly by reading the 'label_asym_id' column in PDBML and the TER line in PDB flat file, respectively.
* version 3.6.4
** Some problems in GUI menu on Mac have been fixed.
* version 3.6.5
** The jV applet can invoke a JavaScript function when it started.
* version 3.7
** Commands 'pdbj_describe' and 'pdbj_execute' have been added.
** Keyword 'xps3' have been replaced by 'pdbj'.
* version 3.7.1
** Default PDBML URLs have been changed.
* version 3.7.2
** Some problems in creating png/jpeg image files have been fixed.
* version 3.8
** Command 'displayatom' has been added.
** The signed jV applet can save PNG/JPEG image files.
* version 3.8.1
** In commands 'cartoon', 'ribbons' and 'trace', a backbone will be drawn instead when a chain does not have enough atoms to draw those models.
** Recognition of amino acids is based on [http://remediation.wwpdb.org/ccd.html Chemical Component Dictionary].
* version 3.8.2
** Command 'ball_and_stick' has been added.
* version 3.8.3
** Binary distribution contains the JOGL library and pre-installation of JOGL is not necessary to use jV.
* version 4.0
** The program supports PDB format version 4.0.
** Atom expression has been extended to handle case-sensitive chain ID and label_asym_id in PDBML.
* version 4.1
** The program runs with new JOGL library (2.0-rc4 or later) which enables jV applets to run on Mac.
** From this release, the program requires JRE 1.6 or later.
** Command 'add_backbone' has been added.
** The program uses MODRES data and chem_comp/type data (PDBML only) to determine residue types.
* version 4.2
** The program reads polygon CGO (PyMOL-specific Compiled Graphics Objects) files distributed at eF-site system. Command 'load polygon_cgo' has been added.
** A parameter 'pdbid' and a method 'loadFTP' have been added to applet.
** When the program loads a PDBML noatom file whose directory is 'all-noatom' or 'XML-noatom', the coordinate file is retrieved from the corresponding directory; '../all-extatom' or '../XML-extatom', respectively.
* version 4.2.1
** The program runs with new JOGL library (2.0-rc11).
* version 4.3
** Anaglyph 3D rendering is added to 'stereo' command.
* version 4.3.1
** A workaround for a cache problem in JRE 1.7 has been added.
* version 4.4
** The program can read and write mmCIF format files.
** The program handles biomolecule structures when reading and writing a molecule file.
** The default setting of PDBMLplus URL has been changed.
* version 4.4.1
** Some problems in reading mmCIF files have been fixed.
** The behavior of mouse picking when measuring the distance between two atoms has been changed. Rotation and translation of molecules between two mouse pickings do not affect the distance measurement.
* version 4.4.2
** The program files are signed with a new certificate.
* version 4.4.3
** Some problems in writing PDB files have been fixed.
* version 4.4.4
** Some problems in rendering polygons have been fixed.
* version 4.4.5
** The program shows an error dialog when an input file has no valid data.
** The program files are signed with an updated certificate.
* version 4.5
** The program can read and display mmCIF files for small molecules.
* version 4.5.1
** A file permission problem in writing image files has been fixed.
* version 4.5.2
** The contact address on the error dialog has been changed.
* version 4.5.3
** In applet parameters, data files on the same server as the web page can be specified by the path part of URL as well as the full URL.
* version 4.5.4
** The program files are signed with a new certificate.
* version 4.5.5
** The program files are signed with a new certificate.
* version 4.5.6
** The program files are signed with a new certificate.
* version 4.5.7
** The program files were signed with a new certificate because of the CA certification renewal.
* version 4.5.8
** PDBML URL to fetch molecule information files has been updated.
** The applet functionality has been removed.
* version 4.5.9
** The format of PDBMLplus files has been changed to JSON.</text>
    <sha1>4514da6e95b9c7d08005dbd340c18ff9a0d6b480</sha1>
  </revision>
  <revision>
    <id>665</id>
    <parentid>657</parentid>
    <timestamp>2023-06-12T06:24:38Z</timestamp>
    <contributor>
      <username>IMSsato</username>
      <id>4</id>
    </contributor>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="7053" xml:space="preserve">Changes and improvements have been made as follows.

* version 3.1
** The following commands have been added; 'animrange', 'set adjustview', 'show godata', and 'show xps3'.
** The xPSSS expression has been added in order to select a group of atoms.
** Several public methods have been added to the applet so as to append molecule or polygon files after the applet started.
** The applet can send information about mouse-picked atoms to JavaScript.
* version 3.1.1
** Some problems in GUI menu [Options]-[Hetero Atoms] and [Hydrogens] have been fixed.
** Some problems in 'trace' command have been fixed.
* version 3.1.2
** eF-site ID has been changed to a new format.
* version 3.1.3
** Some problems in xps3 atom selection have been fixed.
* version 3.1.4
** Some problems in finalization process of openGL rendering have been fixed.
* version 3.1.5
** The output of 'show xps3' command has been modified.
** Some problems in 'save png/jpeg' command have been fixed.
* version 3.1.6
** Some problems in loading an empty polygon file have been fixed.
* version 3.1.7
** Some problems in initialization process of the applet have been fixed.
* version 3.2
** 'show site' command has been added.
* version 3.3 beta 1
** Availabe JOGL version is restricted to JSR-231 beta 5 only.
* version 3.3
** Both the previous JOGL (version 1.1.1) and JSR-231 are available.
** The following commands have been added; 'set viewpoint', 'show viewpoint', 'set imagesize', and 'show imagesize'.
* version 3.3.1
** Some problems in reading a pdbMLplus file have been fixed.
* version 3.4
** PDB format version 3 can be processed.
* version 3.5
** Discrimination of DNA and RNA linking nucleotides is based on [http://remediation.wwpdb.org/ccd.html Chemical Component Dictionary] for PDB format version 3.
** The default representation of the cartoon model has been changed. Commands 'set cartoon_loop_tube', 'set cartoon_round' and 'set ribbonback' have been added.
** The default parameters of lighting have been changed. Commands 'set ambient', 'set diffuse1', 'set diffuse1_direction', 'set diffuse2' and 'set diffuse1_direction' have been added.
** Commands 'set pdbml_noatom_url', 'set pdbml_extatom_url', 'set pdbml_plus_url', 'set efsite_url', 'set ext_site_url', 'show pdbml_url', 'show efsite_url' and 'show ext_site_url' have been added.
** The command-line option '-stdin' has been added to receive commands from stdin stream.
* version 3.6
** Users can specify the JavaScript function name used in Applet-to-JavaScript Communication.
** Applet parameter 'file_load_message' has been added.
* version 3.6.1
** Predefined set of residues has been modified.
** Old JOGL API is not supported.
* version 3.6.2
** Latest version of PDBML can be processed.
** Some problems in mouse control on Mac have been fixed.
* version 3.6.3
** Molecule file parsing has been modified to detect chain breaks properly by reading the 'label_asym_id' column in PDBML and the TER line in PDB flat file, respectively.
* version 3.6.4
** Some problems in GUI menu on Mac have been fixed.
* version 3.6.5
** The jV applet can invoke a JavaScript function when it started.
* version 3.7
** Commands 'pdbj_describe' and 'pdbj_execute' have been added.
** Keyword 'xps3' have been replaced by 'pdbj'.
* version 3.7.1
** Default PDBML URLs have been changed.
* version 3.7.2
** Some problems in creating png/jpeg image files have been fixed.
* version 3.8
** Command 'displayatom' has been added.
** The signed jV applet can save PNG/JPEG image files.
* version 3.8.1
** In commands 'cartoon', 'ribbons' and 'trace', a backbone will be drawn instead when a chain does not have enough atoms to draw those models.
** Recognition of amino acids is based on [http://remediation.wwpdb.org/ccd.html Chemical Component Dictionary].
* version 3.8.2
** Command 'ball_and_stick' has been added.
* version 3.8.3
** Binary distribution contains the JOGL library and pre-installation of JOGL is not necessary to use jV.
* version 4.0
** The program supports PDB format version 4.0.
** Atom expression has been extended to handle case-sensitive chain ID and label_asym_id in PDBML.
* version 4.1
** The program runs with new JOGL library (2.0-rc4 or later) which enables jV applets to run on Mac.
** From this release, the program requires JRE 1.6 or later.
** Command 'add_backbone' has been added.
** The program uses MODRES data and chem_comp/type data (PDBML only) to determine residue types.
* version 4.2
** The program reads polygon CGO (PyMOL-specific Compiled Graphics Objects) files distributed at eF-site system. Command 'load polygon_cgo' has been added.
** A parameter 'pdbid' and a method 'loadFTP' have been added to applet.
** When the program loads a PDBML noatom file whose directory is 'all-noatom' or 'XML-noatom', the coordinate file is retrieved from the corresponding directory; '../all-extatom' or '../XML-extatom', respectively.
* version 4.2.1
** The program runs with new JOGL library (2.0-rc11).
* version 4.3
** Anaglyph 3D rendering is added to 'stereo' command.
* version 4.3.1
** A workaround for a cache problem in JRE 1.7 has been added.
* version 4.4
** The program can read and write mmCIF format files.
** The program handles biomolecule structures when reading and writing a molecule file.
** The default setting of PDBMLplus URL has been changed.
* version 4.4.1
** Some problems in reading mmCIF files have been fixed.
** The behavior of mouse picking when measuring the distance between two atoms has been changed. Rotation and translation of molecules between two mouse pickings do not affect the distance measurement.
* version 4.4.2
** The program files are signed with a new certificate.
* version 4.4.3
** Some problems in writing PDB files have been fixed.
* version 4.4.4
** Some problems in rendering polygons have been fixed.
* version 4.4.5
** The program shows an error dialog when an input file has no valid data.
** The program files are signed with an updated certificate.
* version 4.5
** The program can read and display mmCIF files for small molecules.
* version 4.5.1
** A file permission problem in writing image files has been fixed.
* version 4.5.2
** The contact address on the error dialog has been changed.
* version 4.5.3
** In applet parameters, data files on the same server as the web page can be specified by the path part of URL as well as the full URL.
* version 4.5.4
** The program files are signed with a new certificate.
* version 4.5.5
** The program files are signed with a new certificate.
* version 4.5.6
** The program files are signed with a new certificate.
* version 4.5.7
** The program files were signed with a new certificate because of the CA certification renewal.
* version 4.5.8
** PDBML URL to fetch molecule information files has been updated.
** The applet functionality has been removed.
* version 4.5.9
** The format of PDBMLplus files has been changed to JSON.
* version 4.5.10
** Finished providing the signed version and no longer offering the web start version.
** Default PDBML URLs have been changed.</text>
    <sha1>86626a3aea7ee563594b58475be4ca6d5621b1df</sha1>
  </revision>
</page>
<page arvcontinue="20210426085749|654">
  <title>Main Page</title>
  <ns>0</ns>
  <id>1</id>
  <revision>
    <id>655</id>
    <parentid>649</parentid>
    <timestamp>2021-06-28T06:19:50Z</timestamp>
    <contributor>
      <username>IMSsato</username>
      <id>4</id>
    </contributor>
    <comment>/* Start up */</comment>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="6329" xml:space="preserve">&lt;big&gt;'''Welcome to jV wiki.'''&lt;/big&gt;

jV (formerly known as PDBjViewer) is a program to display molecular graphics of protein and nucleic acids. 
jV supports the following features:
* jV can read and display PDBML files, the canonical XML format for the Protein Data Bank.
* Of course, jV can read and display the traditional PDB format files, too.
* RasMol-like usability.
* jV can process more than one molecules.
* jV can display polygons specified by XML. ([https://pdbj.org/eF-site/schema/polygon12.xsd XML Schema for polygons] is available.)
* Multiple polygons can be processed simultaneously, and be superimposed onto molecular images.
* Animation can be realized.
* jV runs on the Java Runtime Environment ([http://java.com/download/ JRE]) and works as a stand-alone application.
* The graphics of jV is based on OpenGL ([http://jogamp.org/jogl/www/ JOGL]), thereby producing fairly beautiful pictures.


The program 'jV' has been developed by [http://www.sb.ecei.tohoku.ac.jp/index-en.html Kengo Kinoshita] ([https://www.is.tohoku.ac.jp/en/ Graduate School of Information Sciences], [http://www.tohoku.ac.jp/en/ Tohoku University]) and [http://www.protein.osaka-u.ac.jp/rcsfp/pi/index_en.html Haruki Nakamura] ([http://www.protein.osaka-u.ac.jp/en/ Institute for Protein Research], [http://www.osaka-u.ac.jp/en Osaka Univeristy]), with the support from [https://biosciencedbc.jp/en/ JST-NBDC] and [http://www.protein.osaka-u.ac.jp/en/ Institute for Protein Research IPR], [http://www.osaka-u.ac.jp/en Osaka Univeristy].
      

&lt;gallery&gt;
File:Spacefill.jpg
File:Cartoon.jpg
File:Surface.jpg
File:edmap.jpg
&lt;/gallery&gt;


== Start up ==
You can start up jV (4.5.9) with Java Web Start technology immediately from here.
* [https://pdbj.org/eF-site/servlet/stable/jV.jnlp stable JOGL version] (recommended)
* [https://pdbj.org/eF-site/servlet/current/jV.jnlp recent JOGL version]
The current jV requires JRE 1.8 or later.
The previous version, jV version 4.0, can run with JRE 1.4 and 1.5.
* [https://pdbj.org/jv/stable/jV_4_0.jnlp jV 4.0]

== Basic Usage ==
You can execute basic operations such as rotation and translation with mouse action. Major actions are described in the following table:
{| style="margin:auto;border:1px solid gray"
! rowspan="2" style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap;font-weight:bold" |Action
! colspan="2" style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap;font-weight:bold" |Mouse Operation
|-
! style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap;font-weight:bold" |Windows, Linux
! style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap;font-weight:bold" |Mac OS X
|-
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |rotate around X (horizontal) axis&lt;br /&gt;rotate around Y (vertical) axis
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |left drag
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |drag
|-
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |translate along X axis (holizontally)&lt;br /&gt;translate along Y axis (vertically)
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |right drag
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |Command + drag
|-
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |translate along Z axis (zoom in/out)
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |Shift + left drag
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |Shift + drag
|}

Operations such as changing display models and colors and saving the image, can be executed with a menu. The location of the menu is at the top of the application window in Windows and at the top of screen in Mac as the stand-alone application. As an applet usage, a popup menu appears by clicking the right mouse button on the display screen, or clicking with a "Command" button in case of Mac.

{| style="margin:auto;border:0"
|-
| [[File:Jv_menu_win.png|The location of menu in jV stand-alone version in Windows.|250px]]
| [[File:Jv_menu_mac.png|The location of menu in jV stand-alone version in Mac.|250px]]
| [[File:popupmenu_en.png|The location of menu in applet version.|250px]]
|-
| style="text-align:center" |Stand-alone (Windows)
| style="text-align:center" |Stand-alone (Mac)
| style="text-align:center" |Applet
|}

Basic menu operations are following (see also [[GUI]] for details):

{| style="margin:auto;border:1px solid gray;border-collapse:collapse"
! style="padding:0 0.5em;border:1px solid gray" | Operations
! style="padding:0 0.5em;border:1px solid gray" | Menu location
|-
| style="padding:0 0.5em;border:1px solid gray" | Save a static image
| style="padding:0 0.5em;border:1px solid gray" | [File]-[Save]-[PNG/JPEG]
|-
| style="padding:0 0.5em;border:1px solid gray" | Change the expression format
| style="padding:0 0.5em;border:1px solid gray" | [File]-[Display]-[Wireframe/Backbone/Sticks/Spacefill/Ball&amp;amp;Stick/Ribbons/Cartoon]
|-
| style="padding:0 0.5em;border:1px solid gray" | Change the color
| style="padding:0 0.5em;border:1px solid gray" | [File]-[Colors]-[Monochrome/CPK/Shapely/Group/Chain/Temperature/Structure/Charge/Amino]
|}

To execute more complicated operation such as diplaying some piece of the molecule or changing some part of molecule in another style, use command line operation.

See also [[#Other resources]] for details:


== Download ==
You can also download the program and start it up locally.
The following links take you to the download pages. (latest version is 4.5.8@2021/4/26)
* [https://pdbj.org/jv/download/binary binary (4.5.8)] 
* [https://pdbj.org/jv/download/source source code (4.5.8)] (registration will be required)

== Other resources ==
* [[How_to_use]] (in this site in English)
* [https://pdbj.org/jv/manual/index_ja.html Manual] (html in Japanese)

== Contact us ==
If you have any questions about jV, please feel free to contact us from [http://pdbj.org/contact here].</text>
    <sha1>1c193eea461ac2efab99e07b8bf909e444339fba</sha1>
  </revision>
  <revision>
    <id>656</id>
    <parentid>655</parentid>
    <timestamp>2021-06-28T06:20:16Z</timestamp>
    <contributor>
      <username>IMSsato</username>
      <id>4</id>
    </contributor>
    <comment>/* Download */</comment>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="6329" xml:space="preserve">&lt;big&gt;'''Welcome to jV wiki.'''&lt;/big&gt;

jV (formerly known as PDBjViewer) is a program to display molecular graphics of protein and nucleic acids. 
jV supports the following features:
* jV can read and display PDBML files, the canonical XML format for the Protein Data Bank.
* Of course, jV can read and display the traditional PDB format files, too.
* RasMol-like usability.
* jV can process more than one molecules.
* jV can display polygons specified by XML. ([https://pdbj.org/eF-site/schema/polygon12.xsd XML Schema for polygons] is available.)
* Multiple polygons can be processed simultaneously, and be superimposed onto molecular images.
* Animation can be realized.
* jV runs on the Java Runtime Environment ([http://java.com/download/ JRE]) and works as a stand-alone application.
* The graphics of jV is based on OpenGL ([http://jogamp.org/jogl/www/ JOGL]), thereby producing fairly beautiful pictures.


The program 'jV' has been developed by [http://www.sb.ecei.tohoku.ac.jp/index-en.html Kengo Kinoshita] ([https://www.is.tohoku.ac.jp/en/ Graduate School of Information Sciences], [http://www.tohoku.ac.jp/en/ Tohoku University]) and [http://www.protein.osaka-u.ac.jp/rcsfp/pi/index_en.html Haruki Nakamura] ([http://www.protein.osaka-u.ac.jp/en/ Institute for Protein Research], [http://www.osaka-u.ac.jp/en Osaka Univeristy]), with the support from [https://biosciencedbc.jp/en/ JST-NBDC] and [http://www.protein.osaka-u.ac.jp/en/ Institute for Protein Research IPR], [http://www.osaka-u.ac.jp/en Osaka Univeristy].
      

&lt;gallery&gt;
File:Spacefill.jpg
File:Cartoon.jpg
File:Surface.jpg
File:edmap.jpg
&lt;/gallery&gt;


== Start up ==
You can start up jV (4.5.9) with Java Web Start technology immediately from here.
* [https://pdbj.org/eF-site/servlet/stable/jV.jnlp stable JOGL version] (recommended)
* [https://pdbj.org/eF-site/servlet/current/jV.jnlp recent JOGL version]
The current jV requires JRE 1.8 or later.
The previous version, jV version 4.0, can run with JRE 1.4 and 1.5.
* [https://pdbj.org/jv/stable/jV_4_0.jnlp jV 4.0]

== Basic Usage ==
You can execute basic operations such as rotation and translation with mouse action. Major actions are described in the following table:
{| style="margin:auto;border:1px solid gray"
! rowspan="2" style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap;font-weight:bold" |Action
! colspan="2" style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap;font-weight:bold" |Mouse Operation
|-
! style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap;font-weight:bold" |Windows, Linux
! style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap;font-weight:bold" |Mac OS X
|-
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |rotate around X (horizontal) axis&lt;br /&gt;rotate around Y (vertical) axis
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |left drag
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |drag
|-
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |translate along X axis (holizontally)&lt;br /&gt;translate along Y axis (vertically)
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |right drag
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |Command + drag
|-
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |translate along Z axis (zoom in/out)
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |Shift + left drag
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |Shift + drag
|}

Operations such as changing display models and colors and saving the image, can be executed with a menu. The location of the menu is at the top of the application window in Windows and at the top of screen in Mac as the stand-alone application. As an applet usage, a popup menu appears by clicking the right mouse button on the display screen, or clicking with a "Command" button in case of Mac.

{| style="margin:auto;border:0"
|-
| [[File:Jv_menu_win.png|The location of menu in jV stand-alone version in Windows.|250px]]
| [[File:Jv_menu_mac.png|The location of menu in jV stand-alone version in Mac.|250px]]
| [[File:popupmenu_en.png|The location of menu in applet version.|250px]]
|-
| style="text-align:center" |Stand-alone (Windows)
| style="text-align:center" |Stand-alone (Mac)
| style="text-align:center" |Applet
|}

Basic menu operations are following (see also [[GUI]] for details):

{| style="margin:auto;border:1px solid gray;border-collapse:collapse"
! style="padding:0 0.5em;border:1px solid gray" | Operations
! style="padding:0 0.5em;border:1px solid gray" | Menu location
|-
| style="padding:0 0.5em;border:1px solid gray" | Save a static image
| style="padding:0 0.5em;border:1px solid gray" | [File]-[Save]-[PNG/JPEG]
|-
| style="padding:0 0.5em;border:1px solid gray" | Change the expression format
| style="padding:0 0.5em;border:1px solid gray" | [File]-[Display]-[Wireframe/Backbone/Sticks/Spacefill/Ball&amp;amp;Stick/Ribbons/Cartoon]
|-
| style="padding:0 0.5em;border:1px solid gray" | Change the color
| style="padding:0 0.5em;border:1px solid gray" | [File]-[Colors]-[Monochrome/CPK/Shapely/Group/Chain/Temperature/Structure/Charge/Amino]
|}

To execute more complicated operation such as diplaying some piece of the molecule or changing some part of molecule in another style, use command line operation.

See also [[#Other resources]] for details:


== Download ==
You can also download the program and start it up locally.
The following links take you to the download pages. (latest version is 4.5.9@2021/6/28)
* [https://pdbj.org/jv/download/binary binary (4.5.9)] 
* [https://pdbj.org/jv/download/source source code (4.5.9)] (registration will be required)

== Other resources ==
* [[How_to_use]] (in this site in English)
* [https://pdbj.org/jv/manual/index_ja.html Manual] (html in Japanese)

== Contact us ==
If you have any questions about jV, please feel free to contact us from [http://pdbj.org/contact here].</text>
    <sha1>9d1d274f251a324758c83b73d1650188098d76e1</sha1>
  </revision>
  <revision>
    <id>658</id>
    <parentid>656</parentid>
    <timestamp>2021-06-28T07:30:41Z</timestamp>
    <contributor>
      <username>IMSsato</username>
      <id>4</id>
    </contributor>
    <comment>/* Start up */</comment>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="6354" xml:space="preserve">&lt;big&gt;'''Welcome to jV wiki.'''&lt;/big&gt;

jV (formerly known as PDBjViewer) is a program to display molecular graphics of protein and nucleic acids. 
jV supports the following features:
* jV can read and display PDBML files, the canonical XML format for the Protein Data Bank.
* Of course, jV can read and display the traditional PDB format files, too.
* RasMol-like usability.
* jV can process more than one molecules.
* jV can display polygons specified by XML. ([https://pdbj.org/eF-site/schema/polygon12.xsd XML Schema for polygons] is available.)
* Multiple polygons can be processed simultaneously, and be superimposed onto molecular images.
* Animation can be realized.
* jV runs on the Java Runtime Environment ([http://java.com/download/ JRE]) and works as a stand-alone application.
* The graphics of jV is based on OpenGL ([http://jogamp.org/jogl/www/ JOGL]), thereby producing fairly beautiful pictures.


The program 'jV' has been developed by [http://www.sb.ecei.tohoku.ac.jp/index-en.html Kengo Kinoshita] ([https://www.is.tohoku.ac.jp/en/ Graduate School of Information Sciences], [http://www.tohoku.ac.jp/en/ Tohoku University]) and [http://www.protein.osaka-u.ac.jp/rcsfp/pi/index_en.html Haruki Nakamura] ([http://www.protein.osaka-u.ac.jp/en/ Institute for Protein Research], [http://www.osaka-u.ac.jp/en Osaka Univeristy]), with the support from [https://biosciencedbc.jp/en/ JST-NBDC] and [http://www.protein.osaka-u.ac.jp/en/ Institute for Protein Research IPR], [http://www.osaka-u.ac.jp/en Osaka Univeristy].
      

&lt;gallery&gt;
File:Spacefill.jpg
File:Cartoon.jpg
File:Surface.jpg
File:edmap.jpg
&lt;/gallery&gt;


== Start up ==
You can start up jV (4.5.9) with Java Web Start technology immediately from here.
* [https://pdbj.org/eF-site/servlet/stable/jV.jnlp stable JOGL version] &lt;!--(recommended)--&gt;
&lt;!--
* [https://pdbj.org/eF-site/servlet/current/jV.jnlp recent JOGL version]
--&gt;
The current jV requires JRE 1.8 or later.
&lt;!--
The previous version, jV version 4.0, can run with JRE 1.4 and 1.5.
* [https://pdbj.org/jv/stable/jV_4_0.jnlp jV 4.0]
--&gt;

== Basic Usage ==
You can execute basic operations such as rotation and translation with mouse action. Major actions are described in the following table:
{| style="margin:auto;border:1px solid gray"
! rowspan="2" style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap;font-weight:bold" |Action
! colspan="2" style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap;font-weight:bold" |Mouse Operation
|-
! style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap;font-weight:bold" |Windows, Linux
! style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap;font-weight:bold" |Mac OS X
|-
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |rotate around X (horizontal) axis&lt;br /&gt;rotate around Y (vertical) axis
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |left drag
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |drag
|-
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |translate along X axis (holizontally)&lt;br /&gt;translate along Y axis (vertically)
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |right drag
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |Command + drag
|-
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |translate along Z axis (zoom in/out)
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |Shift + left drag
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |Shift + drag
|}

Operations such as changing display models and colors and saving the image, can be executed with a menu. The location of the menu is at the top of the application window in Windows and at the top of screen in Mac as the stand-alone application. As an applet usage, a popup menu appears by clicking the right mouse button on the display screen, or clicking with a "Command" button in case of Mac.

{| style="margin:auto;border:0"
|-
| [[File:Jv_menu_win.png|The location of menu in jV stand-alone version in Windows.|250px]]
| [[File:Jv_menu_mac.png|The location of menu in jV stand-alone version in Mac.|250px]]
| [[File:popupmenu_en.png|The location of menu in applet version.|250px]]
|-
| style="text-align:center" |Stand-alone (Windows)
| style="text-align:center" |Stand-alone (Mac)
| style="text-align:center" |Applet
|}

Basic menu operations are following (see also [[GUI]] for details):

{| style="margin:auto;border:1px solid gray;border-collapse:collapse"
! style="padding:0 0.5em;border:1px solid gray" | Operations
! style="padding:0 0.5em;border:1px solid gray" | Menu location
|-
| style="padding:0 0.5em;border:1px solid gray" | Save a static image
| style="padding:0 0.5em;border:1px solid gray" | [File]-[Save]-[PNG/JPEG]
|-
| style="padding:0 0.5em;border:1px solid gray" | Change the expression format
| style="padding:0 0.5em;border:1px solid gray" | [File]-[Display]-[Wireframe/Backbone/Sticks/Spacefill/Ball&amp;amp;Stick/Ribbons/Cartoon]
|-
| style="padding:0 0.5em;border:1px solid gray" | Change the color
| style="padding:0 0.5em;border:1px solid gray" | [File]-[Colors]-[Monochrome/CPK/Shapely/Group/Chain/Temperature/Structure/Charge/Amino]
|}

To execute more complicated operation such as diplaying some piece of the molecule or changing some part of molecule in another style, use command line operation.

See also [[#Other resources]] for details:


== Download ==
You can also download the program and start it up locally.
The following links take you to the download pages. (latest version is 4.5.9@2021/6/28)
* [https://pdbj.org/jv/download/binary binary (4.5.9)] 
* [https://pdbj.org/jv/download/source source code (4.5.9)] (registration will be required)

== Other resources ==
* [[How_to_use]] (in this site in English)
* [https://pdbj.org/jv/manual/index_ja.html Manual] (html in Japanese)

== Contact us ==
If you have any questions about jV, please feel free to contact us from [http://pdbj.org/contact here].</text>
    <sha1>54e5b411255427c5a8c221eb55498834fcd5ac70</sha1>
  </revision>
  <revision>
    <id>659</id>
    <parentid>658</parentid>
    <timestamp>2021-06-28T07:32:47Z</timestamp>
    <contributor>
      <username>IMSsato</username>
      <id>4</id>
    </contributor>
    <comment>/* Start up */</comment>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="6388" xml:space="preserve">&lt;big&gt;'''Welcome to jV wiki.'''&lt;/big&gt;

jV (formerly known as PDBjViewer) is a program to display molecular graphics of protein and nucleic acids. 
jV supports the following features:
* jV can read and display PDBML files, the canonical XML format for the Protein Data Bank.
* Of course, jV can read and display the traditional PDB format files, too.
* RasMol-like usability.
* jV can process more than one molecules.
* jV can display polygons specified by XML. ([https://pdbj.org/eF-site/schema/polygon12.xsd XML Schema for polygons] is available.)
* Multiple polygons can be processed simultaneously, and be superimposed onto molecular images.
* Animation can be realized.
* jV runs on the Java Runtime Environment ([http://java.com/download/ JRE]) and works as a stand-alone application.
* The graphics of jV is based on OpenGL ([http://jogamp.org/jogl/www/ JOGL]), thereby producing fairly beautiful pictures.


The program 'jV' has been developed by [http://www.sb.ecei.tohoku.ac.jp/index-en.html Kengo Kinoshita] ([https://www.is.tohoku.ac.jp/en/ Graduate School of Information Sciences], [http://www.tohoku.ac.jp/en/ Tohoku University]) and [http://www.protein.osaka-u.ac.jp/rcsfp/pi/index_en.html Haruki Nakamura] ([http://www.protein.osaka-u.ac.jp/en/ Institute for Protein Research], [http://www.osaka-u.ac.jp/en Osaka Univeristy]), with the support from [https://biosciencedbc.jp/en/ JST-NBDC] and [http://www.protein.osaka-u.ac.jp/en/ Institute for Protein Research IPR], [http://www.osaka-u.ac.jp/en Osaka Univeristy].
      

&lt;gallery&gt;
File:Spacefill.jpg
File:Cartoon.jpg
File:Surface.jpg
File:edmap.jpg
&lt;/gallery&gt;


== Start up ==
You can start up jV (4.5.9) with Java Web Start technology immediately from here.
Open the downloaded jV.jnlp file.
* [https://pdbj.org/eF-site/servlet/stable/jV.jnlp stable JOGL version] &lt;!--(recommended)--&gt;
&lt;!--
* [https://pdbj.org/eF-site/servlet/current/jV.jnlp recent JOGL version]
--&gt;
The current jV requires JRE 1.8 or later.
&lt;!--
The previous version, jV version 4.0, can run with JRE 1.4 and 1.5.
* [https://pdbj.org/jv/stable/jV_4_0.jnlp jV 4.0]
--&gt;

== Basic Usage ==
You can execute basic operations such as rotation and translation with mouse action. Major actions are described in the following table:
{| style="margin:auto;border:1px solid gray"
! rowspan="2" style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap;font-weight:bold" |Action
! colspan="2" style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap;font-weight:bold" |Mouse Operation
|-
! style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap;font-weight:bold" |Windows, Linux
! style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap;font-weight:bold" |Mac OS X
|-
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |rotate around X (horizontal) axis&lt;br /&gt;rotate around Y (vertical) axis
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |left drag
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |drag
|-
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |translate along X axis (holizontally)&lt;br /&gt;translate along Y axis (vertically)
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |right drag
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |Command + drag
|-
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |translate along Z axis (zoom in/out)
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |Shift + left drag
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |Shift + drag
|}

Operations such as changing display models and colors and saving the image, can be executed with a menu. The location of the menu is at the top of the application window in Windows and at the top of screen in Mac as the stand-alone application. As an applet usage, a popup menu appears by clicking the right mouse button on the display screen, or clicking with a "Command" button in case of Mac.

{| style="margin:auto;border:0"
|-
| [[File:Jv_menu_win.png|The location of menu in jV stand-alone version in Windows.|250px]]
| [[File:Jv_menu_mac.png|The location of menu in jV stand-alone version in Mac.|250px]]
| [[File:popupmenu_en.png|The location of menu in applet version.|250px]]
|-
| style="text-align:center" |Stand-alone (Windows)
| style="text-align:center" |Stand-alone (Mac)
| style="text-align:center" |Applet
|}

Basic menu operations are following (see also [[GUI]] for details):

{| style="margin:auto;border:1px solid gray;border-collapse:collapse"
! style="padding:0 0.5em;border:1px solid gray" | Operations
! style="padding:0 0.5em;border:1px solid gray" | Menu location
|-
| style="padding:0 0.5em;border:1px solid gray" | Save a static image
| style="padding:0 0.5em;border:1px solid gray" | [File]-[Save]-[PNG/JPEG]
|-
| style="padding:0 0.5em;border:1px solid gray" | Change the expression format
| style="padding:0 0.5em;border:1px solid gray" | [File]-[Display]-[Wireframe/Backbone/Sticks/Spacefill/Ball&amp;amp;Stick/Ribbons/Cartoon]
|-
| style="padding:0 0.5em;border:1px solid gray" | Change the color
| style="padding:0 0.5em;border:1px solid gray" | [File]-[Colors]-[Monochrome/CPK/Shapely/Group/Chain/Temperature/Structure/Charge/Amino]
|}

To execute more complicated operation such as diplaying some piece of the molecule or changing some part of molecule in another style, use command line operation.

See also [[#Other resources]] for details:


== Download ==
You can also download the program and start it up locally.
The following links take you to the download pages. (latest version is 4.5.9@2021/6/28)
* [https://pdbj.org/jv/download/binary binary (4.5.9)] 
* [https://pdbj.org/jv/download/source source code (4.5.9)] (registration will be required)

== Other resources ==
* [[How_to_use]] (in this site in English)
* [https://pdbj.org/jv/manual/index_ja.html Manual] (html in Japanese)

== Contact us ==
If you have any questions about jV, please feel free to contact us from [http://pdbj.org/contact here].</text>
    <sha1>f53354921a11ec5bf94cb04f8be27296c83e7c2b</sha1>
  </revision>
  <revision>
    <id>662</id>
    <parentid>659</parentid>
    <timestamp>2023-05-02T23:48:25Z</timestamp>
    <contributor>
      <username>Cudo29</username>
      <id>5</id>
    </contributor>
    <comment>The URLs were updated.</comment>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="6333" xml:space="preserve">&lt;big&gt;'''Welcome to jV wiki.'''&lt;/big&gt;

jV (formerly known as PDBjViewer) is a program to display molecular graphics of protein and nucleic acids. 
jV supports the following features:
* jV can read and display PDBML files, the canonical XML format for the Protein Data Bank.
* Of course, jV can read and display the traditional PDB format files, too.
* RasMol-like usability.
* jV can process more than one molecules.
* jV can display polygons specified by XML. ([https://pdbj.org/eF-site/schema/polygon20.xsd XML Schema for polygons] is available.)
* Multiple polygons can be processed simultaneously, and be superimposed onto molecular images.
* Animation can be realized.
* jV runs on the Java Runtime Environment ([https://java.com/download/ JRE]) and works as a stand-alone application.
* The graphics of jV is based on OpenGL ([https://jogamp.org/jogl/www/ JOGL]), thereby producing fairly beautiful pictures.


The program 'jV' has been developed by [http://www.sb.ecei.tohoku.ac.jp/index-en.html Kengo Kinoshita] ([https://www.is.tohoku.ac.jp/en/ Graduate School of Information Sciences], [http://www.tohoku.ac.jp/en/ Tohoku University]) and Haruki Nakamura ([http://www.protein.osaka-u.ac.jp/en/ Institute for Protein Research], [https://www.osaka-u.ac.jp/en Osaka Univeristy]), with the support from [https://biosciencedbc.jp/en/ JST-NBDC] and [http://www.protein.osaka-u.ac.jp/en/ Institute for Protein Research IPR], [http://www.osaka-u.ac.jp/en Osaka Univeristy].
      

&lt;gallery&gt;
File:Spacefill.jpg
File:Cartoon.jpg
File:Surface.jpg
File:edmap.jpg
&lt;/gallery&gt;


== Start up ==
You can start up jV (4.5.9) with Java Web Start technology immediately from here.
Open the downloaded jV.jnlp file.
* [https://pdbj.org/eF-site/servlet/stable/jV.jnlp stable JOGL version] &lt;!--(recommended)--&gt;
&lt;!--
* [https://pdbj.org/eF-site/servlet/current/jV.jnlp recent JOGL version]
--&gt;
The current jV requires JRE 1.8 or later.
&lt;!--
The previous version, jV version 4.0, can run with JRE 1.4 and 1.5.
* [https://pdbj.org/jv/stable/jV_4_0.jnlp jV 4.0]
--&gt;

== Basic Usage ==
You can execute basic operations such as rotation and translation with mouse action. Major actions are described in the following table:
{| style="margin:auto;border:1px solid gray"
! rowspan="2" style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap;font-weight:bold" |Action
! colspan="2" style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap;font-weight:bold" |Mouse Operation
|-
! style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap;font-weight:bold" |Windows, Linux
! style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap;font-weight:bold" |Mac OS X
|-
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |rotate around X (horizontal) axis&lt;br /&gt;rotate around Y (vertical) axis
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |left drag
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |drag
|-
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |translate along X axis (holizontally)&lt;br /&gt;translate along Y axis (vertically)
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |right drag
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |Command + drag
|-
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |translate along Z axis (zoom in/out)
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |Shift + left drag
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |Shift + drag
|}

Operations such as changing display models and colors and saving the image, can be executed with a menu. The location of the menu is at the top of the application window in Windows and at the top of screen in Mac as the stand-alone application. As an applet usage, a popup menu appears by clicking the right mouse button on the display screen, or clicking with a "Command" button in case of Mac.

{| style="margin:auto;border:0"
|-
| [[File:Jv_menu_win.png|The location of menu in jV stand-alone version in Windows.|250px]]
| [[File:Jv_menu_mac.png|The location of menu in jV stand-alone version in Mac.|250px]]
| [[File:popupmenu_en.png|The location of menu in applet version.|250px]]
|-
| style="text-align:center" |Stand-alone (Windows)
| style="text-align:center" |Stand-alone (Mac)
| style="text-align:center" |Applet
|}

Basic menu operations are following (see also [[GUI]] for details):

{| style="margin:auto;border:1px solid gray;border-collapse:collapse"
! style="padding:0 0.5em;border:1px solid gray" | Operations
! style="padding:0 0.5em;border:1px solid gray" | Menu location
|-
| style="padding:0 0.5em;border:1px solid gray" | Save a static image
| style="padding:0 0.5em;border:1px solid gray" | [File]-[Save]-[PNG/JPEG]
|-
| style="padding:0 0.5em;border:1px solid gray" | Change the expression format
| style="padding:0 0.5em;border:1px solid gray" | [File]-[Display]-[Wireframe/Backbone/Sticks/Spacefill/Ball&amp;amp;Stick/Ribbons/Cartoon]
|-
| style="padding:0 0.5em;border:1px solid gray" | Change the color
| style="padding:0 0.5em;border:1px solid gray" | [File]-[Colors]-[Monochrome/CPK/Shapely/Group/Chain/Temperature/Structure/Charge/Amino]
|}

To execute more complicated operation such as diplaying some piece of the molecule or changing some part of molecule in another style, use command line operation.

See also [[#Other resources]] for details:


== Download ==
You can also download the program and start it up locally.
The following links take you to the download pages. (latest version is 4.5.9@2021/6/28)
* [https://pdbj.org/jv/download/binary binary (4.5.9)] 
* [https://pdbj.org/jv/download/source source code (4.5.9)] (registration will be required)

== Other resources ==
* [[How_to_use]] (in this site in English)
* [https://pdbj.org/jv/manual/index_ja.html Manual] (html in Japanese)

== Contact us ==
If you have any questions about jV, please feel free to contact us from [http://pdbj.org/contact here].</text>
    <sha1>90d55b4dc39a73214f00f1f3111ce6cd80484e18</sha1>
  </revision>
  <revision>
    <id>664</id>
    <parentid>662</parentid>
    <timestamp>2023-06-12T06:22:44Z</timestamp>
    <contributor>
      <username>IMSsato</username>
      <id>4</id>
    </contributor>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="5860" xml:space="preserve">&lt;big&gt;'''Welcome to jV wiki.'''&lt;/big&gt;

jV (formerly known as PDBjViewer) is a program to display molecular graphics of protein and nucleic acids. 
jV supports the following features:
* jV can read and display PDBML files, the canonical XML format for the Protein Data Bank.
* Of course, jV can read and display the traditional PDB format files, too.
* RasMol-like usability.
* jV can process more than one molecules.
* jV can display polygons specified by XML. ([https://pdbj.org/eF-site/schema/polygon20.xsd XML Schema for polygons] is available.)
* Multiple polygons can be processed simultaneously, and be superimposed onto molecular images.
* Animation can be realized.
* jV runs on the Java Runtime Environment ([https://java.com/download/ JRE]) and works as a stand-alone application.
* The graphics of jV is based on OpenGL ([https://jogamp.org/jogl/www/ JOGL]), thereby producing fairly beautiful pictures.


The program 'jV' has been developed by [http://www.sb.ecei.tohoku.ac.jp/index-en.html Kengo Kinoshita] ([https://www.is.tohoku.ac.jp/en/ Graduate School of Information Sciences], [http://www.tohoku.ac.jp/en/ Tohoku University]) and Haruki Nakamura ([http://www.protein.osaka-u.ac.jp/en/ Institute for Protein Research], [https://www.osaka-u.ac.jp/en Osaka Univeristy]), with the support from [https://biosciencedbc.jp/en/ JST-NBDC] and [http://www.protein.osaka-u.ac.jp/en/ Institute for Protein Research IPR], [http://www.osaka-u.ac.jp/en Osaka Univeristy].
      

&lt;gallery&gt;
File:Spacefill.jpg
File:Cartoon.jpg
File:Surface.jpg
File:edmap.jpg
&lt;/gallery&gt;


== Basic Usage ==
You can execute basic operations such as rotation and translation with mouse action. Major actions are described in the following table:
{| style="margin:auto;border:1px solid gray"
! rowspan="2" style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap;font-weight:bold" |Action
! colspan="2" style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap;font-weight:bold" |Mouse Operation
|-
! style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap;font-weight:bold" |Windows, Linux
! style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap;font-weight:bold" |Mac OS X
|-
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |rotate around X (horizontal) axis&lt;br /&gt;rotate around Y (vertical) axis
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |left drag
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |drag
|-
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |translate along X axis (holizontally)&lt;br /&gt;translate along Y axis (vertically)
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |right drag
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |Command + drag
|-
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |translate along Z axis (zoom in/out)
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |Shift + left drag
| style="border:1px solid gray;text-align:center;padding:5px;width:150px;white-space:nowrap" |Shift + drag
|}

Operations such as changing display models and colors and saving the image, can be executed with a menu. The location of the menu is at the top of the application window in Windows and at the top of screen in Mac as the stand-alone application. As an applet usage, a popup menu appears by clicking the right mouse button on the display screen, or clicking with a "Command" button in case of Mac.

{| style="margin:auto;border:0"
|-
| [[File:Jv_menu_win.png|The location of menu in jV stand-alone version in Windows.|250px]]
| [[File:Jv_menu_mac.png|The location of menu in jV stand-alone version in Mac.|250px]]
| [[File:popupmenu_en.png|The location of menu in applet version.|250px]]
|-
| style="text-align:center" |Stand-alone (Windows)
| style="text-align:center" |Stand-alone (Mac)
| style="text-align:center" |Applet
|}

Basic menu operations are following (see also [[GUI]] for details):

{| style="margin:auto;border:1px solid gray;border-collapse:collapse"
! style="padding:0 0.5em;border:1px solid gray" | Operations
! style="padding:0 0.5em;border:1px solid gray" | Menu location
|-
| style="padding:0 0.5em;border:1px solid gray" | Save a static image
| style="padding:0 0.5em;border:1px solid gray" | [File]-[Save]-[PNG/JPEG]
|-
| style="padding:0 0.5em;border:1px solid gray" | Change the expression format
| style="padding:0 0.5em;border:1px solid gray" | [File]-[Display]-[Wireframe/Backbone/Sticks/Spacefill/Ball&amp;amp;Stick/Ribbons/Cartoon]
|-
| style="padding:0 0.5em;border:1px solid gray" | Change the color
| style="padding:0 0.5em;border:1px solid gray" | [File]-[Colors]-[Monochrome/CPK/Shapely/Group/Chain/Temperature/Structure/Charge/Amino]
|}

To execute more complicated operation such as diplaying some piece of the molecule or changing some part of molecule in another style, use command line operation.

See also [[#Other resources]] for details:


== Download ==
You can also download the program and start it up locally.
The following links take you to the download pages. (latest version is 4.5.10@2023/6/12)
* [https://pdbj.org/jv/download/binary binary (4.5.10)] 
* [https://pdbj.org/jv/download/source source code (4.5.10)] (registration will be required)

== Other resources ==
* [[How_to_use]] (in this site in English)
* [https://pdbj.org/jv/manual/index_ja.html Manual] (html in Japanese)

== Contact us ==
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<page arvcontinue="20210426085749|654">
  <title>Document type of the polygon file</title>
  <ns>0</ns>
  <id>35</id>
  <revision>
    <id>661</id>
    <parentid>504</parentid>
    <timestamp>2023-05-02T23:29:34Z</timestamp>
    <contributor>
      <username>Cudo29</username>
      <id>5</id>
    </contributor>
    <comment>URLs are updated.</comment>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="4981" xml:space="preserve">The contents of a polygon file are organized as follows.

 &lt;?xml version="1.0"?&gt;
 &amp;nbsp;
 &lt;polygon&gt;
  &lt;vertices count="100" id_numbers=”use”&gt;            ←impossible to omit
    &lt;vertex id="1" image="x y z nx ny nz R G B"/&gt;
    &lt;vertex id="2" image="x y z nx ny nz R G B"/&gt;
    ・・・
  &lt;/vertices&gt;
 &amp;nbsp;
  &lt;point_array count="2" size=”3”&gt;                   ←possible to omit
    &lt;point id="1" vertex="v1"/&gt;
    &lt;point id="2" vertex="v1"/&gt;
  &lt;/point_array&gt;
 &amp;nbsp;
  &lt;line_array count="2" width=”2”&gt;                   ←possible to omit
    &lt;line id="1" vertex="v1 v2"/&gt;
    &lt;line id="2" vertex="v1 v2"/&gt;
  &lt;/line_array&gt;
 &amp;nbsp;
  &lt;triangle_array count="2" transparency=”0.5”&gt;      ←possible to omit
    &lt;triangle id="1" vertex="v1 v2 v3"/&gt;
    &lt;triangle id="2" vertex="v1 v2 v3"/&gt;
  &lt;/triangle_array&gt;
 &amp;nbsp;
  &lt;quad_array count="2"&gt;                               ←possible to omit
    &lt;quad id="1" vertex="v1 v2 v3 v4"/&gt;
    &lt;quad id="2" vertex="v1 v2 v3 v4"/&gt;
  &lt;/quad_array&gt;
 &amp;nbsp;
  &lt;polyline_array count="2" width=”1”&gt;               ←possible to omit
    &lt;polyline id="1" vertex="v1 v2 v3 v4 v5 ・・・"/&gt;
    &lt;polyline id="2" vertex="v1 v2 v3 v4 v5 ・・・"/&gt;
  &lt;/quad_array&gt;
 &amp;nbsp;
 &lt;/polygon&gt;

The ‘vertices’ element contains the sequence of vertices and the number of vertices is specified by the ‘count’ attribute. If the value of the ‘id_numbers’ attribute is ‘ignore’, the vertex id is automatically numbered starting from 1. If the ‘id_numbers’ attribute is set to be ‘use’, users can assign arbitrary numbers to each vertex id. In the ‘vertex’ element, x, y and z represent the x, y and z coordinates of the vertex, respectively, and nx, ny and nz represent the x, y and z components of the normal vector at the vertex, respectively. They are assigned real numbers. The color of each vertex is defined according to the RGB color scheme; R, G and B take the real numbers from 0 to 255. The ‘point_array’, ‘line_array’, ‘traiangle_array’, ‘quad_array’ and ‘polyline_array’ elements contain the sequence of polygons such as dots, lines, triangles, quadrangles and polylines, respectively. They can be omitted. The v1, v2, v3, v4 and v5 describe id of the vertices constructing the polygon. For these elements, the ‘transparency’ attribute that is omissible can be used to set the transparency of the image. To specify the size of dots and the width of lines, the ‘point_array’ element has the omissible ‘size’ attribute and ‘line_array’ and ‘polyline_array’ elements have the omissible ‘width’ attribute, respectively. The XML schema file that describes the type definitions and element declarations is published at https://pdbj.org/jv/polygonSchema. A simple example of a polygon is shown below. It represents a colored cube. The file is published at https://pdbj.org/eF-site/jV/cube.xml. Before you open this polygon, you should close all files currently loaded to the application to get an appropriate viewpoint for the cube. To do this, you can use [File] – [Close] menu, or execute ‘zap’ in the command line.

 &lt;?xml version="1.0"?&gt;
 &amp;nbsp;
  &lt;polygon&gt;
   &lt;vertices count="24" id_numbers="use"&gt;
    &lt;vertex id="1"  image=" 1  1  1  0  0  1 255   0   0"/&gt;
    &lt;vertex id="2"  image="-1  1  1  0  0  1 255   0   0"/&gt;
    &lt;vertex id="3"  image="-1 -1  1  0  0  1 255   0   0"/&gt;
    &lt;vertex id="4"  image=" 1 -1  1  0  0  1 255   0   0"/&gt;
    &lt;vertex id="5"  image="-1  1 -1  0  0 -1   0 255 255"/&gt;
    &lt;vertex id="6"  image=" 1  1 -1  0  0 -1   0 255 255"/&gt;
    &lt;vertex id="7"  image=" 1 -1 -1  0  0 -1   0 255 255"/&gt;
    &lt;vertex id="8"  image="-1 -1 -1  0  0 -1   0 255 255"/&gt;
    &lt;vertex id="9"  image=" 1  1  1  1  0  0   0 255   0"/&gt;
    &lt;vertex id="10" image=" 1 -1  1  1  0  0   0 255   0"/&gt;
    &lt;vertex id="11" image=" 1 -1 -1  1  0  0   0 255   0"/&gt;
    &lt;vertex id="12" image=" 1  1 -1  1  0  0   0 255   0"/&gt;
    &lt;vertex id="13" image="-1  1 -1 -1  0  0 255   0 255"/&gt;
    &lt;vertex id="14" image="-1 -1 -1 -1  0  0 255   0 255"/&gt;
    &lt;vertex id="15" image="-1 -1  1 -1  0  0 255   0 255"/&gt;
    &lt;vertex id="16" image="-1  1  1 -1  0  0 255   0 255"/&gt;
    &lt;vertex id="17" image=" 1  1  1  0  1  0   0   0 255"/&gt;
    &lt;vertex id="18" image=" 1  1 -1  0  1  0   0   0 255"/&gt;
    &lt;vertex id="19" image="-1  1 -1  0  1  0   0   0 255"/&gt;
    &lt;vertex id="20" image="-1  1  1  0  1  0   0   0 255"/&gt;
    &lt;vertex id="21" image=" 1 -1 -1  0 -1  0 255 255   0"/&gt;
    &lt;vertex id="22" image=" 1 -1  1  0 -1  0 255 255   0"/&gt;
    &lt;vertex id="23" image="-1 -1  1  0 -1  0 255 255   0"/&gt;
    &lt;vertex id="24" image="-1 -1 -1  0 -1  0 255 255   0"/&gt;
   &lt;/vertices&gt;
   &lt;quad_array count="6"&gt;
    &lt;quad id="1" vertex=" 1  2  3  4"/&gt;
    &lt;quad id="2" vertex=" 5  6  7  8"/&gt;
    &lt;quad id="3" vertex=" 9 10 11 12"/&gt;
    &lt;quad id="4" vertex="13 14 15 16"/&gt;
    &lt;quad id="5" vertex="17 18 19 20"/&gt;
    &lt;quad id="6" vertex="21 22 23 24"/&gt;
   &lt;/quad_array&gt;
  &lt;/polygon&gt;</text>
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  </revision>
  <revision>
    <id>663</id>
    <parentid>661</parentid>
    <timestamp>2023-05-09T06:45:39Z</timestamp>
    <contributor>
      <username>IMSsato</username>
      <id>4</id>
    </contributor>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="4993" xml:space="preserve">The contents of a polygon file are organized as follows.

 &lt;?xml version="1.0"?&gt;
 &amp;nbsp;
 &lt;polygon&gt;
  &lt;vertices count="100" id_numbers=”use”&gt;            ←impossible to omit
    &lt;vertex id="1" image="x y z nx ny nz R G B"/&gt;
    &lt;vertex id="2" image="x y z nx ny nz R G B"/&gt;
    ・・・
  &lt;/vertices&gt;
 &amp;nbsp;
  &lt;point_array count="2" size=”3”&gt;                   ←possible to omit
    &lt;point id="1" vertex="v1"/&gt;
    &lt;point id="2" vertex="v1"/&gt;
  &lt;/point_array&gt;
 &amp;nbsp;
  &lt;line_array count="2" width=”2”&gt;                   ←possible to omit
    &lt;line id="1" vertex="v1 v2"/&gt;
    &lt;line id="2" vertex="v1 v2"/&gt;
  &lt;/line_array&gt;
 &amp;nbsp;
  &lt;triangle_array count="2" transparency=”0.5”&gt;      ←possible to omit
    &lt;triangle id="1" vertex="v1 v2 v3"/&gt;
    &lt;triangle id="2" vertex="v1 v2 v3"/&gt;
  &lt;/triangle_array&gt;
 &amp;nbsp;
  &lt;quad_array count="2"&gt;                               ←possible to omit
    &lt;quad id="1" vertex="v1 v2 v3 v4"/&gt;
    &lt;quad id="2" vertex="v1 v2 v3 v4"/&gt;
  &lt;/quad_array&gt;
 &amp;nbsp;
  &lt;polyline_array count="2" width=”1”&gt;               ←possible to omit
    &lt;polyline id="1" vertex="v1 v2 v3 v4 v5 ・・・"/&gt;
    &lt;polyline id="2" vertex="v1 v2 v3 v4 v5 ・・・"/&gt;
  &lt;/quad_array&gt;
 &amp;nbsp;
 &lt;/polygon&gt;

The ‘vertices’ element contains the sequence of vertices and the number of vertices is specified by the ‘count’ attribute. If the value of the ‘id_numbers’ attribute is ‘ignore’, the vertex id is automatically numbered starting from 1. If the ‘id_numbers’ attribute is set to be ‘use’, users can assign arbitrary numbers to each vertex id. In the ‘vertex’ element, x, y and z represent the x, y and z coordinates of the vertex, respectively, and nx, ny and nz represent the x, y and z components of the normal vector at the vertex, respectively. They are assigned real numbers. The color of each vertex is defined according to the RGB color scheme; R, G and B take the real numbers from 0 to 255. The ‘point_array’, ‘line_array’, ‘traiangle_array’, ‘quad_array’ and ‘polyline_array’ elements contain the sequence of polygons such as dots, lines, triangles, quadrangles and polylines, respectively. They can be omitted. The v1, v2, v3, v4 and v5 describe id of the vertices constructing the polygon. For these elements, the ‘transparency’ attribute that is omissible can be used to set the transparency of the image. To specify the size of dots and the width of lines, the ‘point_array’ element has the omissible ‘size’ attribute and ‘line_array’ and ‘polyline_array’ elements have the omissible ‘width’ attribute, respectively. The XML schema file that describes the type definitions and element declarations is published at https://pdbj.org/eF-site/schema/polygon20.xsd. A simple example of a polygon is shown below. It represents a colored cube. The file is published at https://pdbj.org/eF-site/jV/cube.xml. Before you open this polygon, you should close all files currently loaded to the application to get an appropriate viewpoint for the cube. To do this, you can use [File] – [Close] menu, or execute ‘zap’ in the command line.

 &lt;?xml version="1.0"?&gt;
 &amp;nbsp;
  &lt;polygon&gt;
   &lt;vertices count="24" id_numbers="use"&gt;
    &lt;vertex id="1"  image=" 1  1  1  0  0  1 255   0   0"/&gt;
    &lt;vertex id="2"  image="-1  1  1  0  0  1 255   0   0"/&gt;
    &lt;vertex id="3"  image="-1 -1  1  0  0  1 255   0   0"/&gt;
    &lt;vertex id="4"  image=" 1 -1  1  0  0  1 255   0   0"/&gt;
    &lt;vertex id="5"  image="-1  1 -1  0  0 -1   0 255 255"/&gt;
    &lt;vertex id="6"  image=" 1  1 -1  0  0 -1   0 255 255"/&gt;
    &lt;vertex id="7"  image=" 1 -1 -1  0  0 -1   0 255 255"/&gt;
    &lt;vertex id="8"  image="-1 -1 -1  0  0 -1   0 255 255"/&gt;
    &lt;vertex id="9"  image=" 1  1  1  1  0  0   0 255   0"/&gt;
    &lt;vertex id="10" image=" 1 -1  1  1  0  0   0 255   0"/&gt;
    &lt;vertex id="11" image=" 1 -1 -1  1  0  0   0 255   0"/&gt;
    &lt;vertex id="12" image=" 1  1 -1  1  0  0   0 255   0"/&gt;
    &lt;vertex id="13" image="-1  1 -1 -1  0  0 255   0 255"/&gt;
    &lt;vertex id="14" image="-1 -1 -1 -1  0  0 255   0 255"/&gt;
    &lt;vertex id="15" image="-1 -1  1 -1  0  0 255   0 255"/&gt;
    &lt;vertex id="16" image="-1  1  1 -1  0  0 255   0 255"/&gt;
    &lt;vertex id="17" image=" 1  1  1  0  1  0   0   0 255"/&gt;
    &lt;vertex id="18" image=" 1  1 -1  0  1  0   0   0 255"/&gt;
    &lt;vertex id="19" image="-1  1 -1  0  1  0   0   0 255"/&gt;
    &lt;vertex id="20" image="-1  1  1  0  1  0   0   0 255"/&gt;
    &lt;vertex id="21" image=" 1 -1 -1  0 -1  0 255 255   0"/&gt;
    &lt;vertex id="22" image=" 1 -1  1  0 -1  0 255 255   0"/&gt;
    &lt;vertex id="23" image="-1 -1  1  0 -1  0 255 255   0"/&gt;
    &lt;vertex id="24" image="-1 -1 -1  0 -1  0 255 255   0"/&gt;
   &lt;/vertices&gt;
   &lt;quad_array count="6"&gt;
    &lt;quad id="1" vertex=" 1  2  3  4"/&gt;
    &lt;quad id="2" vertex=" 5  6  7  8"/&gt;
    &lt;quad id="3" vertex=" 9 10 11 12"/&gt;
    &lt;quad id="4" vertex="13 14 15 16"/&gt;
    &lt;quad id="5" vertex="17 18 19 20"/&gt;
    &lt;quad id="6" vertex="21 22 23 24"/&gt;
   &lt;/quad_array&gt;
  &lt;/polygon&gt;</text>
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